Description
University of Colorado Denver Anschutz Medical Campus Core Facilities
University of Colorado
Denver| Anschutz Medical Campus
Core Facilities
Prepared by
Richard J. Traystman, PhD
Vice Chancellor for Research
and
Paula McGuigan
Executive Assistant
Office of the Vice Chancellor for Research
Fees & Services are not guaranteed
Tab
Core Name Director/Contact Name
A
Administration (IDDRC) Karl H. Pfenninger, MD
Administration (UCCC) Dan Theodorescu, MD, PhD
Adult CTO (CCTSI) Barbara DiMercurio, RN, MBA
Advanced Microscopy Core Facility
Andrew Millard, PhD
Moshe Levi, MD
Altitude Research Center
Ben Honigman, MD
Robert Roach, PhD
Animal Models (IDDRC) Ken Maclean, PhD
B
A
Bard Center for Entrepreneurship Catherine Kunst, MBA, PhD
Bio-Imaging Research Laboratory (BIRL) David Miller, PhD
Bimolecular NMR Core Facility David Jones, PhD
Biophysics Core Facility Robert Hodges, PhD
Biorepository Core Facility Scott Lucia, MD
Biostatistics & Bioinformatics (UCCC) Anna Baron, PhD
B
C
Cellular Systems and Analysis (IDDRC) Karl Pfenninger , PhD
Center for Computational Mathematics (CCM) Jan Mandel, PhD
CCTSI CTRC Behavioral Medicine (NJH) Fred Wamboldt, MD
CCTSI CTRC Inflammation & Immunology (NJH) Lisa Maier, MD
CCTSI CTRC Nursing Diane Branham, RN, BSN
CCTSI CTRC Nutrition Janine Higgins, PhD
CCTSI CTRC Research Nursing & Facilities (NJH) Donald Leung, MD., PhD
CCTSI CTRC Research Nursing & Facilities (UCB) Elizabeth Connick, MD
Clinical Investigations Core (CFAR) Cara Wilson, MD
Clinical Investigations Core (UCCC) Anthony Elias, MD
Clinical Sciences PhD & MS Program Lisa Cicutto, PhD., RN
Clinical Trials Organization Jill McHale
Colorado Advanced Photonics Technology (CAPT) Larry Scherrer
Colorado Biostatistics Consortium John Neal
Colorado Genetics Lab
Karen Swisshelm, Ph.D., FACMG
Loris McGavran, Ph.D., FACMG
Colorado Health Outcomes Program (COHO) David West, PhD
Colorado Multiple Institutional Review Board (COMIRB) Marie Wade
Computational Biology Core Robert Hodges, PhD
Cytogenetic Core Laboratory (UCCC) Marileila Varella-Garcia, PhD
D
C
Developmental Core (CFAR) Myron Levin, MD
Diabetes & Endocrinology Research Center (DERC) John C. Hutton, PhD
DNA Diagnostic Laboratory Elaine Spector, PhD
DNA Sequencing and Analysis Core (UCCC) Christopher Korch, PhD
E Evaluation Center Bonnie Walters
D
Tab
Core Name Director/Contact Name
Flow Cytometry and Cell Sorting (CFAR) Brent Palmer, PhD
Flow Cytometry Services (UCCC) Christopher J. Hogan, PhD
Gene Expression, Microarray & PCR(UCCC) Mark Geraci, MD
Gene-Targeting/Viral Vector Core Mark Dell'Acqua, PhD
Grants & Contracts Pam Jones, PhD
High-Throughput Genome Sequencer David Pollock, PhD
HLA (Histocompatibility) Testing and Umbilical Cord Blood Bank Brian M. Freed, PhD
Histology Core Roberto Gianani, MD
Informatics Core (UCCC) Jessica Bondy, MHA
Institutional Animal Care and Use Committee (IACUC) Mark Douse, PhD
Interdisciplinary Transcranial Magnetic Stimulation Benzi Kluger, MD
Laboratory Science Core Elizabeth Connick, MD
Laser Capture Core Wilbur Franklin, MD
Light Microscopy Bill Betz, PhD
Machine Shop Ulli Bayer, PhD
Mass Spectrometry (CNRU) Uwe Christians, PhD., MD
Mass Spectrometry Facility (NJH) Nichole Reidorph, PhD
Medicinal Chemistry Core Facility Michael F. Wempe, PhD
Metabolomics Core (NMR) Natalie Serkova, PhD
Metabolic Core (CNRU) Jed Friedman, PhD
Molecular discovery (IDDRC)
Frank Frerman, PhD
Elaine Spector, PhD
Morphology and Phenotyping Core Maranke I. Koster, PhD
Musosal and Vaccine Research Colorado (MAVRC) Ed Janoff, MD
Pathology Core (UCCC) Wilbur Franklin, MD
Peptide and Protein Chemistry Core Robert Hodges, PhD
Pharmacology (UCCC) Daniel L. Gustafson, PhD
Pregnancy Core Peggy Neville, PhD
Protein Production-Moab-Tissue Culture (UCCC) Steven Nordeen, PhD
Proteomics (Mass Spectrometry) (UCCC) Mark Duncan, PhD
RADScience Clinical Trials Physics Support Ann Scherzinger, PhD
Research Design & Analysis Core (CFAR) Samantha MaWhinney, ScD
Rodent In Vivo Neurophysiology Core Yogendra Raol, PhD
Shared Analytical Service Laboratory Jeff Boon
Statistical Consulting Service Loren Cobb, PhD
Small Animal Imaging Core (UCCC) Natalie Serkova, PhD
S
M
P
R
F
L
H
G
I
Tab
Core Name Director/Contact Name
Transgenic and Gene Targeting Core Peter Koch, PhD
Translational Nexus (IDDRC) Cordelia Robinson, PhD
U UCH-CTRC Core Laboratory (CCTSI) Bryan Haugen, MD
V Vivarium - Animal Housing & Care Jori Leszczynski, DVM DACLAM
X X-Ray Crystallography Mair Churchill, PhD
Z Zebrafish Transgenic Angie Ribera, PhD
UCCC - University of Colorado Cancer Center
CFAR - Center for Aids Research
CCTSI - Colorado Clinical and Translational Sciences Institute
IDDRC - Intellectual and Developmental Disabilities Research Center
CAPT - Colorado Advanced Photonics Technology
COHO - Colorado Health Outcomes
ARC - Altitude Research Center
NJH - National Jewish Hospital
NMR - Nuclear Magnetic Resonance
T
Administration (IDDRC-UCD)
The Colorado Intellectual & Developmental
Disabilities Research Center (IDDRC)
The Administrative Core unit provides the Center’s personnel and fiscal management
infrastructure, as well as the interface with the NICHD, other IDDRCs, the AUCD, the
University, and the public. Furthermore, this core acts as the information hub of the IDDRC and
organizes educational activities, junior faculty mentoring, and collaborator referral.
Contacts:
Karl H. Pfenninger, MD
Director
303-724-3466
[email protected]
Frank Frerman, PhD
Associate Director
303-724-3809
[email protected]
Carrie John
IDDRC Administrator
303-724-3839
[email protected]
Carmel Harberg
Program Assistant
303-724-4349
[email protected]
http://www.ucdenver.edu/academics/colleges/medicine/Centers/IDDRC/research/admincore/Pages/IDDR
CAdministration.aspx#directors
The IDDRC Administration is located in the RC-1 North Building of the University of Colorado
Denver Anschutz Medical Campus in Aurora, CO. Click here for IDDRC contact information.
Services
1) Educational Activities
Contact: Alberto Costa, MD, PhD ([email protected])
Goals: to advance knowledge, to enhance interaction among IDDRC members, and to explore
and stimulate collaborations in IDD research.
The Administrative Core organizes annually three or four workshops or mini-symposia focused
on a particular topic of IDD. The format of these conferences is interdisciplinary, with only brief
presentations from individuals working in epidemiology, basic science, clinical research, and
rehabilitation as they relate to the selected topic. Most of the meeting time is spent on
discussion.
2) Collaborator Referral and Faculty Mentoring
Contact: Karl Pfenninger, MD ([email protected])
Goals: To assist with the identification of potential collaborators for interdisciplinary projects.
The CCTSI hosts InfoEd software to facilitate the search for appropriate collaborators. The
Center Director also assists with advice regarding potential collaborators and identifying
appropriate faculty mentors for young investigators. The IDDRC is committed to not only
recruiting new investigators to IDD research but also helping them develop strong and
competitive research programs.
3) Liaisons with other IDDRCs and local entities that deal with IDD
Contact: Karl Pfenninger, MD ([email protected])
4) Community Outreach
Contact: Karl Pfenninger, MD ([email protected])
Goals: To educate the public in the area of IDD and to share information on important research
advances and new treatments. The Colorado IDDRC present public lectures about twice a year.
The IDDRC’s website (see below) has a special section for public use that is designed to
disseminate information on access to appropriate clinics, the performance of clinical trials in
specific areas of IDD, and progress in research on IDD. Furthermore, there are links to NIH
websites and to those of specific support groups in the area and nationally.
The IDDRC also maintains contact with a number of State and local agencies that serve people
with IDD and with local support groups, such as the Mile High Down Syndrome Association,
Autism Society of Colorado, Colorado Family Voices, the Colorado Arc, and the Colorado
Developmental Disabilities Council.
Administrative Core
University of Colorado Cancer Center
The Administrative Core provides administrative and fiscal oversight for the University of
Colorado Cancer Center (UCCC) entities as described in the NCI Cancer Center Support
Grant that funds UCCC, for the Lung Special Program of Research Excellence (SPORE)
and any other grants in the Cancer Center.
Contacts:
Dan Theodorescu, MD, PhD
Director
303-724-3150
[email protected]
Mark Kochevar
Associate Director for Administration & Finance
303-724-5724
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/administration/Index.aspx
Administration
Sets business objectives, mission, vision
• Manages daily operations
• Negotiates contracts
• Manages relationships with affiliates
Manages & allocates physical space
•
Grants & Contracts Management
• Administers daily business procedures for all multidisciplinary funded grants routed
through UCCC
• Pre- and post-award
• Manages the CCSG and Lung SPORE
• Manages subcontracts
Supports all multidisciplinary funded grants and contracts held by UCCC members
• Manages the American Cancer Society Institutional Research Grant/UCCC Seed
Grants program
• Maintains membership publication database
Human Resources and Finances
• Recruitment, hiring, personnel issues and payroll
• Manages institutional funds, gift accounts and facility funds
• Manages compliance with Federal, State and CU policies
• Grant account reconciliation
• Accounts payable/accounts receivable
• Budgeting
• Audits
Membership, Education & Career Development
Coordinates the UCCC membership program, including applications and database
• Coordinates the weekly UCCC Symposium
• Coordinates the Lung SPORE and Thoracic Oncology Program seminars
• Manages the UCCC Student Cancer Research Fellowship Program
Public Relations & Communications
• Publications, including the weekly Director’s Newsletter and TOPICS, a three-times
yearly external newsletter
• Web site development and management
• Media relations
• Internal communications, including monthly newsletter Six Things from the Sixth Floor
• UCCC marketing/marketing communications
• Event management
• Legislative communications
• Fundraising communications
Fundraising
UCCC employs one full-time fundraiser. The University of Colorado Foundation and
AMC Cancer Research Center both also employ development staff who raise money
for UCCC.
• Donor cultivation, solicitation and stewardship
• Fundraising events
• Grateful patient program
• Manages the Community Advisory Board
• Maintains relationships with Cancer League of Colorado, Cancer Cure,
the American Cancer Society and other groups that support UCCC
No fees
Adult CTO
Barbara DiMercurio, RN, MBA
Clinical Nursing Director
Colorado Clinical and Translational Sciences Institute
Clinical Translational Research Centers
UCH/TCH/UCB/NJH
12605 East 16th Street, Room 12.062
Aurora, CO 80045
[email protected]
Office: 720-848-6420 Fax: 720-848-7347
Cell: 303-524-5967
SIMS
CODE
Facility Fee Charge
1672 CTO Review Fee $525.00
1600 Inpatient Med Surg Room Rate $857.74
1601 Inpatient Med Surg with Tele Room Rate $1,000.00
1602 Inpatient Step Down Room Rate $1,500.00
1603 Inpatient ICU Room Rate $1,566.92
1604 Inpatient Short stays (0-4 hours) $142.96
1605 Inpatient Short stays (5-13 hours) $464.62
1606 Inpatient Short Stays (14-23 hours) $822.00
1607 Telemetry monitoring $50 per hour
1609 Outpatient exam room 20 mins $60.00
1610 Outpatient exam room 20 mins without RN $40.00
1611 Outpatient exam room 21-39 mins $70.00
1612 Outpatient exam room 21-39 mins without RN $50.00
1613 Outpatient exam room 40-59 mins $85.00
1614 Outpatient exam room 40-59 mins without RN $60.00
1615 Outpatient exam room 60-120mins $130.00
1616 Outpatient exam room 60-120mins without RN $80.00
1617 Outpatient exam room > 120 mins $200.00
1618 Outpatient exam room > 120 mins without RN $110.00
1619 Infusion Chair 1st Hour $125 1st hour
1621 Infusion Chair each additional hour $30 each additional hour
1620 Infusion Chair 1st Hour without RN $60 1st hour
1622 Infusion Chair each additional hour without RN $20 each additional hour
Physician Assistant (PA) Services
1683 Investigator Initiated (A) study PA consult $15 per 15 min.
1684 CTO PA consult $ 25 per 15 min.
1685 CTO PA ON CALL $ 200 per night
1686 Investigator Initiated (A) study PA ON CALL $100 per night
1687 CTO PA H&P $100.00
1688 Investigator Initiated (A) Study H&P $50.00
1689 Investigator Initiated (A) PA Stress Treadmill Testing $50.00
1690 Investigator Initiated (A) PA + RN Treadmill Testing $100.00
1633 CTO Stress Treadmill Testing ( basic) $375.00
1634 CTO VO2 Max Testing $375.00
Inpatient and Outpatient Testing Charge
1692 TB Skin Testing $50.00
1623 Venipuncture ( 1 time only) $25.00
1640 After Hours Blood draw $40.00
1624 Port or central line blood draw $100.00
1625 Pharmacokinetics ( + 1 Venipuncture charge) $12 per draw
1691 Pharmacokinetics Sample processing $ 5 per draw
1626 Pulse Ox ( 1 time only) $20.00
1627 Pulse Ox ( serial or continuous) $100.00
1681 ECG ( low) $50.00
1628 ECG ( 1 time only) $100.00
1629 ECG ( serial) $200.00
1608 One to One RN charge ( hourly) $100 per hour
1630 Intravenous Glucose Tolerance Test (IVGTT) $300.00
1631 Oral Glucose Tolerance Test (OGGT) $200.00
1632 Mix Meal Tolerance Test (MMT) $200.00
1633 Stress Treadmill Testing ( basic) $375.00
1634 VO2 Max Testing $375.00
1635 Calorimetry Room stay (per hour) $100 hour
1636 Calorimetry Room stay $800.00
1637 RMR ( includes interpretation) $300.00
1638 Bike Exercise Testing $375.00
1679 D-Xylose Absorption Test $300.00
1682 Liver Biopsy ( ultrasound) $50.00
1677 Kidney Biopsy $300.00
1680 Complex Infusion $620.00
1678 6 Min Walk Test $24.99
1641 Supplies (low) $30.00
1642 Supplies (mod) $60.00
1643 Supplies (high) $90.00
1644 DXA Lumbar spine $250.00
1645 DXA Proximal femur $250.00
1646 DXA Total body $250.00
1647 DXA SPINE, FEMUR, WHOLE BODY $500.00
Core Echo Laboratory
1648 Ejection Fraction (EF) ONLY $150.00
1649 2-D ECHO BASIC $250.00
1650 2-D ECHO DOPPLER & FLOW MAP $400.00
1651 Tissue Doppler /Tissue Track/Stain $450.00
1652 Exercise Stress Echocardiogram $500.00
1653 Stress ECHO-PHARM $600.00
1654 3-D Echocardiogram $450.00
1655 Arterial INTIMA-MEDIAL Thickness (IMT ONLY) $100.00
1656 Femerol Artery imaging $100.00
1657 BRACHIAL ARTERY FLOW MED VASODIL(FMD) $250.00
1658 CAROTID DUPLEX-BILATERAL $350.00
1659 US MACHINE W ASSISTANCE 60 MIN UNITS $75.00
Nutrition Services Cost
Inpatient meals $0.00
1668 Breakfast ( Basic select menu) $8.00
1669 Lunch ( Basic select menu) $13.00
1670 Dinner ( Basic select menu) $19.00
1671 Snack ( Basic select menu) $5.00
1673 Breakfast-metabolic $16.00
1674 Lunch -metabolic $22.00
1675 Dinner -metabolic $32.00
1676 3 day weighed, metabolic diets $195.00
1660 Gourmet meals $38.00
1661 Personalized eating plan $200.00
1662 Recipe modification (simple) $40.00
1663 Recipe modification (complex) $85.00
1664 Weight loss counseling $65/hour (plus personalized eating plan
1665 Food preparation classes $65/hour plus ingredients at cost
1666 Supermarket tours $65/hour
1667 Travel $30/hour
Advanced Microscopy Core Facility
Contacts:
Andrew C. Millard, PhD
Tel: 303-724-4856
[email protected]
For reservation and equipment questions
Moshe Levi, MD
Tel: 303-724-4825
[email protected]
Rachael Fuhrman
Tel: 303-724-4849
[email protected]
For invoice and billing questions
Facility Overview
We have several microscopes in the R2 DOM-SOM Facility including: 1) a Laser-Scanning
Confocal/Multiphoton-Excitation (MPE) and Second Harmonic Generation (SHG) fluorescence
microscope with a Meta spectral detection system (Zeiss NLO 510 with META) and an
environmental chamber; 2) a Total Internal Reflection Fluorescence (Zeiss TIRF) microscope
with an environmental chamber; 3) a Fluorescence Correlation Spectroscopy (FCS) and
Fluorescence Lifetime Imaging Microscope (FLIM) (ISS) equipped with an environmental
chamber; and 4) a forthcoming Coherent Anti Stokes Raman Scattering (CARS) Microscope
equipped with an environmental chamber. These microscopes allows for the high-resolution
analysis of fixed samples as well as the time-resolved imaging of live cells. These microscopes
are also set up to conduct biophysical studies in live cells such as fluorescence recovery after
photobleaching (FRAP), fluorescence resonance energy transfer (FRET), fluorescence
correlation spectroscopy (FCS) and fluorescence lifetime imaging (FLIM). These techniques are
of considerable use in studying the dynamics of lipids and protein in live cells and the
interactions of transcription factors and signaling molecules.
Recent Publications
PTH-Induced Internalization of Apical Membrane NaPi2a: Role of Actin and Myosin VI by
Judith Blaine et al., American Journal of Physiology - Cell Physiology (Sept. 2009)
Liver Cyst Cytokines Promote Endothelial Cell Proliferation and Development by Kelley
Brodsky et al., Experimental Biology and Medicine (July 2009)
Noggin Enhances Dopamine Neuron Production from Human Embryonic Stem Cells and
Improves Behavioral Outcome after Transplantation into Parkinsonian Rats by Shunmai
Chiba et al., Stem Cells (Sept. 2008)
Advisory Committee
William Betz, PhD, University of Colorado Denver
Eric Betzig, PhD, Howard Hughes Medical Institute
Emily Gibson, PhD, University of Colorado Denver
Enrico Gratton, PhD, University of California, Irvine, Lab for Fluorescence Dynamics
Tim Lei, PhD, University of Colorado Denver
Jennifer Lippincott-Schwartz, PhD, National Institute of Child Health and Human
Development
William Mantulin, PhD, University of California, Irvine, Lab for Fluorescence Dynamics
George Patterson, PhD, NIBIB (National Institute of Biomedical Imaging and
Bioengineering)
Eric Olaf Potma, PhD, University of California Irvine
Diego Restrepo, PhD, University of Colorado at Denver and Health Sciences Center
Bruce Tromberg, PhD, University of California, Irvine, Beckman Laser Institute
Paul Wiseman, PhD, McGill University
X. Sunney Xie, PhD, Harvard University
UC Denver Participants
Kurt Beam, PhD, Department of Physiology and Biophysics
Peter Buttrick, MD, Division of Cardiology
Sean Colgan, MD, Division of Gastroenterology and Hepatology
Elizabeth Connick, MD, Division of Infectious Diseases
Brian Doctor, PhD, Division of Gastroenterology and Hepatology
Curt Freed, MD, Division of Clinical Pharmacology and Toxicology
Glenn Furuta, MD, Gastrointestinal Eosinophil Disease Center
Mark Geraci, MD, Division of Pulmonary Sciences and Critical Care Medicine
Emily Gibson, PhD, Department of Physics
Michael Holers, MD, Division of Rheumatology
John Hutton, PhD, Barbara Davis Center for Childhood Diabetes
Richard Johnson, MD, Division of Renal Diseases and Hypertension
Chifong (Tim) Lei, PhD, Department of Electrical Engineering
Simon Rock Levinson, PhD, Department of Physiology and Biophysics
Susan Majka, PhD, Division of Cardiology
James McManaman, PhD, Department of Physiology and Biophysics
Raphael Nemenoff, PhD, Division of Renal Diseases and Hypertension
Jane Reusch, MD, Division of Endocrinology, Metabolism and Diabetes
Hugo Rosen, MD, Division of Gastroenterology and Hepatology
Pepper Schedin, PhD, Division of Medical Oncology
Robert Schrier, MD, Division of Renal Diseases and Hypertension
Natalie Serkova, PhD, Department of Anesthesiology
Kurt Stenmark, MD, Department of Pediatrics
Lisa Wise-Faberowski, PhD, Department of Anesthesiology and Pediatric Cardiology
The Zeiss LSM 510 META microscope system (in conjunction with the Coherent
Chameleon for both two-photon and confocal fluorescence imaging) is available for routine
use, including demonstrations, hands-on training and research support.
The other microscope systems are also available for specialized projects.
Advanced Microscopy Core Facility
From: Levi, Moshe
Sent: Wednesday, December 02, 2009 1:46 PM
.
a) How is the quality of your measurements evaluated – quality control?
We have quality controls depending on the individual microscopes and individual
techniques that we use to align our lasers, optics, and images.
b) What is the turn-a-round time for the service you provide?
In our case the investigators/technicians sign up depending on the available spots and
they perform their imaging usually within the same week.
c) Who documents the data provided and signs off on the data?
Dr. Andrew Millard
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Yes: for each microscope and imaging technique.
f) How will you track billing and financial aspects of your core?
We have administrative personnel who takes care of the billing and Dr. Andrew
Millard and Dr. Moshe Levi go over the finances on a periodic basis.
Altitude Research Center (ARC)
Benjamin Honigman, MD
Director ARC
Professor of Emergency Medicine
F524 - PO Box 6508
12469 East 17th Place
Aurora, CO 80045-0508
[email protected]
Robert Roach, PhD
Research Director
Associate Professor of Emergency Medicine
303-724-1641
[email protected]
For clinical consultations at the
Altitude Clinic: 720-848-2631
ARC-Foundation: 720-284-7074
http://www.altituderesearch.org/
The Importance of Oxygen
A continuous supply of oxygen i s essential f or proper physical and mental f unctioning. If t his
supply is compromised for any reason, a condition called hypoxia, or a lack of oxygen, results.
Everyone who t ravels t o hi gh a ltitude e xperiences s ome de gree of h ypoxia b efore t heir bod y
adapts to the lower oxygen levels, and they know the feeling well. Simple physical tasks become
much more difficult and mental deficits begin to appear. But altitude isn't the only factor causing
hypoxia: millions of people experience chronic hypoxia and these same symptoms every day at
sea level due to common cardiovascular and respiratory diseases.
Despite this s ignificant i mpact on quality of lif e, large gaps s till exist in our understanding of
how the body is impacted by hypoxia. There is little to no research exploring how altitude affects
vulnerable popul ations, s uch a s aging popul ations with unde rlying c ardiovascular, respiratory,
and metabolic di seases. The pr essing ne ed t o u nderstand s uch ba sic p roblems be comes e ven
clearer when the economic impact of hypoxia is considered. The Altitude Research Center exists
to address these problems using the full array of modern medical research tools.
Our Mission
Improving life through research on how hypoxia affects health and performance
Our Goal
Developing distinguished research programs in four key areas:
1. epidemiology of altitude problems in travelers and the impact of hypoxia on common
diseases in residents of altitude
2. clinical outcomes research
3. integrative physiology
4. cell, molecular and genomic mechanisms of hypoxia
The Impact of Hypoxia
A continuous supply of oxygen i s essential f or proper physical and mental f unctioning. If t his
supply is compromised for any reason, a condition called hypoxia, or a lack of oxygen, results.
Everyone who t ravels t o hi gh a ltitude e xperiences s ome de gree of h ypoxia be fore t heir bod y
adapts t o t he l ower oxygen l evels. At hi gh altitude, s imple physical t asks become much more
difficult and mental deficits begin to appear. But altitude isn't the only factor causing hypoxia:
millions of pe ople a t sea l evel experience c hronic h ypoxia e very day due t o common
cardiovascular and respiratory diseases.
Despite this s ignificant i mpact on quality of lif e, large gaps s till exist in our understanding of
how the body is impacted by hypoxia. There is little to no research exploring how altitude affects
vulnerable popul ations, such as elderly people with underlying cardiovascular, r espiratory, and
metabolic diseases. The pressing need to understand such basic problems becomes even clearer
when t he economic i mpact o f h ypoxia i s co nsidered. The Altitude Research Center ex ists t o
address these problems using the full array of modern medical research tools.
The center has research programs in four distinct areas:
1. epidemiology
2. clinical outcomes research
3. integrative physiology
4. cellular, molecular, and genetic biology
Each a pproach bui lds o n t he ot hers i n or der t o a chieve t he m ost c omplete unde rstanding
possible. Epidemiological s tudies qua ntify t he s cope of a ltitude r elated problems a nd i dentify
specific at risk populations. Integrative studies look at physiological changes on t he level of the
organism w hile c ellular, m olecular, and genomic i nvestigations e xamine t he f undamental
mechanisms underlying these changes. This understanding ultimately improves clinical treatment
of problems related to altitude.
Research
The Altitude Research Center studies hypoxia to improve health and
performance. The Center conducts international, cutting edge work in
hypoxia research from the basic physiological to the molecular level.
The Altitude Research Center Laboratory staffs 6 renowned
scientists:
• Robert Roach, PhD
• Andrew Subudhi, PhD
• Benjamin Honigman, MD
• Colleen Julian, PhD
• Megan Wilson, PhD
• Deborah Thomas, PhD
The ARC laboratory is equipped with a state-of-the-art altitude chamber, comprehensive
laboratory facilities, extensive computing resources, and novel instrumentation.
Original research at the Altitude Research Center:
• Brain Response to Low Oxygen and Relation to Acute Mountain Sickness
• Genetics of Acute Mountain Sickness
• Genetics of Human Athletic Performance
• Genetics of Low Birth-weight Babies at High Altitude
A natural pr ogression i n s cience i s pr oof of concept by s mall, i nnovative exploratory r esearch
programs that can lead into larger, fully funded programs. This is key because at the University
of Colorado Denver Anschutz Medical Campus our ARC researchers and their staffs are 100%
supported by research funding. We support a number of exploratory i nternally funded research
programs that we hope lead to funding opportunities:
• Multiple Sclerosis Progression at Altitude versus Sea Level
• Longevity and Cardiovascular Disease at Altitude
• Malaria and Altitude
Hypobaric Chamber CORE
The hypobaric chamber is an i ntegral CORE of the Altitude Research Center ( ARC). It has 2
sealed rooms in series and each room has a port connected to a vacuum source. When vacuum is
applied to either the main chamber or the lock using chamber controls, air is removed from the
room(s) causing t he pressure i nside t o drop. This pressure drop creates a simulated i ncrease i n
altitude and the resultant hypoxia associated with the specific elevation attained. Hypoxia can be
controlled easily by adjusting the altitude and the pressure and the rooms can then be used for a
variety of research experiments testing the effects of hypoxia on humans.
The CORE can h ouse b etween 2 -4 r esearch s ubjects an d an eq ual n umber o f r esearchers i n
addition t o e quipment which c an measure c erebral f low, ve ntilation a nd ox ygenation, NIRS,
ECHO and a number of other cardiac and pulmonary functions. Any device that is portable can
be used in the chamber in order to measure other physiologic functions such as EEG, EKG etc.
Areas of research interest of the ARC for which the CORE can be used include:
Migraine Headaches
Genetic testing and exercise performance
Cerebral blood flow and auto regulation
CSF vascular dynamics
Pulmonary functions
Cardiac function
Drug metabolism and Kinetics
Hypoxia based Drug development
Prices for CORE use:
Chamber testing: 1 subject-- $1000/day; 2 subjects $1500/day; 3 -4 subjects--$2000/day—may
vary depending on the protocol needs
Protocol Development and Consultation: $200/hr
Animal Models Core (IDDRC)
Director:
Ken Maclean, PhD
303-724-3818
[email protected]
Co-Directors:
Tim BenkeMD, PhD (Design of behavioral studies)
303-724-3568
[email protected]
Michael Mesches, PhD (Behavioral testing operations)
[email protected]
Natalie Serkova, PhD (Imaging and Metabolomics)
303-724-1086
[email protected]
Mission
The objectives of the Animal Models core are three-fold: (1) to provide animal husbandry and
genotyping services to IDDRC investigators; (2) to provide expertise, assistance and facilities for
assessing the behavioral phenotype of genetically modified or other experimental rodents; (3) to
provide access to equipment and expertise for small-animal radiologic imaging and for in-situ
and in-vitro metabolomic analysis using NMR spectroscopy.
Staffing
Consultants
Albee Messing, PhD, DVM Mouse genetic engineering
Elaine Spector, PhD PCR genotyping [email protected]
Gary Zerbe, PhD Biostatistics (behavioral assessment) [email protected]
Technical Staff
Hua Jiang, PhD [email protected]
Marian Maslak [email protected]
Megan Ferguson [email protected]
Services
1. Use of Animal Models; Protocols
Contact Person: Ken Maclean ([email protected])
Dr. Maclean advises IDDRC investigators in the development phase of grant proposals involving
animal models and provides assistance with preparation of animal protocols (he is a member of
the IACUC). A variety of approved standard protocols are maintained in a database and available
for incorporation by investigators into their animal protocols.
2. Animal Husbandry and Genotyping.
Contact Person: Ken Maclean ([email protected])
The Animal Models core maintains a number of colonies of mouse models of IDD and normal
control animals, together with a comprehensive database on the animals, including normative
data on control subjects on each genetic background.
List of Wild-Type and Mutant Mice Currently Available
C57BL/6J wild-type controls
FVB/N wild-type controls
Ts65Dn (female offspring that carry the
Ts65Dn mutation are bred with hybrid
C57BU6J Ei x C3H/HeSnJ F1 males)*
Down syndrome model
Maeda CBS knockout** CBS-deficient
1181*** Transgenic for human CBS gene; Down
syndrome
ho.CBSDH (selective crossing of 1181
with heterozygous Maeda knockout mice)
CBS-deficient homocystinuria
GCDH knockout**** glutaric acidemia
* Reeves, R.H., et al., 1995. Nat. Genet. 11, 177-84.
** Watanabe, M., et al., 1995. Proc. Natl. Acad. Sci., USA 92, 1585-9.
*** Butler, C., et al., 2006. Behav. Genet. 36, 429-38.
**** Koeller, D.M., et al., 2002. Hum. Mol. Genet. 11, 347-357.
The core, in consultation with IDDRC investigators, breeds the mice, provides timed generation
of pregnancies and newborn mice, administers special diets and collects blood and/or tail
samples for genotyping. PCR and FISH-based genotyping are available. The core also provides
training in the correct technique for making blood smears suitable for FISH analysis.
Fees: Occasional use of mice from the Center’s breeding stocks is free. However, the
investigators’ grants must pay for extra mouse cages needed to breed and supply mice on a
regular basis. Please contact Ken MacLean for information regarding these fees.
3. Transgenic/knockout/knockin mouse generation.
Contact: Ken Maclean ([email protected])
In addition, the IDDRC has a collaborative agreement with the Rodent Models Core of the
Waisman Center under the leadership of Dr. Messing whereby vectors can be sent to the
Waisman Center, where all cell and animal work required to generate transgenic/knockout/
knockin mice is performed. Founder mice are then shipped back to Colorado (the investigator
pays for this service, at the Waisman Center’s IDDRC rate). The Colorado IDDRC Animal
Models core breeds and maintains these mice.
The Waisman Center guarantees injection of a minimum of 100 eggs or at least two transgenic
founders. For investigators who require transgenics to be made in non-standard genetic
backgrounds, such as C57BL/6J, special arrangements can be made at an additional cost.
Vectors: The IDDRC’s Molecular Discovery Core provides a vector design and production
service.
4. Behavioral Assessment.
Contact persons: Tim Benke ([email protected]) and Mike Mesches
([email protected])
The Animal Models Core provides animal housing in close proximity to testing with identical
light/dark cycles to avoid artifacts involved in transportation from housing to testing rooms; the
testing suite is sound-proofed and offers the ability to provide a wide range of behavioral tests.
The Animal Models Core provides IDDRC investigators with a battery of standard behavioral
assays to assess cognition, emotionality, motor and sensory function in mice and rats:
Cognition: Morris water maze, radial arm water maze, novel place and novel object recognition,
contextual fear conditioning, stimulus discrimination, learning by instrumental conditioning,
inhibitory avoidance, and conditioned taste aversion.
Altered emotionality: Elevated plus maze, light/dark discrimination, tail suspension, acoustic
startle, and prepulse inhibition.
Motor function: Rotorod, open field, grip strength, and cat walk gait analysis.
Sensory tasks: Visual cliff test, tail flick, and foot shock assessment.
IDDRC investigators with little experience in rodent behavioral analysis can consult with Drs.
Benke or Mesches to develop an experimental strategy (including choice of tests, design of
protocols and power analysis for proper selection of animal numbers).
Limited technical assistance for behavioral testing is available. Typically, Dr. Michael Mesches
trains technical personnel of the investigator’s laboratory in the performance of behavioral tests.
Dr. Mesches also can establish contact with qualified part-time personnel to conduct the
behavioral studies (at the investigator’s cost). Some projects may be beyond the scope of the
standard behavioral phenotyping services offered by the core. In these cases, the Core assists the
investigator with establishing additional behavioral assays designed to enable critical secondary
or follow-up studies. From the design stage to data interpretation of behavioral studies, Dr. Zerbe
is available for biostatistics consultation.
5. Small-Animal Radiologic Imaging
Contact Person: Natalie Serkova ([email protected])
Website
Non-invasive imaging technologies allow for the assessment of anatomical as well as functional
parameters in rodents and enable longitudinal studies of time-dependent effects in the same
animal. The core provides access to the following imaging technologies, at reduced fees to
IDDRC investigators, through the University of Colorado Cancer Center:
• Anatomic MRI: provides high-resolution brain images with superb soft tissue contrast.
The spatial resolution is approximately 90 ?m, which allows both visualization and
volumetric measurements of various parts of the brain (as small as the pituitary gland - 4
mm3) without the use of ionizing radiation or contrast agents.
• Anatomic CT: provides high-resolution images (50 ?m) of bone and soft-tissue structures
(soft tissue resolution is poorer than that of MRI).
• Functional FDG-PET: Injection of radioactive 18fluorine-D-deoxyglucose (FDG) allows
for assessment of brain activity during a 1-hour uptake period (no anesthesia required for
the uptake period). Higher brain activity will correspond to higher intensity on FDG-PET
scans. This is a novel and, to our knowledge, unique imaging application that is currently
under development in the facility.
• Gadolinium-enhanced MRI: Clinically used gadolinium-based contrast agents (for MRI)
are incapable of crossing the blood-brain barrier. Therefore, a disruption of the blood-
brain barrier can be visualized using gadolinium-enhanced MRI.
• Diffusion-weighted MRI: allows for assessment of brain edema and brain necrosis based
on diffusion coefficients (ADC mapping) for tissue water.
• In-Vivo 1H-MRS: allows (after localized MRI) to determine non-invasively major brain
endogenous metabolites, such as the MR neuronal marker N-acetyl-aspartate, glial
marker myo-inositol, neurotransmitters GABA and glutamate, as well as total choline
(membrane biosynthesis) and total creatine (energy metabolism). Additional, expanded
(ex vivo) metabolic profiling can then be achieved by high-resolution NMR after tissue
sampling (see below).
• Molecular Imaging: Using novel radiolabeled or MR relaxing reporters (for PET and
MRI, respectively) attached to a specific compound (e.g., metabolic substrate/precursor),
it is possible to visualize molecular targets (such as certain proteins or metabolic activity)
in vivo.
6. Metabolomics.
Contact Person: Natalie Serkova ([email protected]).
Website
Metabolomics refers to technologies that detect and quantify the low- molecular weight
molecules or metabolites (constituents of the metabolome) produced by active, living cells under
different conditions and times in their life cycles. The metabolomics facility offers IDDRC
investigators the opportunity to analyze genotype-phenotype as well as genotype-envirotype
relationships. N. Serkova is an expert in the field and offers access to the following metabolomic
technologies:
High-resolution one-dimensional metabolic analysis (including 1H-, 13C-, and 31P-NMR
analysis). Over 50 metabolites are quantified simultaneously from a single tissue biopsy/cell
extract:
• From 1H-NMR: neuronal markers, such as neurotransmitters, amino acids, ketone body,
and lipid metabolism;
• From 13C-NMR: glucose and fatty acid fluxes;
• From 31P-NMR: high-energy phosphates and phospholipid precursors.
High-resolution two-dimensional NMR analysis (2D-COSY, NOESY, HSQC) for structural
elucidation of metabolites (see above for the list of metabolites, or identification of unknown
metabolites.
Data Interpretation
Chemical Shift libraries for spectral interpretation (including in-house generated data sets, the
Human Metabolome Database and the NMR Database are available). These databases include
NMR chemical shifts for over 200 endogenous metabolites.
Fees
This section is under construction. For information on pricing, please contact the core director
Ken MacLean.
Bard Center for Entrepreneurship Business Incubator
Contact Information:
Bard Center for Entrepreneurship
535 16th Street, Suite 300
Denver, CO 80202
Office: 303-620-4050
Office Fax: 303-217-8064
[email protected]
www.business.ucdenver.edu/bard
Catherine Kunst, MBA, PhD
Executive Director
Bard Center for Entrepreneurship
Business School at the University of Colorado Denver
Start or Grow Your Company with the Bard Center
The Richard H. and Pamela S. Bard Center for Entrepreneurship was established in 1996 to foster economic
development in Denver and the Rocky Mountain Region. Richard and Pamela Bard's generous endowment turned their
dream into a reality, creating a program that prepares future leaders for success in any business venture.
As part of the Business School at the University of Colorado Denver, the Bard Center provides people with
opportunities to create partnerships with the business community through academics, mentoring, and programs
designed to foster innovation and entrepreneurial development. The Bard Center provides all of the necessary
resources to build a successful business. Our unique combination of experiential courses, scholarships, internships,
access to mentors and alumni networks, on-site incubation and funding allow entrepreneurs to make their dreams
become real. The Bard Center Incubator is open to early stage Colorado companies who meet our admission criteria.
Admission Criteria*
• Executive Summary on Innovative Business Idea
• Growth strategy to exit incubator within 12 to 18 months
• Goals & objectives to execute strategy
• Successful interview(s) with Advisory Council member(s)
*Preference given to University of Colorado (Faculty, Staff, Students, & Alumni) or Bard Center (e.g. Business Plan Winner) affiliates
Incubation Process
• Matched to specific business mentor for optimal growth & success of the company
• Potential for meetings with mentors-in-residence for legal, accounting, public relations & others as needed
• Quarterly updates on financial progress and goals toward meeting milestones to Incubation & Mentorship
Committee or Bard Center Advisory Council
• Access to Rutt Bridges VC Fund or Angel Investors in our community ?
Office Amenities
• Furnished Offices
• Private Kitchen & Meeting
Room
• Wireless and Wired Internet
Service
• Nightly Cleaning Service
• Moderate Fax/Copy Usage
• Scheduled use of shared
conference and class rooms
Leasing Options (per month):
• 6 month lease to start
• Virtual - $150 (mailing address,
usage of shared spaces up to 10
hrs per month)
• Small Office - $500
• Medium Office - $750
• Large Office - $1000
320B
Large
$1000
320C
Medium
$750
320D
Small
$500
320E
Medium
$750
320F
Small
$500
320G
Small
$500
300E
Large
$1000
Computer
Lab
300F
Small
$500
Conf
Kitchen
Shared
Meeting
Space
Large
Classroom
Shared
Meeting
Space
Copy
320H
Large
$1000
300G
Medium
$750
closet
Library
Kitchen
Small
Classroom
BC/GA
Office
BC
Office
BC
Office
Computer
Lab
11 M
MBA
Office
Incubator
Shared Spaces
University of Colorado
11 M
MBA
Office
Shared
UCD
office
320B
Large
$1000
320C
Medium
$750
320D
Small
$500
320E
Medium
$750
320F
Small
$500
320G
Small
$500
300E
Large
$1000
Computer
Lab
300F
Small
$500
Conf
Kitchen
Shared
Meeting
Space
Large
Classroom
Shared
Meeting
Space
Copy
320H
Large
$1000
300G
Medium
$750
closet
Library
Kitchen
Small
Classroom
BC/GA
Office
BC
Office
BC
Office
Computer
Lab
11 M
MBA
Office
Incubator
Shared Spaces
University of Colorado
11 M
MBA
Office
Shared
UCD
office
Bio-Imaging Research Laboratory (BIRL)
David Miller, PhD
Associate Professor
303-724-3464
[email protected]
http://www.uchsc.edu/ucbirl/index.php
UCD Home | Campus Directory | Anschutz Medical Campus
A sampling of UC BIRL clients and tested pharmaceuticals.
The University of Colorado Bio-Imaging Research Laboratory (UC BIRL) provides image
analysis and radiology review services for all clinical phases of drug development, ranging
from small Phase I studies to large, international trials. Our services have been instrumental in
the testing of new compounds, particularly in multiple sclerosis and the approval of Avonex™.
The lab is composed of GCP and HIPAA trained professionals who have extensive
training and experience in radiology, medical physics, computer science and clinical
trials management. UC BIRL provides experienced project managers, interfacing with
both sponsors and sites to ensure the timely receipt, review and reporting of quality
data.
The UC BIRL facility supports both film and digital data, with the ability to convert between
the two. Fully digital (filmless) studies can be accommodated. 21 CFR 11 compliant systems
allow UC BIRL to electronically receive, QA, process, and archive medical image data in a
secure manner.
Typical analyses include lesion counting and volumetrics, focal or whole-brain atrophy measures, serial
registration, RECIST evaluation and lung histogram analysis. The laboratory also has the ability to
process more complicated acquisitions, including diffusion tensor imaging (DTI), magnetization-transfer
(MTR), and functional imaging (fMRI) using BOLD contrast. Custom data analysis for new or emerging
biomarkers is available.
UC BIRL prides itself on providing high quality site management, image analysis, and radiology review.
Our on-staff radiology, medical physics, and technologist support ensure that trials are performed in a
competent, technically sound, professional manner. Please contact us for more information regarding
our services or to schedule a facility visit.
Complete Analysis Support
UC BIRL offers a comprehensive list of services to aid sponsors in their clinical
investigations.
Our services include:
Protocol Design
o Selection of Relevant Imaging Biomarkers
o Determination of Sample Size
o Imaging Intervals
o Image Acquisition Parameters
Site Selection and Training
International Site Management
Image Quality Assurance
Centralized Image Review and Analysis
o Lesion Tracking
o Semi-automated Segmentation and Volumetrics
o RECIST Evaluation
o Brain Atrophy
o Serial Registration
o fMRI
o Dynamic Imaging
o CT Fat Quantification
o Magnetization Transfer
o Diffusion Tensor Imaging
o Perfusion
o MRS
HIPAA Compliant Image Archiving
Experienced Project Management
The Project Managers of UC BIRL are some of the best trained in the industry, with over 25
years combined experience in regulatory compliance, imaging site management and quality
control, data analysis and reporting. Project managers work with both imaging sites and
sponsors, while supervising research associates who assist with data receipt and analysis.
Fees: Under Construction
UC BIRL Image Processing offers state-of-the-art analysis and review capabilities. New technologies
are constantly being explored, developed and integrated into the processing toolbox. Below is a
sampling of current capabilities
• Digital Image Receipt (Internet, MOD, CD, DVD, DAT)
• mini-PACS
• Film Digitization
• Light Box Viewing
• Inter- and Intra-modality Image Registration
• Automated and semi-automated segmentation (Whole Brain, Gray / White Matter, CSF, lesion
volumetrics, etc.)
• fMRI Analysis
• Magnetization Transfer Imaging
• MRS with multinuclear capability
• Tractography
• Dynamic Studies (e.g., DCE-MRI, perfusion)
• Bone density CT measures
• Automated CT fat measures
• ROI Analysis
• Multi-planar reconstruction with sinc or trilinear interpolation
• Inhomogeneity Correction
• Adaptive Filtering
• Motion Correction
• Annotation
• File Format Conversion (ANALYZE, DICOM, ACR-NEMA, vendor specific formats)
Bio-Imaging Research Laboratory (BIRL)
From: Miller, David E
Sent: Thursday, October 01, 2009 2:32 PM
a) How is the quality of your measurements evaluated – quality control?
As part of our standard operating procedures we require training and testing of
core staff prior to their participation on new projects. Additionally we perform
periodic evaluation of our measurement techniques, within and across analysts.
b) What is the turn-a-round time for the service you provide?
Turnaround time is variable, based on the needs of the client and their funding
capabilities. We have turnaround times of less than 24 hours and some on the
order of weeks.
c) Who documents the data provided and signs off on the data?
Signoffs vary based on regulatory requirements and the nature of the research.
A trained PRA or project manager may approve some analysis results while a
medical physicist or radiologist signoff may be required for FDA reviewed
research.
d) Have you had experience providing data for industry?
We have provided image analysis, protocol development and program
management services for phase I-IV clinical trials. Some of our past clients
include Biogen-Idec, BMS and Genentech.
e) Do you have a standard operating procedure manual?
We have standard operating procedures for all laboratory activities. Our SOPs
have been reviewed by quality experts and auditors from a number of different
pharmaceutical companies and clinical research organizations.
f) How will you track billing and financial aspects of your core?
BIRL project managers track study billing and coordinate with the lab director
and Dept. of Radiology Research/Business Manager for all billing activities.
Biomolecular NMR Core Facility
Contacts:
David Jones, PhD
NMR Director
[email protected]
303-724-3600
Website:http://biomol.uchsc.edu/cores/nmr/
Geoffrey Armstrong, PhD
Operational Specialist
800/900 MHz NMR
Phone: 303-724-3331
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Here you will find information about the facilities available, a brief introduction to NMR, the
sort of information can get from it and how can it help your research.
Introduction and History
Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides high resolution
information about the structure and dynamics of molecules in solution at the atomic level. It used
to study a wide variety of molecules from small drug like molecules to macromolecules such as
proteins and nuceic acids.
The NMR Core facilities provideaccess to state of the art
instrumentation to researchers at UCHSC and its affiliated
institutions for the study of the structure and function of biological
macromolecules. NMR core staff and faculty provide assistance to
other users through training or through the development of
collaborations.
The NMR core was established in 1996 through a grant from the
Howard Hughes Medical Institue and the National Cancer Institute.
Ongoing support for the NMR facility is provided primarily by the
University of Colorado Cancer Center and the School of Medicine.
The NMR facility is located in Room L18-1300 on the first floor of
the RC-1 South Building on UCHSC campus at Fitzsimons.
The facility has Varian INOVA spectrometers operating at 500
MHz and 600 MHz, and an 800 MHz NMR spectrometer, which is
located at the UC Boulder campus. Recently a 900 MHz
spectrometer was installed in the facility as part of the Rocky
Mountain Regional NMR Resource. A variety of probes are
available that are suitable for the solution NMR studies of
biological macromolecules including proteins, nucleic acids and
carbohydrates. There is a small wet lab that can be used for sample
manipulations, and an office/computer room for visitors while
using the facility.
Information on access to the core, user fees, documentation etc, can
be found through the links at the top of this page.
Policies and Rates
• Management Committee
• Access to the Facility
• Financial Resposibility
• Acknowledgements
NMR Management Committee
All policies for the the NMR Core are formulated in consultation with the NMR
Management Committee, which consists of faculty members with research programs in
NMR spectroscopy. The commitee meets on an as needed basis.
Access to the NMR Facility and its Services
The NMR facility is open to all researchers from UCHSC and its affiliated institutions,
including other groups within the CU system. The NMR facility is a Cancer Center Core
facility, and members of the Cancer Center are given priority in using the instruments.
Private-sector customers are also welcome to discuss use of the facility with the facility
director.
The NMR Core facility is funded in part by the National Istitutes of Health. Therefore all
users of the facility are required to submit a short annual report on their research efforts
in the core. This report should summarize the results obtained, all grants that are
dependent on the core facility and any publications arising from use of the facility. This
information is used to ensure continued funding of the core.
Successful completion of a BiSMaRC User Training Course by individuals responsible
for executing the NMR experiments will be required, unless prior NMR experience can
be demonstrated. This one week training course will be held several times a year or
whenever there is sufficient demand.
Faculty, staff, and students who have undergone user training and/or certification may
operate the instruments without direct supervision, provided:
1. Financial responsibility is implicitly agreed to as a result of this use (see below).
2. Such use of the Center falls within the guidelines for sponsored research at the in-
house rates for UCHSC research. The associated charges must be charged to a
valid UCHSC account.
3. The only instrumental techniques attempted are routine ones or are those for
which the user has received relevent instruction.
Only those who have been issued a password and told by the NMR Manager that they
may operate the instruments unsupervised may do so.
Individuals who have not undergone training and checkout may submit samples to be
run by qualified facility personnel at the in-house rates plus an additional $20/hr that
applies only to the time the personnel are setting up the data acquisition or working up
the data (minimum 1 hr charge). This option is recommended for users who have
infrequent need for NMR data, or for those who have temporary need of advanced
techniques.
Private sector clients who wish to use the NMR facility should BiSMaRC personnel,
even if they have arrangements with UCHSC personnel for the performance of non-
UCHSC research. Although some arrangements with the private sector fall under the
guidelines for "sponsored UCHSC research," more often they do not.
Financial Responsibility for Charges and Damages
Users are responsible for applicable charges and for damage that results from samples
that are explosive, pressurized, chemically corrosive, radioactive, biologically
dangerous, or that otherwise pose unusual hazards to instrumentation or personnel. In all
such cases, prior advice should be sought with regard to these special samples, but
permission does not absolve any user from responsibility for harm their samples may
cause the Center.
UCHSC researchers use the Center with the understanding that the account used may be
charged up to $5000 for damages incurred as a result of careless or negligent use of the
instrumentation. This obligation does not extend to responsibility for damage that occurs
accidentally and unavoidably during normal use.
Acknowledgements
All publications resulting from use of the NMR core facilities must acknowlege use of the core.
A suitable acknowledgement would be "The NMR core facilities are funded by the University of
Colorado Comprehensive Cancer Center and the UCHSC Program in Biomolecular Structure".
Use of the 800 MHz Spectrometer must also include the following statement. "The 800 MHz
NMR sectrometer was purchased with funds provided the W.M. Keck Foundation"
Bimolecular NMR
From: David Jones [mailto:[email protected]]
Sent: Monday, November 02, 2009 5:25 PM
a) How is the quality of your measurements evaluated – quality control?
The performance of all NMR instruments is routinely calibrated against known standard
samples that are the industry standard. Performance for all user samples is assured by
addition of internal controls that are widely recognized to be inert. Alternatively,
external standards contained within a capillary can be included in the sample. These
controls provide a set of known benchmarks for calibration and optimization of the NMR
spectrometer. The effects of sample on performance can be directly inferred from the data
from these controls.
b) What is the turn-a-round time for the service you provide?
This depends on complexity of experiments to be performed and the number of samples.
Simple 1D proton or carbon spectra can be acquired rapidly within several days. More
complex experiments, turnaround is between 1 - 2 weeks
c) Who documents the data provided and signs off on the data?
The Core Director
d) Have you had experience providing data for industry?
Yes
e) Do you have a standard operating procedure manual?
f) How will you track billing and financial aspects of your core?
Billing is tracked automatically through a program designed to capture the name of the
instrument operator, a descriptor of the project or service, and the individual to be billed
for the service. Billing accounts for actual instrument time used and operator Assistance
fees. The Financial Aspects of the Core are maintained by the Program in Structural
Biology and the University of Colorado Cancer Center and are thoroughly reviewed on
an annual basis.
Biophysics Core Facility-
The Program in Biomolecular Structure
Contacts:
Dr. Robert S. Hodges, PhD
Director
303-724-3253
[email protected]
Jackie Newnam,
Administrator and primary
contact for information
regarding The Program
including graduate studies.
303-724-3268
[email protected]
Brooke Hirsch, PhD
Facility Manager
303-724-3322
[email protected]
Website:http://biomol.uchsc.edu/cores/biophysics/
Biophysical Studies
The Biophysics Core Facility is a user facility owned and operated by The Program in
Biomolecular Structure at the University of Colorado Health Sciences Center. We opened our
doors in early 2001 and have since served a wide variety of researchers on diverse projects in
both academia and industry.
We currently have resources to study biomolecular structure and thermodynamics with Biacore
surface plasmon resonance phenomonen, CD/ORD, ITC, DSC, fluorescence spectroscopy, and
analytical ultracentrifugation (AUC). Mass spectroscopy, LC/MS/MS, HPLC, amino acid
analysis are also available.
Facility Users
The Facility provides professional collaborations, training, and instrument time to researchers
associated with both nonprofit organizations and private institutions. After a user is trained, they
may use the instruments independently. Please contact us if you would like the Biophysics Core
Staff to run or analyze your samples.
Training
The Biophysics Core Staff are available to train users on each of the instruments located in the
core. We offer one-on-one and group training to those interested in operating the instruments.
Every user must be trained on each instrument before they are allowed independent use. There
will be a one-time charge for training each individual per machine. After the user is trained,
instrument user fees will be assessed. All fees associated with training and instrument use are
listed on the Rates and Policies page.
Scheduling
All scheduling is done with the online calendar. After you are trained to operate an instrument,
you may request an account from Brooke Hirsch. Priority is generally on a first-scheduled first-
served basis. Users must sign up for an instrument at least 48 hours in advance. Similarly, users
must cancel reservations at least 48 hours in advance. If a user fails to cancel an instrument
reservation 48 hours before the reserved start time, a charge will be accessed for instrument time.
Rates
Fees for University of Colorado and Affiliated Users
Instrument
Training
Session
(cost per user)
Trained users at CU and
affiliates independent
users
Biophysics Core handles samples
for CU and affiliates
JASCO 815 CD $80 $15.00 $36.00
Fluoromax-3 $50 $9.00 $30.00
Microcal VP-
DSC
$50 $10.00 or $80 per day $40.00 or $125 per day
Microcal VP-ITC $50
$15.00 (4 hr. min.) or
$80 per day
$35.00 (4 hr. min.) or $200 per day
Biacore 3000 $150
$20.00 (4 hr. min.) or
$110 per day
$50.00 (4 hr. min.) or $200 per day
Analytical
Ultracentrifuge
$150
$20.00 (for velocity) or
$160 per day $5.00 (for
equilibrium) or $100
per day
$30.00 (for velocity) or $240 per
day $8.00 (for equilibrium) or $200
per day
Amino acid
analysis
$60 $30 per sample $40 per sample
Fees for Industry/Company Users
Instrument
Training
Session
(cost per user)
Trained
Industry/Company user
independent user
Biophysics Core handles samples
JASCO 815 CD $100 $16.00 $40.00
Fluoromax-3 $100 $12.00 $37.00
Microcal VP-
DSC
$75 $19.00 or $100 per day $43.00 or $250 per day
Microcal VP-ITC $75
$19.00 (4 hr. min.) or
$100 per day
$43.00 (4 hr. min.) or $250 per day
Biacore 3000 $200
$25.00 (4 hr. min.) or
$135 per day
$62.00 (4 hr. min.) or $250 per day
Analytical
Ultracentrifuge
$200
$25.00 (for velocity) or
$200 per day $7.00 (for
equilibrium) or $125 per
day
$37.00 (for velocity) or $300 per
day $10.00 (for equilibrium) or
$250 per day
Amino acid
analysis
$100 $37 per sample $50 per sample
Biorepository Core Facility
Contact Information:
Director
M. Scott Lucia, MD
303-724-3470
Email: [email protected]
Website: under construction
The University o f Colorado Denver Biorepository ( UCDBCF) hous ed i n t he Department of Pathology
functions as a campus-wide bi orepository facility offering a wide range of services t o the University of
Colorado Denver (UCD) research community and beyond. UCDBCF manages a l arge number of organ-
specific biorepositories i n support of research projects at UCD and its affiliated hospitals. In addition,
UCDBCF is active on a national level providing centralized biorepository and pathology services for
multi-institutional SWOG, NIH, and NIDDK r esearch networks. UCDBCF has the flexibility to offer a
full r ange of services ranging f rom pr otocol development an d p atient r ecruitment to simple sp ecimen
storage. Situated in a department that bridges basic and clinical sciences, the UCDBCF is in an ideal
position to promote and support interdisciplinary research.
Facilities
• Full Service Pathology Lab
• Automated Tissue Processing
• Automated H&E Staining
• Automated Immunostaining
• Freezer Repository
• Badge Access
• UCD Security equipment monitoring
• Network based temperature monitoring
• 4300 sq ft
• Slide and Block Repository
• Badge Access
• Environmental Control
• 1700 sq ft
• Advanced Imaging Facility
• Aperio Scanscope
• 10 terabytes of storage
• Web access to images
Services
• Protocol & SOP Development
• IRB Assistance
• Collection Kit Design
• Patient Consent
• Specimen Collection
• Phlebotomy
• Inventory Management
• Histology
• Tissue Processing
• Routine H&E
• Microtomy / Cryomicrotomy
• Immunohistochemistry
• Special Stains
• Special Processing
• Tissue Microarrays
• Laser Capture Micro dissection
• DNA/RNA/Protein Isolation
• Imaging
• Whole Slide Imaging
• Image Analysis
• Epidemiology / Biostatistics
• Molecular & Clinical Diagnostics
Experience
Our biorepository staff brings over 70 combined years
of experience in biorepository management and
coordination of multi-institutional pathology and
biorepository core operations.
Our ex tensive ex perience i ntegrating research w ith
routine c linical p ractice, specimen co llection an d
storage, and information technology has enabled us to
maximize efficiency and accuracy in all aspect of our
biorepository m anagement. Advanced p athology,
histology and laboratory expertise allow us to provide
researchers w ith hi ghly s pecific di agnostic
characteristics and r eliable d ata for t he specimens
stored in our biorepository.
Price List: 8/01/09
Detailed services: UCD External
Database query and specimen tracking $50.00 per hr $70.00 per hr
Histology of archived tissue (Includes costs of specimen maintenance):
Unstained section from block $4.10 per slide $7.00 per slide
H&E stained section from block $9.10 each $15.00 each
Immunohistochemistry $50.00 per slide $75.00 per slide
Creation of tissue microarray $665.00 $1000.00
Acquisition of serum aliquot $15.00 per aliquot $75.00 per aliquot
Acquisition of tissue sample $50.00 per hr $75.00 per hr
Biobank services
Monitor probe $300.00 per freezer N/A
Monitor relay $600.00 (up to 8 freezers) N/A
Freezer monitoring and maintenance: $1.00 per day per freezer N/A
Inventory database creation: $75.00 per hour N/A
Inventory restructure: $75.00 per hour N/A
Inventory management: $30.00 per hour N/A
Biorepository Core Facility
From: Lucia, Scott
Sent: Thursday, October 08, 2009 11:20 AM
a) How is the quality of your measurements evaluated – quality control?
We do not make measurement per se. The services provided by the biorepository
core consist of assistance in the procurement, storage, processing and distribution
of patient bi ospecimens for r esearch us e. Therefore, quality i s opt imized by 1)
proper collection and handling techniques, 2) assuring integrity of the data, and 3)
assuring p roper usage o f bi ospecimens. 1) To opt imize pr oper c ollection a nd
handling, s pecimens a re c ollected us ing s tandardized c ollection ki ts a nd
protocols. E ach s pecimen container/tube i n t he kits has a uni que barcode l abel
that links it to the c ollection kit barcode a nd uni que pa tient ID t o he lp pr event
misidentification of samples. Data collected on the accompanying tracking forms
include t he date and t ime of collection, t ime of blood f low i nterruption, time of
centrifugation, time s ample was s tored in -80, etc. At points where s amples ar e
handed ove r t o ot her p ersons, s uch a s t he t ime it i s transferred from clinic to
processing l ab, we have s ign-offs for t he person who handled t he s ample up t o
that poi nt. The da ta o n t he t racking f orm i s e ntered i nto t he bi orepository
database by a biorepository technician and r eceives a finalizing signature by t he
core d irector o r co -director i f e verything i s i n or der. If pr oblems a re f ound,
personnel that handled the specimen will be contacted for clarification.
Data en try q uality i s c hecked on w eekly b asis b y a s upervisor us ing a random
selection of previously entered forms. If errors are found, additional checking of
forms will be initiated. As previously mentioned, our freezers are monitored by
an alarm system that records temperatures in real time and has automatic dial-out
when t he t emperature exceeds a s et t hreshold. We p hysically i nspect t he
biorespository on a da ily b asis dur ing w hich e ach i ndividual c ryo unit i s
examined. Problems a nd a ctions t aken t o r esolve t he situation ar e r ecorded. In
situations where l iquid samples a re of >10 years i n s torage, evaporation may
occur due to deterioration of tube seals. In addition to visual inspection, samples
may b e monitored b y t esting f or s odium or a lbumin l evels. If t he v alues ar e
within the acceptable range, samples are considered adequate and may be released
for di stribution. Additional quality control assays will be provided i f required or
requested by individual projects. RNA and DNA concentration and integrity can
be assessed using Nanodrop or the Agilent Bioanalyzer instruments. If necessary,
the l ab ha s a de dicated ABI 7700 s equence a nalyzer f or qua ntitative r eal-time
(RT-) PCR us ing T aqman or S YBR-green t echnology t hat c an be us ed i f
additional analysis and/or quality control is needed.
A committee composed of members of t he UCD departments i ncluding but not
limited t o t he de partments of pa thology, s urgery and m edicine s erves a s a n
advisory committee, th e Tissue P rocurement Committee ( TPC) f or th e general
operation of t he B CF. T he c ommittee w ill a lso be c harged w ith r eview of
specimen requests and prioritizing studies for the utilization of materials from the
biorepository. O nce a n i nvestigator h as c ontacted t he M edical Director or
Supervising Technologist t hat he/she wishes to obtain biological materials f rom
the B CF, a que ry i s made i n t he da tabase t o a ssess w hether or not a dequate
samples f or t he research i n que stion i s available. T he i nvestigator w ill t hen
submit to the Medical Director a short (2-3 pages) proposal as t o t he nature and
importance of the study, the need for biorepository samples, and the likelihood for
success. This proposal will then be distributed to members of the TPC for review
and, if satisfactory, approval to begin distributions.
b) What is the turn-a-round time for the service you provide?
This de pends on t he na ture of t he s ervices r equested a nd t he t otal nu mber of
specimens. Collections occur on same day. Pulls and processing requests must
be preapproved (see above) and then may take up to two weeks depending on how
much labor is required.
c) Who documents the data provided and signs off on the data?
See number 1 above.
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Yes.
f) How will you track billing and financial aspects of your core?
A c ost pe r s pecimen a nd/or hour ly charge r ate a pplies f or ou r s ervices ( see
attached cost sheet). F or on-campus i nvestigators, requests for services must be
accompanied b y a s peed t ype. Industry i s di rect bi lled. E xpenses a re t racked
through the biorepository expense account set up in the Department of Pathology.
University of Colorado Cancer Center
Biostatistics and Bioinformatics
Shared Core Service
Contacts:
Anna E. Barón, PhD,
Director
303-315-7502
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/biostat/index.aspx
The University of Colorado Cancer Center Biostatistics and Bioinformatics Core provides
quantitative and information science support for the planning, design, analysis and presentation
of basic science, clinical, and epidemiological investigations by Cancer Center members.
Services
• Consultation on study design (clinical and basic science, including gene expression arrays
and proteomics experiments)
• Consultation on sample size and power
• Development of data collection, storage, and quality control procedures (basic science
and clinical studies, protocol review and monitoring)
• Data analysis, including genomic and proteomic data
• Collaboration on manuscript and oral presentation preparation, and grant proposal
development
Rather than charging users for services, we ask Cancer Center investigators to write in funding
for biostatistics and bioinformatics support on grants and contracts, then to acknowledge the
Core in any publications.
How to Use the Core
Your study's initial design and data collection strongly affect its analysis and interpretation.
Please involve us during the design phase to we can help make sure your project is successful.
Our work is usually done as part of protocol development for clinical trials or during project
design for other cancer-related research.
To get started, please contact Anna Barón, director.
• You will meet with one of our Core biostatisticians or bioinformaticians to present your
hypothesis and goals.
• We will help you put together a basic scope of work and general timeline and identify
key collaborators to include.
• We will work with you throughout your project.
No fees
Biostatistics & Bioinformatics (UCCC)
From: Baron, Anna
Sent: Thursday, November 05, 2009 12:51 PM
NONE OF THIS APPLIES TO THE Biostatistics & Bioinformatics (UCCC)
a) How is the quality of your measurements evaluated – quality control?
n/a
b) What is the turn-a-round time for the service you provide?
n/a
c) Who documents the data provided and signs off on the data?
n/a
d) Have you had experience providing data for industry?
n/a
e) Do you have a standard operating procedure manual?
n/a
f) How will you track billing and financial aspects of your core?
n/a
Cellular Systems and Analysis Core Unit (IDDRC)
Director:
K. Pfenninger, MD (cell culture and biochemical analysis of the brain)
303-724-3466
[email protected]
Associate Director:
John R. Sladek, PhD (neuroanatomy and histology)
303-724-0629
[email protected]
Mission:
The overall mission of this core is to stimulate and facilitate IDD-related research at the cellular
and tissue levels. This core also performs lymphoblast immortalization for bio-banking and
genomic analysis.
The Cell Systems and Analysis Core has two sections focused on cell culture and one on brain
tissue, respectively. This core is designed not only to advance ongoing in-vitro studies but to
assist investigators without experience in the area with the adoption of in-vitro approaches. In
addition, this core provides the technology and assistance to analyze brain tissue with
neuroanatomical and cell labeling techniques as well as with approaches of subcellular
fractionation and biochemistry.
Staffing:
Renata Collard, PhD
Barbara Blanchard, MS
Services:
Cell Culture
Services include advice and assistance with the use and analysis of in-vitro model systems and
interpretation of results. The cell culture bank stores and carries a collection of cell lines that can
be grown for research use. In addition, the cell culture core performs lymphoblast
immortalization for biobanking by the IDDRC’s Translational Nexus.
If you are interested in any of the below listed Cell Culture services for your research please
contact Dr. Karl Pfenninger at [email protected].
1. In-vitro System Consulting.
K. Pfenninger is available to IDDRC investigators for the evaluation of experimental approaches
involving in-vitro systems. Options include the possibility of culturing primary neurons or glial
cells from genetically engineered rodents, the use of wild-type rodent neurons or glial cells for
transfection, and/or the use of cell lines for a particular study. Also part of the service is advice
on the feasibility of visualizing particular functions or functional changes in cells using optical
methods or biochemical approaches. This consulting service is designed primarily for those
investigators with little or no experience with in-vitro models or neuronal/glial cultures.
2. Cell Lines and Primary Neural Cells.
The Core is a repository for a variety of cell lines and fibroblasts for IDD-related research use
(see Table, below). Investigators can order from the list, the thawing and initial culture of cell
lines for further expansion and experimentation by the investigator’s laboratory. In addition, the
core can grow newly acquired cell lines for investigators and bank them for later use. In
collaboration with the IDDRC’s Molecular Discovery Core, the Cell Systems and Analysis Core
DNA-profiles human cell lines as needed to authenticate their identity. For investigators who
wish to have many cell lines grown in large quantity, the core can provide this service if the
work load permits, but the grant supporting the investigator’s study must buy personnel time in
the core to perform this service. For pilot studies or small projects the Core provides cells at no
charge.
Species Cell Type Designation
African green
monkey
male kidney Cos-7
Drosophila Schneider S2
Hamster
Chinese hamster
ovary
CHO K1
Human
cervical cancer HeLa
glioblastoma 10-08, 13-06, U373
hepatocell. Carcinoma HEPG2
kidney (embryonic) HEK293
lung, small cell
carcinoma
SCLC H510, N-417, NC1-146, NC1-H345
melanoma WM-35, WM-1617, WM-1158
melanocytes
(epidermal, normal)
NHEM 693
prostate carcinoma LNCaP, PC3, PC3M-MM2, TSU Prl
Mouse
myoblasts C2C12
melanoma B16, B16 MC1
pheochromocytoma MPC12
Rat
pheochromocytoma PC12
prostate carcinoma At-3, Mat-Lu, Mat-LyLu
The Core also provides training and assistance with the preparation of primary neural cell
cultures. For experimentation with very limited scope or pilot studies, the Core prepares cultures
of rat or mouse cortical explants or dissociated cells. For larger studies the principal
investigator’s laboratory receives appropriate training and advice. Training also may include the
establishment of other neuron populations (those from hippocampus, cerebellum, olfactory bulb,
peripheral ganglia and others) or of glial cell types.
3. Lymphoblast Immortalization.
Immortalized lymphoblasts provide DNA in essentially unlimited quantities and enable analysis
of chromosomes, copy number variations, RNA, etc. R. Collard was trained in lymphoblast
immortalization using EBV and is now performing this function for the Translational Nexus. R.
Collard spends about half of her time on lymphoblast immortalization.
4. Other Cell Culture Services.
a) Mycoplasma Testing: The cell culture core routinely tests cells for potential mycoplasma
contamination and provides this service for cultures grown and maintained in the different
IDDRC investigator laboratories.
b) Cell Transfection: The Cell Culture Core has acquired an Amaxa Nucleofector
electroporator, which is the best currently available instrument for introducing vectors into
difficult-to-transfect cell types, including primary neurons. This equipment, and advice on how
to use it, are available to IDDRC members.
c) Cell Processing and Analysis: K. Pfenninger (with members of his laboratory) and R. Collard
provide advice and training on how to handle cultures for live-cell imaging and how to process
them for, e.g., immunolabeling or a variety of biochemical approaches.
Brain Tissue Services
If you are interested in any of the Brain Tissue services listed below for your research please
contact Dr. Karl Pfenninger at [email protected] or Dr. John Sladek at
[email protected].
1. Subcellular fractionation and biochemical analysis.
K. Pfenninger provides advice for the preparation and analysis of subcellular fractions such as
synaptosomes from adult rodent brain, growth cones from fetal rodent brain, myelin,
mitochondria, and other membrane fractions. Tools and instrumentation to perform such
analyses are readily available in the IDDRC (see Molecular Discovery Core).
2. Neuroanatomy and Histology.
J. Sladek is available to advise investigators on the optimal neuroanatomical and -histological
techniques to be used for examining the brains of experimental animals and on the interpretation
of results. B. Blanchard is in charge of the various histology services.
a) Stereotaxic implantation of cells, factors and viral vectors. The Sladek laboratory has a rodent
stereotaxic apparatus with a digital positioning manipulator that allows for a high degree of
precision and reproducibility.
b) Brain perfusions can be performed on a wide variety of animal models that include rats, mice,
guinea pigs, rabbits, and non-human primates with a range of routine to specialized fixatives
including paraformaldehyde, Bouin’s, glutaraldehyde, and others. B. Blanchard is familiar with
the advantages and disadvantages associated with a particular fixative or fixation method and can
advise the members of the IDDRC of best uses and potential obstacles depending on their
experimental needs. Expertise also is available in the perfusion of embryonic and postnatal
animals, which requires special technical skill and knowledge of the appropriate fixation
methods.
c) Neurohistochemical Preparation: B. Blanchard can produce consistent, uniform tissue
sections ranging in thickness from less than 5? to 100?m or more, with the use of different
embedding techniques, and with a rotary microtome, freezing sliding-blade microtome, cryostat,
or Vibratome (for fresh tissue).
d) Staining: Routine histological preparation of tissue sections can be done with a variety of
staining and counterstaining approaches, with dyes such as cresyl violet, methyl green,
hematoxylin, and many others depending on the structure(s) needing to be visualized.
e) Immunohistochemical staining for various neuronal and glial markers, synaptic markers,
indicators of differentiation or development, receptors, transmitters, enzymes and markers of
inflammation. This may involve the application of double-labeling techniques, with the use of
permanent dyes and chromagens, such as diaminobenzidine, nickel-enhanced diaminobenzidine,
Vector Red, Vector Blue, and others, or fluorescent conjugated markers, such as fluorescein,
rhodamine, Cy2, Cy3, Cy5, and AlexaFluors. The principal investigator’s laboratory provides
the appropriate antibodies.
User Fee Table: Under construction. For information about pricing, please contact
Dr. Karl Pfenninger.
Center for Computational Mathematics (CCM)
Jan Mandel, PhD, Professor
Director
303-556-4475
[email protected]
Russel Boice
System administrator
[email protected]
303-556-5394
http://ccm.ucdenver.edu/facilities
Facilities
The Center for Computational Mathematics and the Department of Mathematical and Statistical
Sciences provide high-end scientific computing facilities, including professional technical
support, to research projects, graduate education, and affiliated faculty.
The cost of the facilities will be allocated based on total FTEs of all users. Internal use is covered
by existing UCD internal funding. Users who are paid from externally funded projects will need
to include a Computer Services item in the proposal budget and the services will be charged to
their project based on their total FTEs worked on the project. Federal rules require that all usage
is treated consistently. Approvals are pending for exact rules and rates.
On-Site Computing Facilities
• Beowulf cluster with 72CPUs, 72GB memory, and 10Gb/s interconnect
• machine room with independent air-conditioning
• numerous Linux servers with up to 16 Cores and 64 GB RAM
• NVIDIA Tesla S1070 GPU supercomputing system (960 cores) with CUDA development tools
• Linux and Windows workstations in public areas and offices, including 10 public workstations
with 30in monitors
• multiple laser printers, including high-speed color printers
• gigabit optical fiber backbone
• scientific and software development software, including Matlab, Mathematica, compilers, and
debuggers
• disk arrays with disk-to-disk backup of users' files
The Center for Computational Mathematics and the Department of Mathematical and Statistical
Sciences has a professional full time system administrator.
Front Range Consortium Supercomputing Facilities
• IBM BlueGene/L, one rack with 2048 cores. Front end with 4 POWER 5 nodes, disk array, and
connection to NCAR's mass storage. The computer is located at the National Center for
Atmospheric Research in Boulder.
• SUN Blade Constellation, 10 racks with total 7680 cores and aggregate performance of over
100TeraFLOP/s. One of the racks accelerated by NVIDIA Tesla S1070 GPUs. Disk array with
raw capacity 768 TB. The computer is currently on order and will be located at CU Boulder.
The Front Range Consortium supercomputers are funded by joint NSF grants to UCD, CU Boulder, and
the National Center for Atmospheric Research. Their use is free, but users who require support or access
from CCM on-site facilities are subject to the Computing services fee.
*Core approval pending
Center for Computational Mathematics
From: [email protected] [mailto:[email protected]]
Sent: Thursday, October 01, 2009 7:44 PM
a) How is the quality of your measurements evaluated – quality control?
We do not measure anything.
b) What is the turn-a-round time for the service you provide?
We do not provide separate track able services. For support issues, it
is generally same or next day. Computer jobs run immediately.
c) Who documents the data provided and signs off on the data?
Not applicable. We do not provide any data.
d) Have you had experience providing data for industry?
Not applicable. We do not provide any data.
e) Do you have a standard operating procedure manual?
No.
f) How will you track billing and financial aspects of your core?
With the help of the Dean's office.
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Behavioral Medicine Core (NJH)
Mailing Address:
Room K340b Goodman
National Jewish Health
1400 Jackson Street
Denver, CO 80206
Contacts
Fred Wamboldt, MD Mary Klinnert, PhD Joshua Miller
Lab Director Core Lab Supervisor Technical Assistance
303.398.1827 303.398.1231 303.398.1710
Overview
The Behavioral Medicine Core Lab (BMCL), located at the National Jewish Health site, is part of
the UCD Colorado Clinical and Translational Sciences Institute (CCTSI) and provides a variety of
services to assist CTRC investigators with behavioral and psychological components of Adult and
Pediatric protocols.
Services Include
• Treatment Adherence Monitoring
• Generic and Illness-Specific Quality of Life and Psychosocial Questionnaires (On-Line
and Off-Line Questionnaire Service and Support)
• Structured Psychiatric Diagnostic Interviews
• Family Asthma Management System Scale
• Structured Interpersonal Assessment and Scoring
• Consultation: BMCL Members can consult on including Behavioral Medicine measures in
your research.
The BMCL strongly encourages consulting members of the lab about inclusion of behavioral
medicine measures in your research. For consultation and additional information concerning any
of our provided services, please contact the BMCL staff.
Treatment Adherence Monitoring Systems
Four objective systems are available for tracking treatment and assay adherence.
• MDILog - electronic inhaler sleeves containing a microprocessor that records and stores
medication adherence.
• Doser - used to track adherence of inhaled medications (metered dose inhalers).
• MEMs Cap - used to track adherence with oral medication (pills). It can also be used to
track at-home sample collection such as salivary cortisol samples.
• EncoreAnywhere and/or Restraxx - CPAP adherence solution for gathering and
monitoring patients' adherence data over the web.
The adherence tracking devices, except for EncoreAnywhere and Restraxx, are provided to the
investigator with technical support, including set-up, data downloading, data verification, and
delivery of complete data sets. EncoreAnywhere and Restraxx is strictly a data monitoring
service.
Structured Interpersonal Assessment and Scoring
• Five Minute Speech Sample (FMSS) – brief measure of expressed emotion (EE) derived
from a speech sample.
• Family Asthma Management System Scale (FAMSS) - assesses eight aspects of asthma
management from a family systems perspective.
Full on-site or off-site training is available for both assessments via teleconferencing. Training
includes proper administration of the interviews, rating and coding the interviews, and how to
interpret the coding system. The BMCL will also help code a sample of the interviews for your
specific protocol to help maintain reliability with the measure.
Questionnaires
The following questionnaires are provided on-line* or off-line for protocols needing Generic and/or
Illness Specific Quality of Life assessments:
• Baseline Dyspnea Index and Transitional Dyspnea Index (BDI-TDI) (off-line)
• Clarke Survey of Hypoglycemia Awareness (on-line)
• Diabetes Distress Scale (on-line)
• Dyspnea-12 Questionnaire (off-line)
• Epworth Sleepiness Scale (on-line)
• Fatigue Severity Scale (FSS) (off-line)
• GEMS Activity Questionnaire (off-line)
• Hypoglycemic Fear Survey (on-line)
• Impact of Weight on Quality of Life (IWQOL-Kids) (off-line)
• Obesity Quality of Life Questionnaire (off-line)
• Pediatric Asthma Caregiver’s QoL Questionnaire (PACQLQ) (off-line)
• Pediatric Quality of Life Questionnaire (PedsQL) (off-line)
• Pittsburgh Sleep Quality Index (PSQI) (on-line)
• SF-36 Health Survey (version1) (off-line)
• SF-36 Health Survey (version 2) (on-line)
• World Health Organization Quality of Life (WHOQOL-100) (off-line)
• Youth/Adolescent Questionnaire (YAQ) (off-line)
The following questionnaires are provided on-line or off-line for protocols needing
Psychosocial/Mental Health Domain assessments:
• Behavior Assessment System for Children (BASC-2) (off-line)
• Brief Symptom Inventory (BSI) (off-line)
• Center for Epidemiologic Studies-Depression Scale (CES-D) (on-line)
• Child Behavior Checklist (CBCL) (off-line)
• Prime MD-Generalized Anxiety Disorder (GAD-7) (on-line)
• Prime MD-Patient Health Questionnaire (PHQ-9) (on-line)
• Semi-structured Interview for DSM-IV (SCID PQ-X, computer screening version) (off-line)
• State-Trait Anxiety Inventory (off-line)
*New instruments may be developed for on-line use at the investigator’s request.
NJH CTRC Behavioral Medicine Core Lab Assay Pricing
BMCL- Procedures Name/Device
Full 100%
Pri cing
Adherence Monitoring
MDILog $42.25
-MDILog computer
-Sleeves
-Docking station
-PC Software License
Doser
-regular Doser $27.03
-Doser CT $30.70
Canister weight tracking $11.40
MEMs Cap
-Mems Track Cap $25.00
-Mems Smart Cap $30.50
-Mems Smart Cap 38mm CR $32.50
-Mems Track Cap 38mm CR $26.00
-Powerview software
-Plastic Bottles
Encore Anywhere CPAP monitoring $152.30
On-line questionnaire
service
Quality of Life SF-36 Health Survey (version 2) $19.25
Pediatric Quality of Life Questionnaire
(PedsQL)
$13.60
Generic Core Scales
Family Impact Module
Mental Health
Center for Epidemiologic Studies-Depression
Scale (CES-D)
$17.40
Prime MD-Patient Health Questionnaire (PHQ-
9)
$11.70
Prime MD-Generalized Anxiety Disorder (GAD-
7)
$11.70
Child Behavior Checklist (CBCL) $19.60
Sleep Epworth Sleepiness Scale $11.70
Pittsburgh Sleep Quality Index (PSQI) $17.40
Diabetes Clarke Survey of Hypoglycemia Awareness $11.70
Diabetes Distress Scale $17.40
Hypoglycemic Fear Survey $17.40
Off-line questionnaire
support
Quality of Life- general SF-36 Health Survey (version 1) $23.10
World Health Organization Quality of Life
(WHO-QOL)
$21.20
Obesity QoL
Impact of Weight on Quality of Life (IWQOL-
Kids) $22.80
Obesity Quality of Life Questionnaire
Asthma QoL
Pediatric Asthma Caregiver’s QoL
Questionnaire (PACQLQ) $24.70
Pedatric Asthma Quality of Life Questionnaire
(PAQoLQ) $26.60
Mental Health Brief Symptom Inventory (BSI) $23.33
Child Behavior Checklist (CBCL) $25.20
Semi-structured Interview for DSM-IV (SCID) $21.20
State-Trait Anxiety Inventory Intro Kit $14.80
Behavior Assessment System for Children
(BASC-2) $26.17
Sleep Fatigue Severity Scale (FSS) $11.70
Breathing BDI-TDI $15.50
Diet Youth/Adolescent Questionnaire (YAQ) $34.15
Activity GEMS Activity Questionnaire $24.70
Pubertal Development Tanner stages – Male and Female $7.60
Interpersonal
Coding/Training
Five Minute Speech Sample (FMSS)-Advanced
Training $2,810
FMSS Consensus/Reliability Coding $28.10
Family Asthma Management System Scale $1,867
System for Coding Affect Regulation in
Families
Lab Director: Fred Wamboldt, MD
Behavioral Medicine Core Laboratory Service
a)
Quality control procedures depend on the nature of the service provided. For example,
with standardized questionnaires we develop electronic surveys if possible, with multiple
checks for accurate scoring. For data collected with psychological measures we are able
to provide psychometric calculations of internal consistency, test-retest reliability, etc.
For interpersonal assessment systems, multiple staff and trainees code the data, and we
assess reliability among coders using kappas or ICCs. Data sets derived from any
procedure are examined on a pre-set schedule for complete and accurate entries.
How is the quality of your measurements evaluated – quality control?
b)
Turn-a-round times depend on the service provided. Some procedures require daily
checks while for others weekly or bi-weekly data management is sufficient. For example,
adherence monitoring involves dispensing and receiving/downloading monitoring devices
in real time as Investigators are collecting data from subjects.
What is the turn-a-round time for the service you provide?
c)
Fred Wamboldt, MD, Mary Klinnert, PhD, or Joshua Miller, Lab Tech, provide
documentation and sign-off for different procedures.
Who documents the data provided and signs off on the data?
d)
No
Have you had experience providing data for industry?
e)
We have standard operating procedure manuals for each service or procedure that we
provide.
Do you have a standard operating procedure manual?
f)
Ronnie Calzada ([email protected]), the NJH CTRC administrator, tracks services
and manages billing and financial aspects of the BMCL.
How will you track bil ling and financial aspects of your core?
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Inflammation and Immunology Core Lab (NJH)
Mailing Address:
Room A442d Smith
National Jewish Health
1400 Jackson Street
Denver, CO 80206
Contacts
Lisa Maier, MD
Core Director
3030-398-1983
Beth Canono
Lab Manager
3030-398-1658
Website:http://cctsi.ucdenver.edu/Research-Resources/Clinical-Research-
Resources/Pages/NJHCoreLab.aspx
About This Lab
The NJH Core Lab is part of the UCD Colorado Clinical and Translational Sciences Institute (CCTSI).
With rare exceptions, the NJH Core lab is unique from the TCH and UCH Core Labs. The focus here is
specialized immunologic assays relevant to immunity and inflammation and not clinical diagnostic assays.
We have access to coordinate with the NJH clinical immunology labs with in-house pricing, providing
investigators access to unique immunology and inflammation assays.
Some examples of our capabilities include:
• Immunofluorescent Cell Staining (PBMCs, lymphyocytes, RBCs, BAL and induced sputum)
• Flow Cytometry analysis (Cell quest Pro and Flojo)
• Lymphocyte Proliferation Assays (including responses to beryllium and various steroids)
• Cell Culturing +/- various stimulation
• DNA extraction from various tissues
• Cell isolations
• RNA extraction from whole blood
• ELISA (routine cytokines plus many other markers and capacity to develop new assays in
collaboration with Elisa Tech, Inc.)
We also isolate and store serum, plasma, PBMCs, BAL, catalog multiple sample types, cryopreserve and
snap free cells and perform differential cell counts.
The NJH Core Lab is a 100-percent customer-based operation. We’re here to help you do your research.
Contact us for technical consultation, developing new assays, or training.
CTRC Core Lab I - Fee Schedule
# of
Samples
Supply Cost
Net
Time
Labor
Cost
Tier 1
Direct Supply
Cost only
Tier 1
Price per
sample
Tier 2
Service Cost
A Studies
Tier 2
Price per
sample
Tier 3
Total
Service Cost
Tier 3
Price per
sample
(Net * Rate)
(Labor + Supplies
+20% Discount)
All Costs-
NO Discounts
Isolation of PBMC 13.10 30cc 0.50 29.81 13.25 34.50 43.25
Isolation of BAL 24.78 240cc 1.00 59.63 25.00 67.75 84.75
Isolation of PMN 15.00 40cc 1.00 59.63 15.00 59.75 74.75
Standard Bronchoscopy Prep 43.12 2.00 119.26 43.25 130.00 162.75
DNA Extraction (10-12cc whole blood - Promega method)) 1 20.00 1.00 59.63 20.00 20.00 63.75 63.75 79.75 79.75
DNA Extraction (10-12cc whole blood - Promega method)) 5 100.00 2.00 119.26 100.00 20.00 175.50 35.25 219.50 44.00
DNA Extraction (10-12cc whole blood - Promega method)) 10 200.00 4.00 238.51 200.00 20.00 351.00 35.25 438.75 44.00
DNA Extraction (10-12cc whole blood - Promega method)) 20 400.00 6.00 357.77 400.00 20.00 606.25 30.50 758.00 38.00
DNA Extraction (8cc whole blood - Paxgene method)) 1 17.58 1.00 59.63 17.75 17.75 62.00 62.00 77.50 77.50
DNA Extraction (8cc whole blood - Paxgene method)) 5 87.90 2.00 119.26 88.00 17.75 166.00 33.25 207.50 41.50
DNA Extraction (8cc whole blood - Paxgene method)) 10 175.80 4.00 238.51 176.00 17.75 331.75 33.25 414.75 41.50
DNA Extraction (8cc whole blood - Paxgene method)) 20 351.60 6.00 357.77 351.75 17.75 567.75 28.50 709.75 35.50
Note - an additional $1.75 per sample (one time charge) is applicable if a second tube is drawn for storage and $5 per sample per year for storage at -80 C. Storage fee applies only after the protocol is completed.
DNA Extraction (mouthwash - 20cc) 1 10.24 1.00 59.63 10.25 10.25 56.00 56.00 70.00 70.00
DNA Extraction (mouthwash - 20cc) 5 51.20 2.00 119.26 51.25 10.25 136.50 27.50 170.75 34.25
DNA Extraction (mouthwash - 20cc) 10 102.40 4.00 238.51 102.50 10.25 273.00 27.50 341.25 34.25
DNA Extraction (mouthwash - 20cc) 20 204.80 6.00 357.77 205.00 10.25 450.25 22.75 563.00 28.25
DNA extraction (buccal swab - Qiagen method) 1 5.00 1.00 59.63 5.00 5.00 51.70 51.70 64.65 64.65
DNA extraction (buccal swab - Qiagen method) 5 25.00 1.50 89.45 25.00 5.00 91.55 18.31 109.65 21.93
DNA extraction (buccal swab - Qiagen method) 10 50.00 2.00 119.26 50.00 5.00 135.40 13.54 169.26 16.93
DNA extraction (buccal swab - Qiagen method) 20 100.00 3.00 178.89 100.00 5.00 223.00 11.15 278.89 13.95
DNA extraction (skin lesion swab - Qiagen method) 1 7.50 1.00 59.63 7.50 7.50 53.70 53.70 67.15 67.15
DNA extraction (skin lesion swab - Qiagen method) 5 37.50 1.50 89.45 37.50 7.50 101.55 20.31 126.95 25.39
DNA extraction (skin lesion swab - Qiagen method) 10 75.00 2.00 119.26 75.00 7.50 155.40 15.54 194.25 19.43
DNA extraction (skin lesion swab - Qiagen method) 20 150.00 3.00 178.89 150.00 7.50 263.15 13.15 328.90 16.45
RNA Extraction (Paxgene Method-2.5ml whole blood) 1 17.00 1.25 74.53 17.00 17.00 73.25 73.25 91.75 91.75
RNA Extraction (Paxgene Method-2.5ml whole blood) 5 85.00 2.50 149.07 85.00 17.00 187.50 37.50 234.25 47.00
RNA Extraction (Paxgene Method-2.5ml whole blood) 10 170.00 3.50 208.70 170.00 17.00 303.00 30.50 378.75 38.00
RNA Extraction (Paxgene Method-2.5ml whole blood) 20 340.00 5.00 298.14 340.00 17.00 510.75 25.75 638.25 32.00
note: currently testing DNA & RNA isolation from saliva using kits from Oragene
Differential cell count 5.00 1.00 59.63 5.00 51.75 64.75
Plasma/serum isolation 2.50 0.20 11.93 2.50 11.75 14.50
Lymphocyte proliferation 35.00 3.00 178.88 35.00 171.25 214.00
Note: Ask about current pricing for the following items
Cryopreservation of cells 1.50 per vial 1.50
Cell culture Initial Set-up cost $2.00 to $8.00 - Other costs depend upon culturing variable
ELISA (non-high sensitivity) 157.00 per plate 157.00
ELISA (high sensitivity - $450 to $500 per plate) 450 to 500 per plate 450.00
Flow cytometry 58.00 per hour 1.00 58.00
Flow data analysis Labor intensive - cost is per hour 1.00 59.63 47.75 59.75
Genetic Studies variable
Immunofloursecent cell staining Will run $50 plus number and cost of antibodies used variable
PCR no Set-up, Fragment 15.00 20.00 40.00
PCR Set-up exon, Fragment 50.00 65.00 100.00
PCR Multiplier (set-up) 250.00 325.00 500.00
Sputum Processing 30.00 30.00
Notes:
Tier 1 is Direct Supply costs only for CCTSI SAC approved
Tier 2 is Direct Supply costs plus labor related for other CTSI/GCRC studies
Tier 3 is for Industry Studies
NJH CTRC Inflammation and Immunology Core Lab
a)
Appropriate positive and negative controls are run for each assay and recorded. Reagents are
routinely checked for expiration dates. Equipment is routinely cleaned. Other quality control
measures include but are not limited to annual calibration and preventative maintenance, safety
inspections and upgrading of equipment to meet the highest standards possible.
How is the quality of your measurements evaluated – quality control?
b)
Most services are completed immediately as required. For example, peripheral blood cell
separation, bronchoalveolar lavage cell isolation and induced sputum cell isolation and
processing are conducted the day that they are available. Likewise, proliferation assays and
stimulation assays requiring culture are also set up the same day as cells are available. Once
harvested the cells or supernatant may be frozen for future batch processing. Others such as
DNA, RNA extractions and Elisa assays can be batched and run in a timely manner for technical
and cost efficiency. DNA and RNA extractions are performed weekly as needed. Elisa’s are
performed as needed and as soon as the appropriate immunoassay kits are available. Usually
these are batched and run at one time to ensure comparability of data. However, if faster
turnaround is needed, our Core lab is happy to work with the investigator.
What is the turn-a-round time for the service you provide?
c)
Samples received in to the lab are logged in to a password protected ACCESS data base with
appropriate HIPAA protection, as well as in individual folders for each protocol by a study specific
identifier. The data is always stored in a de-identified manner. Data generated within the lab is
stored in the ACCESS data base and in files created for each protocol within locked file cabinets
housed in a locked office and separate from the lab. The lab manager reviews the data and, if
appropriate, is reviewed with the core lab director.
Who documents the data provided and signs off on the data?
d)
We have experience providing data for industries. For example, we have provided data for an
industrial protocol from Gambro, for protocols supported by pharmaceutical companies including
investigator initiated protocols, such as Centocor/Johnson and Johnson, and others, and also for
a collaborative protocol with Colorado State University. Procedures performed included but were
not limited to: PMBC isolation, differential cell counts, cell cryopreservation, serum and plasma
isolation, sputum tracking and storage, urine sample aliquotting and tracking, immunofluorescent
cell staining of isolated PMBC and whole blood, flow cytometry, and flow data analysis.
Have you had experience providing data for industry?
e)
We have a standard operating procedures (SOP) manual where procedures performed in the lab
are described in detail. Special procedures or those requiring variation from the standard are
also written in detail with a protocol number for reference. These SOPs include quality control
measures to ensure that the tests and procedures are run in a standard manner.
Do you have a standard operating procedure manual?
f)
This is in the process of being set up across the CTRC administrative groups. Our administrative
contact is Ronnie Calzada ([email protected]).
How will you track billing and financial aspects of your core?
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Nursing Core
Contacts
Diane Branham, RN, BSN
Clinical Nursing Director/TCH CTRC Nurse Manager
720-777-3195
Detra Bliton, RN, BSN
UCH CTRC Nurse Manager
720-848-6430
Christine Reed, RN
Perinatal CTRC Nurse Manager
720-777-4694
Debra Coady, RN
UCB CTRC Nurse Manager
303-735-3587
Trudi Madigan, RN
NJH CTRC Nurse Manager
303-398-1717
The Nursing Core provides expert clinical research support during protocol development,
implementation, and data collection. We have dedicated facilities at four sites, University of
Colorado Hospital (UCH), The Children's Hospital (TCH), University of Colorado Boulder (UCB),
National Jewish Health (NJH), and our Perinatal Nursing Team capable of accommodating visits
at these sites and additional hospitals. Some sites have specialized equipment and services,
forming a well-networked nursing service for clinical investigators. We have five well-coordinated
groups of professionals:
• Registered Nurses with extensive experience caring for participants in complex research
protocols.
• Advanced Practitioners and Physician’s Assistants who aid the Principal Investigators in
H&Ps and research procedures.
• Professional Research Assistants and Healthcare Technicians who work closely with the
nursing staff to assist with research procedures and processing of samples.
• Sonographer skilled in collection of research images
• Administrative Staff who schedule participants, assist in creating budgets, and track the flow
of all research activity.
UCH Inpatient 15 inpatient beds, all with telemonitoring capability
UCH Outpatient Clinic 14 rooms with a 5-chair infusion room and a 7-chair blood draw room
TCH Inpatient Unit 10 inpatient beds, all with telemonitoring capability
TCH Outpatient Clinic 6 exam rooms, 5 infusion rooms PLUS the ability to send staff to other areas of
the hospital to collect samples for research (example-PICU, OR, Cath lab)
NJH Clinic 5 clinic rooms
UCB Clinic 5 rooms, 1 DXA room, 1 exercise room
Perinatal Nursing Team Conducts research in Labor & Delivery (UCH, Denver Health, St. Joes)
and the NICUs (UCH, TCH, St. Joes, Denver Health)
Services and Resources
The Nursing Core has a multi-disciplinary role in the CCTSI. Their roles include:
• Clinical Expertise
• Intensive Care/Step-Down Care
• Medical /Surgical Care
• Pediatric Care
• Perinatal Care
• Healthy Volunteer Care
• Feasibility Assessments for Study Implementation/Protocol Oversight
• Consultation Services/Study Design and Consent Development
• Investigator and Study Coordinator Support
• Data and Sample Collection
Note: Specific sites have screening, enrollment, and participation follow up.
Specialized Research Services
Please note that all four sites are well-networked and your protocol needs may be met for
patients enrolled at any of the sites (site availability in parentheses).
• High and Low Risk Exercise Testing (UCH, TCH, UCB)
• Ultrasound Core with Echocardiogram Imaging (UCH, TCH)
• Complex Drug Administration (UCH, TCH, UCB, NJH)
• Allergy Testing (UCH, NJH)
• Biopsies-Muscle, Adipose, Skin (All)
• Endothelial Cell Harvesting (UCH, TCH, UCB)
• Specialized Endocrine Testing (OGTT, IVGTT, Metabolic Clamp) (UCH, TCH, UCB)
• Hemodynamic Monitoring (UCH, TCH, UCB)
• Invasive Pressure Monitoring (UCH, UCB)
• Chemotherapy Infusions (UCH)
Specialized Equipment (site availability in parentheses)
• Metabolic (RMR) Carts (PARVO/VMAX) (UCH, TCH, UCB)
• Dual Energy X-ray Absorptiometry (DXA) (UCH, TCH, UCB)
• Calorimetry Chamber (UCH)
• Exercise Testing Equipment with a Treadmill or Bike (UCH, TCH, UCB)
• Bronchoscopy (UCH, TCH, NJH)
• Sleep Laboratory (UCH, TCH, UCB)
• PCT 3000 Scanner (UCH)
• Cardiac Monitoring Equipment (All Sites)
• ECG Machines (All Sites)
• GE Vivid 9 Ultrasound Machine (TCH, Perinatal)
• GE Vivid Q Portable Ultrasound Machine (UCH, TCH, Perinatal)
• KINCOM (UCH)
• PEA Pod (UCH, TCH, Perinatal)
• BodPod (TCH)
• Faraday Cage (UCB)
CCTSI CTRC Nursing Core
a) How is the quality of your measurement evaluated-quality control?
Each site follows the Quality Control mandated by that institution.
b) What is the turn-a-round time for the service you provide?
N/A
c) Who documents the data provided and signs off on the data?
The nursing staff provides documentation to support the protocol. The protocol is reviewed by
the site which will be implementing the research.
d) Have you had experience providing data for industry?
The nursing staff at each site has developed documentation to implement the protocol.
e) Do you have a standard operating procedure manual?
Each site has operating procedure manuals specific to that institution
f) How will you track billing and financial aspects of your core?
Billing and the financial aspects of the protocol are tracked by the administrative personnel at
each specific site.
Colorado Clinical and Translational Sciences Institute (CCTSI)
Clinical Translational Research Center (CTRC)
Nutrition Core
Contacts
Janine Higgins, PhD Archana Mande Melanie Kasten
Nutrition Research Director Nutritionist, UCH (Adult) Nutritionist, TCH (Peds)
720 777-2955 720 848-6683 720 777-2994
[email protected] [email protected] [email protected]
Core Informationhttp://cctsi.ucdenver.edu/Research-Resources/Clinical-Research-Resources/Pages/Nutrition.aspx
Availability
All Nutrition Core services are available to approved CTRC and Clinical Trials Organization (CTO) protocols.
Services may be available to other protocols on a fee-for-service basis. All fee-for-service protocols must
provide a copy of current COMIRB approval.
Cost
The Nutrition Core tracks monthly usage by protocol. Billing is handled on a case-by-case basis. Prior-
payment arrangements will be made by Janine Higgins and Pat Kittelson ([email protected]).
Prices for each service (see following table) fall into two categories: 1) CTRC cost, and 2) industry/CTO
cost:
1) CTRC cost includes food/materials cost only with minimal or no labor cost as this is subsidized by the
CCTSI. This pricing is available only Scientific Advisory and Review Committee (SARC)-approved,
investigator-initiated studies. Studies in this category are generally federally-funded (e.g. NIH) although
some are funded via private foundations and non-profit institutes.
2) Industry/CTO cost is a non-subsidized fee-for-service cost. This pricing is available for SARC- approved
CTO protocols and other industry protocols. Studies in this category are generally funded by private
companies or corporations (e.g. drug companies).
Services
Item CTRC Cost Industry/CTO Cost
Weighed, Metabolic Meal $6.00 $25.00
3-Day Metabolic Diet $42.00 $122.00
Dietary Instruction/Counseling $28.00/hr $40.00/hr
3-Day Diet Diary Analysis* $28.00 $44.00
24-Hour Dietary Recall $26.00 $40.00
Food Frequency Questionnaire $24.00 $38.00
Resting Metabolic Rate (Peds only) $35.00 $50.00
* This cost is for analysis ONLY does not include instructions at issuance which would be charged at $30/hr. It is recommended that
PRAs learn how to issue the diet diary which would incur a one-time hourly instruction charge rather than an instruction charge/subject.
National Jewish Health (NJH)
Clinical Translational Research Center (CTRC)
Research Nursing and Facilities (NJH)
Contacts
Donald Leung, MD, PhD
Associate Program Director
303-398-1186
Trudi Madigan, RN
Nurse Manager
303-398-1717
The NJH CTRC is part of the UCD Colorado Clinical & Translational Sciences Institute (CCTSI). At the
NJH CTRC clinical research visits will take place at National Jewish Health, the #1 Respiratory Hospital in
America specializing in Pulmonary, Immunology, and Allergy. National Jewish is accredited by the Joint
Commission on Accreditation of Healthcare Organizations. The subjects will be consented and seen in
the CTRC outpatient clinic. The clinic consists of three exam rooms, one interview room, and one
procedure room. The clinic is staffed by a Nurse Practitioner and RNs. History and physicals, spirometry,
EKGs, skin testing, blood draws etc. are performed in the area. An adjacent laboratory is available for
handling clinical samples. The study agent will be stored and prepared for administration by the National
Jewish Health Research Pharmacy Service. A -80
0
F freezer and biosafety cabinet is available for
storage and preparation.
• Administering Questionnaires
Services
• Adverse Event Reporting
• EKG 12 Leads Restin
• Emla Administration (PEDS topical)
• Height and Weight
• History and Physical (long and short) NP
• Informed Consent/Assent
• IRB/SARC Submission
• IRB Continuing Review
• IV Insertion – IV CATHETER INSERT
• Medication administration
• Moderate Sedation/Assistance and Supplies
• Observation Hourly
• Observation Post Medication Administration
• Pharmacokinetics
• Review of Inclusion/Exclusion Criteria
• Six Minute Walk
• Skin Test Delayed – Skin Testing
• Spriometry pre and post – Spiro Clinic Pre/P
• Spirometry pre only – Spiro Clinic Flow
• Sputum Induction
• Urine Collection
• Urine Pregnancy
• Venipuncture Vital Signs
NJH CTRC
a)
Staff performances are evaluated on an annual basis to ensure quality services.
How is the quality of your measurements evaluated – quality control?
b)
Services are provided on the day subjects are scheduled for their visits.
What is the turn-a-round time for the service you provide?
c)
MD’s and RN’s
Who documents the data provided and signs off on the data?
d)
Yes
Have you had experience providing data for industry?
e)
We follow Nursing Policies and Procedures
Do you have a standard operating procedure manual?
f)
The billing and financial aspects are handled by our administrative staff. Our administrative
contact is Ronnie Calzada.
How will you track bil ling and financial aspects of your core?
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Research Nursing and Facilities (UCB)
Contacts
Elizabeth Connick, MD
UCB Medical Director
303-724-4930
Debra Coady, RN
Nurse Manager
303-735-3587
The UCB CTRC located at the University of Colorado Boulder is part of the UCD Colorado
Clinical and Translational Sciences Institute (CCTSI) and delivers nursing care in a research
clinic utilizing a systematic approach to nursing practices incorporating assessment, planning,
implementation, and evaluation; thus providing continuing health care to research volunteers.
New clinical procedures or techniques will be incorporated into nursing core services based upon
funding and potential overall use and is dependent on SARC and IRB approvals. Training for
new procedures or techniques will be provided by the principal investigator.
Due to the unique location of the UCB CTRC on a Ph.D. driven campus, the nursing core also
provides consultation on all medical aspects of protocol design and consent form development.
Rooms
• 1 exam room
• 4 protocol rooms
• 1 DXA room
• 1 exercise physiology room
• 1 Faraday room with nerve traffic analysis system
Services
• Phlebotomy
• Medical histories
• Medication instruction
• Intravenous catheter placement
• ECG recordings and interpretation
• Endothelial harvest collection
• Assisting with arterial line placement
• Drug infusions
• Assisting with biopsies
• 24 hour nursing and physician telephone coverage
• Health and procedural instructions to students and research volunteers
UCB CTRC
a) How is the quality of your measurements evaluated – quality control?
There is on-going review of each staff’s performance maintained by the supervisor. There
is continuing review of interventional outcomes through on-going medical assessments
and tracking of adverse events through the UCB study monitoring committee.
b) What is the turn-a-round time for the service you provide?
Services provided on the day that research volunteers are scheduled.
c) Who documents the data provided and signs off on the data?
Clinical staff (registered nurses and medical doctors) sign off on all forms relating to
procedures performed.
d) Have you had experience providing data for industry?
Yes. A clinical trial was conducted by one of our principal investigators several years
ago which utilized the nursing core.
e) Do you have a standard operating procedure manual?
Yes. Policies and procedures are kept on the unit and signed off by the UCB Medical
Director, Elizabeth Connick, MD.
f) How will you track billing and financial aspects of your core?
Billing is tracked and handled by the UCB Administrative Manager.
Clinical Investigation Core
Center for Aids Research (CFAR)
Cara Wilson, MD
Core Director
303-724-4601
[email protected]
Website:http://www.uchsc.edu/ccfar/cores/clinical.htm
The goal of the Clinical Core to provide focused yet comprehensive support of human
HIV/AIDS-related studies from their conception through implementation.
The overall mission of the Clinical Investigation Core is:
• To provide comprehensive support of HIV-related clinical investigation with a special
emphasis on providing support to junior investigators, investigators new to AIDS clinical
research, and investigators new to patient-oriented research in general.
• To ensure the recruitment of HIV-1 infected persons with diverse racial, cultural, and
gender characteristics at multiple sites throughout Colorado for participation in CFAR
clinical and translational research studies.
• To provide integrated antiretroviral clinical pharmacology expertise and resources to
support the clinical and translational research by D-CFAR investigators in Colorado and
by AIDS investigators throughout the United States.
• To ensure the quality of CFAR-supported clinical investigation through training and
certification of CFAR investigators in the principles of clinical research and human
subject protections.
• To encourage collaborative interactions among laboratory-based, translational and
clinical investigators, thereby promoting the growth of cutting edge clinical HIV/AIDS
research in Colorado.
• To pro-actively identify and correct gaps in HIV/AIDS clinical investigation in Colorado
and to provide core facilities and services that will enhance interdisciplinary
collaborations and eliminate gaps.
The Clinical Investigation Core will provide three main resources to support clinical research of
CFAR investigators: a clinical research resource, a clinical pharmacology resource, and a
specimen management resource.
To request one of our services contact [email protected].
Your form will be forwarded to the Clinical Investigation Core steering committee to work out
the funding and personnel who can help you with the project. You will receive a response to your
request within 1-2 weeks.
Clinical Investigations Core
University of Colorado Cancer Center
(UCCC)
Contacts:
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/cic/index.aspx
The UCCC Clinical Investigations Core (CIC) mission is to optimize the quality and quantity of
cancer clinical trials research for UCCC. The specific objectives are to:
• Ensure the provision of exceptional patient care at UCCC sites by offering new
approaches to cancer management through cancer clinical trials
• Support of all aspects of cancer clinical investigations headed by UCCC investigators
• Provide a conduit for activation of UCCC investigator-initiated cancer clinical trials
• Ensure opportunities for clinical trials education
• Offer a final common pathway for UCCC translational research applications
Almost 70 CIC clinical, regulatory and administrative staff manage performance of more than
400 clinical studies with a total accrual of nearly 7,500 subjects.
Services We Offer
• Regulatory submission and monitoring
• Protocol Development
• Budget development and contract negotiation
• Enrollment of eligible patients
• Data collection and monitoring
• Specimen procurement and processing
• Adverse event reporting
• Coordination of patient treatment
• Training and education of clinical and regulatory staff
• Training of Phase I oncology fellows
• General Good Clinical Practice Training
• Maintenance of the UCCC Clinical Trials Database
• Quality Assurance
• Protocol Review and Monitoring
• PQASC-audit schedule & Data Safety Management Plan
Anthony Elias, MD
Associate Director for
Clinical Research
[email protected]
720-848-1622
Madeleine Kane, MD, PhD
Medical Director
[email protected]
720-848-0354
Andrea Buchmeier, CCRC
Clinical Research Director
[email protected]
720-848-0635
University of Colorado Cancer Center
Clinical Investigations CoreAnschutz
Cancer Pavilion
1665 AuroraCT, RM 3200
Mail Slop F-700
Aurora, Colorado 80045-0510 Fax:
720-848-0671
STATEMENT OF FEES-FISCAL YEAR 2009-2010
(Effective J une 1, 2009-May 31, 2010)
1. Overhead
It is the policy of the University of Colorado Denver (UCD) to obtain the appropriate, approved
facilities and administrative cost recovery rate on all sponsored programs whether they are from
private or public sources. The overhead rate applicable to clinical research at the University of
Colorado Cancer Center (UCCC) Clinical Investigations Core (CIC) is 26% established under
the F & A policy of UCD. This rate is applied to all non-patient care costs (i.e. applied only to
labor and administrative charges). The amount is taken directly from the payments received and
retained by UCD. The overhead collected is in no way applied to the compensation provided to
either the site research staff or the UCCC principle investigator. Please see the attached link for
more detailed information regarding this subject:
2. Study Start Up Feeshttp://www .uchsc.edu/ ogc/pp/fa.php
The University of Colorado Cancer Center Clinical Investigations Core assesses the
following fees to all industry-sponsored clinical trials:
a) Informatics Fee
: The Informatics administrative fee is a flat fee charged to all protocols to
cover the expenses of maintaining on-site monitor workstations, providing computer
monitors at these workstations, providing monitors with access to UCH EMR, and IT
support for this access.
1
b) Pharmacy Fee
c)
: The Pharmacy administrative fee is a flat fee charged to all protocols that
require the dispensing services of The University of Colorado Hospital Pharmacy. This
fee is in addition to the drug dispensing fee.
Laboratory Fee
d)
: The Laboratory administrative fee is a flat fee charged to any protocol
that requires specific sample handling and shipping of specimens. This fee is in addition
to specimen processing, handling, storage and shipment fees
Research Office Start Up Fee
e)
: The Research Office Start Up fee is a flat fee that covers
the costs associated with opening a clinical trial through the University of Colorado. This
process includes regulatory document preparation for protocol submission to the UCCC
Protocol Review and Monitoring Committee (reviews for scientific merit), the IRE, and
the University of Colorado Hospital Research Review Committee (reviews for
compliance and resource utilization). It covers the costs associated with budget and
contract preparation, negotiation, finalization and implementation.
University of Colorado Hospital Research Compliance Review
f)
: The University of
Colorado Hospital (UCH) Research Compliance Review is required to review any new
protocol prior to its opening. This review process typically takes 2-6 weeks.
University of Colorado Hospital Research Compliance Fast Track Review Fee
g)
: This fee is
in addition to the fee stated above. The UCH fast track review fee guarantees a 48-72 hour
turnaround time for initial review and a 24 hour turnaround if there are questions that need
addressed prior to approval. This fee assesses an additional $250 for the expedited request;
this fee is assessed only if the sponsor requests the fast track review process.
Clinical Translational Research Center CCTRC-formerly known as OCRC): This fee
supports the work associated with preparation and submission of the protocol and all
required documentation to the CTRC. The CIRC consists of both in-patient and outpatient
research units that specialize in the conduct of clinical trials. These units are used when the
research procedures cannot be carried out in the outpatient setting or during out-patient
clinic hours. For example: around the clock PK collection. This fee is only assessed if the
study requires the use of the Clinical Translational Research Center.
The CIC will consider reduction of study start up fees if the study is considered a rollover or
extension of study previously conducted in the CIC by the same sponsor. This reduction in
startup fees will be at the discretion of the CIC Director.
Study start up fee exceptions
2
3. Items Invoiced to the Sponsor:
Regulatory Affairs Fees Administrative Category
Frequency
$1800 Regulatory Continuing Review
a
Annually
$125 Regulatory Amendment
B
Per Amendment
A. The regulatory affairs continuing review fee is assessed by the CIC to cover all expense
for annual study submission to Western Institutional Review Board (WIRB). This fee
also includes yearly regulatory maintenance of the study such as safety reporting,
adverse event reporting and other protocol related duties.
B. The regulatory affairs amendment fee is assessed by the CIC to cover all expense pertaining
to each protocol amendment.
All fees listed above are subject to overhead as described in item one. The overhead
collected is not applied to compensation provided to either the clinical research staff or the
UCCC principle investigator. All fees are invoiced to the sponsor and are due upon receipt
of invoice.
Note: The above regulatory fees are subject to a late charge for payments received later
than 60 days of Invoice date, $100 will be applied to the balance for each month payment
is not received.
For studies eligible for WIRB
submission:
FEES*
Administrative Category
$3000
$825
$1800
$350 per submission
$250 per submission
WIRB Initial Review-includes (1) consent form
WIRB Six Month Review (if applicable)
WIRB Annual Continuing Review
Changes to Research Involving Consent Form Review
Changes to Research not Involving Consent Form Review
For studies not eligible for WIRB submission, such as investigator-initiated and/or studies
requiring bio-safety committee review, our local IRB (COMIRB-Colorado Multiple
Institution Review Board) will be used.
FEES*
$2000 COMIRB Initial Review
Administrative Category
$1500 COMIRB Continuing
Annual Review
*The fees listed above are not subject to overhead.
3
4. University of Colorado Hospital pricing
Every protocol that involves the use of University of Colorado facilities is sent to the
applicable department for review and pricing. The applicable department (radiology, clinical
laboratory, pharmacy) reviews the protocol and provides the CIC with a price quote for the
procedures required. The prices quoted are offered to the CIC, and subsequently to the
sponsor, at a reduced research rate. These prices are effective for a period of 12 months
following the department's initial review. The prices set by the hospital are non-negotiable. In
addition, a CIC bill processing fee in the amount of $944 (overhead to be assessed) will be
applied to the total per patient amount. This fee supports the CIC billing process assuring that
research procedures are billed appropriately, to include compliance review of all research
invoices to ensure billing remains compliant with all federal laws.
If a protocol is not open within 12 months of initial budget agreement, prices are subject to
change. If this occurs, a revised budget will be sent for review and approval.
Protocol complexity may result in additional fees as deemed necessary by CIC
administration.
Additional Fees
Additional fees such as Principal Investigator fees, RN/Coordinator fees, Research
Administration fees (general administrative oversight of study to include payments applied,
account reconciliation, invoicing, sponsor contact for query resolution, coordinator budget or
enrollment issues, study close out, contract/amendment issues; in addition, medical and clinical
director oversight of study to include review of protocol, monitoring of site, review of
monitoring letters to ensure GCP compliance, quality and assessment of training issues and
needs), data management and archive fees are included in the body of the site's budget.
4
Clinical Science PhD and MS Program
Contact:
Lisa Cicutto, PhD, RN
Program Director
University of Colorado Denver
303-398-1538
[email protected]
http://www.uchsc.edu/clinicalscience/index.htm
The Clinical Science PhD and Masters Program
This innovative program is designed for qualified individuals who are interested in obtaining
either a Ph.D. (doctoral) or Master's degree in Clinical Science. The primary applicant audience
includes those having earned a health sciences graduate degree or a health care professional
degree (e.g., physicians, MSPH graduates, biostatisticians, epidemiologists, nurses, pharmacists,
physical therapists and dentists).
The overall goal of the University of Colorado Denver (UCD) Graduate Program in Clinical
Science (CLSC) is to train Clinician Scientists by providing a formal, structured, and rigorous
educational program in Clinical Investigation (CI), Health Information Technology (HIT), or
Health Services Research (HSR).
These three fields of clinical science are important areas of study for translational research
activities in the evolving health care environment. Graduates of our program are highly qualified
and well-trained Clinician Scientists who will be nationally competitive for grant funding and
career advancement in the health sciences.
Core Personnel
Lisa Cicutto, PhD, RN (Program Director) specializes in Allergy, Asthma, COPD/Chronic
Obstructive Pulmonary Disease/Emphysema, and other Pulmonary Disease Research. She is
Associate Professor, Colorado School of Public Health and the College of Nursing and Associate
Director, Clinical Science Graduate Program.
Welcome to the Clinical Trials
Organization
Contacts:
Jill McHale
Interim Director
(720) 777-8430
[email protected]
Website;http://research.childrenscolorado.org/content/clinical-trials-organization
The Clinical Trials Organization (CTO) supports the research mission of Children’s Hospital Colorado. The CTO
provides a variety of services to researchers who conduct clinical research, including those required for study
start up and initiation, ongoing trial management and study close out. Studies range from non-interventional
database collections to more complex treatment trials using investigational agents or devices.
Please visit our links, indexed at left, to find out more about our research and clinical activities.
Clinical Trials Organization Research
The Clinical Trials Organization (CTO) supports the research mission of Children’s Hospital Colorado. The CTO
provides a variety of services to researchers who conduct clinical research, including those required for study
start up and initiation, ongoing trial management and study close out. Studies range from non-interventional
database collections to more complex treatment trials using investigational agents or devices.
If you have questions about clinical research studies at Children’s Hospital Colorado, or would like
information regarding our current studies, please call 720-777-8430 or e-mail:
[email protected].
Clinical Trials Organization Clinical Services
The Clinical Trials Organization serves the children and primary care providers of the Rocky Mountain
region by translating cutting-edge research into clinical care. Internationally recognized leaders in
pediatric health care research are involved in a variety of groundbreaking studies working towards
advancements in pediatric health care. The Clinical Trials Organization conducts studies throughout all
arenas of pediatric medicine and exists to advance the health and welfare of children through the careful
coordination of state-of-the-art pediatric clinical research.
If you have questions about clinical research studies at The Children’s Hospital, or would like information
regarding our current studies, please call 720-777-8430 or e-mail: [email protected].
Colorado Advanced Photonics Technology Center (CAPT)
Larry Scherrer
Director
303-556-4175
[email protected]
http://www.captcenter.org/about/Default.htm
The Colorado Advanced Photonics Technology (CAPT) Center has several labs with equipment
that give companies access to state of the art measurement and fabrication equipment.
Companies are welcome to come to the center and use equipment, or contract service
measurements are also available. CAPT has a 2000 square foot facility. There is also a dark room
for photolithography, a general optics and development lab, office space, and conference room.
The four major areas of concentration are:
• Optical Characterization and Metrology Lab
• Photonics and General Developmental Lab
• Prototype Packaging and Photolithography Lab
• Environmental Test and Evaluation Lab
CAPT is conveniently located in Longmont which is close to Boulder and Denver, and easily
accessible from interstate I-25 ( see map).
As a non-profit organization, the CAPT Center provides cutting-edge technical services and
human resources to its corporate and educational partners. The CAPT Center is the only
photonics resource in Colorado that can deliver: surface roughness measurements, optical testing
, contract measurement services, prototyping, precision metrology, environmental testing, use of
photonics equipment and facilities, training for current employees, and connections with future
employees.
The CAPT Center provides access to state-of-the-art facilities and equipment:
• $5 million in equipment for material characterization, prototype packaging, measuring,
inspection and environmental testing.
• 2,000 sq. ft. of support laboratories
• Design, processing, characterization, packaging and quality labs
• CAPT Incubator Program
Before you commit to purchasing expensive equipment, test your product ideas at the CAPT
Center.
How can CAPT help you?
• By providing sophisticated equipment and tools for testing, fabrication, packaging,
environmental test and design.
• By providing clean room facilities
• By assisting in use of equipment and tools
• By training your employees through photonics short courses
• By giving you access to photonics students
CAPT also offers the following services
• surface roughness measurements
• optical testing
• Contract measurement services
• component evaluation
• Contract optical testing
• photonic and optical systems engineering
Tell us what you need!
Facility Rates and Usage
You can come and use the equipment at the CAPT Center, or we offer surface roughness
measurements, optical testing , and other contract measurement services. Use of the facility
should be reserved in advance and the use of any particular item is subject to availability. Call
your CAPT representative to schedule usage and assure availability.
Equipment Cost
CAPT Facility Rates depend on three factors: the sophistication of the equipment that is being
utilized (Equipment Classification); the commitment to use the equipment over a period of time;
and CAPT Membership status. See our complete Equipment List and Classification.
CAPT Facility Rate Schedule
Equipment
Class
Hourly Rate
($/hr)#
Daily Rate
($/day)#
Weekly Rate ($/5
Days)*
Monthly Rate
($/22 days)*
A $25 $160 $720 $2,808
B $50 $320 $1,440 $5,616
C $75 $480 $2,160 $8,424
D $100 $640 $2,880 $11,232
E $150 $960 $4,320 $16,848
F $200 $1,280 $5,760 $22,464
# Terms Net 15 days with approved credit
* Payment due in advance (days use may be non-contiguous)
Non CAPT Members pay a 50% premium
Usage Discount
The CAPT Facility Rate Schedule provides discounts for long-term usage from the hourly rate. If
equipment is utilized for 1 full day (8 hours), an automatic discount of 20% will be extended to
the user.
Weekly and monthly rates are also available at substantial discounts. The benefit of these rates is
that they apply to 40 hours of usage for the weekly rate and 176 hours of usage for the monthly
rate. The usage dates do not have to be contiguous. This payment approach offers the
opportunity for long term planning and provides flexibility that standard lease programs cannot
provide. The weekly and monthly usage fees must be paid in full in advance.
Technical Assistance and Contract Measurements
CAPT will provide Engineering level and/or Technician level technical assistance at the
following rates:
Technician: $50 per hour
Engineering: $83 per hour
Payment Terms
Terms are NET 15 days upon invoice for CAPT Members.
Terms are Due on Receipt for non CAPT Members.
Colorado Biostatistics Consortium (CBC)
Contacts:
John Neal
[email protected]
Administrator
303-724-4370
Website:http://cbc.uchsc.edu/
The Colorado Biostatistics Consortium (CBC) is a unit in the Department of Biostatistics &
Informatics, Colorado School of Public Health, University of Colorado Denver (UCD). The
CBC is a shared resource for biomedical investigators at UCD, Colorado State University (CSU),
University of Northern Colorado (UNC) and other institutions. It provides biostatistical
expertise for centers, programs, departments, and individual investigators to facilitate the design
of studies, data acquisition protocols, data analysis, and the preparation of grants
and manuscripts.
Colorado Clinical and Translational Sciences Institute (CCTSI) The CBC administers the
Biostatistics, Epidemiology, and Research Design (BERD) core function of the CCTSI.
Biostatistical consultation is provided to CCTSI award/grant recipients at no charge. BERD
hosts courses and seminars in study design, data collection and results analysis for medical
researchers who desire to deepen their understanding of these topics. For more information
about the CCTSI, please visit:http://cctsi.ucdenver.edu.
Research Consulting Laboratory (RCL) Medical investigators needing a "quick question"
answered and students working on theses, dissertations and research projects can obtain support
from the CBC Research Consulting Lab. Staffed by graduate students in Biostatistics &
Informatics, and supervised by Kim McFann, PhD, the RCL provides tutoring on the design of
studies, sample size calculations, data analysis, and other biostatistical subjects. Located in
Historic Building 500, Third Floor, West Wing, Room W3132, the RCL is open during normal
business hours every weekday. Call 303-724-4619 to schedule an appointment.
How to contact the CBC:
Contact John Neal (CBC Administrator) to arrange a meeting with a senior biostatistician.
CBC Fees
Medical researchers working under the auspices of the Colorado Clinical and Translational
Sciences Institute (CCTSI) should contact the CBC regarding their biostatistical needs.
For investigators who have their own funding, there are two options for obtaining biostatistics
support, provided that the CBC has the resources and expertise to meet the client’s needs:
1. Agreement
For ongoing, long-term grants or departmental support requiring a variety of services.
? A monthly retainer for a specified time period for the anticipated work involved.
? To be negotiated on a case-by-case basis with the Director of the CBC.
2. Hourly Rates
For one-time, short-term projects requiring specific services within a limited time frame.
? $125 per hour for University departments and affiliated organizations or institutions.
? For non-affiliated organizations, the hourly rate will be negotiated, depending on scope of
work, plus travel costs, if incurred.
Frequently Asked Questions:
1. Why would I use the CBC instead of hiring my own biostatistician?
? Rather than relying on a single person’s education and background, you would have access to
a range of levels (MS / junior to PhD / senior level biostatisticians), as well as taking advantage
of the wide array of expertise within the CBC collaborative pool of colleagues. See Faculty for
details.
? Consortium statisticians are mentored by senior faculty, providing a depth of shared
experience that cannot be found in a single individual.
? You avoid the management responsibility and facilities expense associated with a “regular”
employee, while having the flexibility to obtain part-time or short-term support as needed.
? You can control the specific costs associated with a project or grant.
? You can secure intellectual collaboration on short notice, without undergoing a time-
consuming hiring process.
? The CBC works with you to help structure your research and analyses. As a collaborative
partner, the CBC can assist you in preparing grant proposals, designing studies, analyzing their
results – all the way through to helping you write manuscripts, reports to funding agencies, and
presentations of findings.
2. What do the hourly rates include?
? Support for staff salaries and benefits.
? Support for the CBC infrastructure, including computer hardware/software, professional
development, administrative and financial management.
? Built-in “capacity” to respond to and collaborate on new projects as they arise.
4. Do I have to pay the CBC if I just have a quick question?
? No. We are happy to share our expertise with the University community by addressing quick
biostatistical questions or providing short consultations at no charge.
? The CBC also includes a “Research Consulting Lab” which offers walk-in statistical
consultation at no charge. This is primarily targeted toward students. However, faculty
investigators are welcome to utilize this service as well, although they may be referred to the
CBC for more in-depth collaboration.
? If the question isn’t really “quick” and requires comprehensive analysis or treatment, the CBC
will work with you to structure a longer term collaboration. 5.
How do I incorporate the CBC into my research?
? Contact John Neal, Administrator: 303-724-4370 or [email protected]
? We will set up an initial meeting to discuss your project. (Note: There is no charge for the
initial meeting.)
Core Facility
Contacts
Directors
Karen Swisshelm, PhD, FACMG
(303) 724-5701
[email protected]
Loris McGavran, PhD, FACMG
(303) 724-5701
[email protected]
Genetic Counselors
Janine Gessner, MS
(303) 724-5723
[email protected]
Michelle Springer, MS, CGC
(303) 724-5710
[email protected]
Client Services
Susan Mountain-Morgan
(303) 724-5701
[email protected]
Website: www.coloradogeneticslab.com
CAP #2182823
CLIA # 06D0644362
Colorado Genetics Laboratory
About Colorado Genetics Laboratory
Colorado Genetics Laboratory (CGL) is nationally recognized for excellence and strives to provide the
highest quality cytogenetic testing. Based in Denver and serving the Rocky Mountain region, CGL
specializes in prenatal, postnatal, and cancer cytogenetics; fuorescence in situ hybridization (FISH); and
microarray (cytogenomic) technologies. With decades of experience, our cytogenetic technologists
are outstanding in the feld. Certifed genetic counselors are on staf to aid in test interpretation and
answer your questions. We provide the most up-to-date information on chromosome abnormalities
and microarray fndings. Client services representatives are available to assist with transport of samples,
copies of reports and other special requests.
1) How is the quality of your measurements evaluated - quality control?
Colorado Genetics Laboratory (CGL) is accredited by Clinical Laboratory Improvement Amendments (CLIA) and the College of
American Pathologists (CAP). Internal quality controls are performed and evaluated to ensure our services are superior. CGL
participates in the Children’s Oncology Group, the Eastern Cooperative Oncology Group (ECOG) and the Southwest Oncology
Group peer-reviewed cytogenetic cancer studies.
2) What is the turn around time for the service you provide?
Turn around times are accommodated to meet your research and clinical trial needs. Please contact CGL at (303) 724-5701 to
discuss your testing timeline.
3) Who documents the data provided and signs of on the data?
Our certifed cytogenetic technologists analyze and document their fndings in a written report. The report is reviewed and
signed by the laboratory directors.
4) Have you experience providing data for industry?
Colorado Genetics Laboratory has been working with private industry for over 14 years.
5) Do you have a standard operating procedure manual?
Colorado Genetics Laboratory is accredited by CLIA and CAP. Our operating procedure manual is annually reviewed and
updated as required by these regulators.
6) How will you track billing and fnancial aspects of your core?
Billing and expenses are tracked though CGL administration. Please contact our Business Manager, Kathy Taylor, at
(303) 724-5705, to discuss pricing for your specifc cytogenetic testing needs.
Services
Chromosomal Microarray (CMA)
• High-resolution DNA
array containing 180,000
oligonucleotide clones
• Follows International
Standards for Cytogenomic
Array in chip design
• Clones spaced ~16 Kb
along the backbone
• Increased
coverage in disease regions
• Targeted coverage of 500+ disease genes, microdeletion/
duplication syndrome regions, and subtelomeres
• Abnormalities detected at a resolution of 100-200 Kb
• Two diferent software platforms available for analysis
to increase overall accuracy and for quality control.
• Confrmation studies performed on abnormal cases
• Autism referrals cross-referenced with current autism
databases for the most up-to-date copy number
associations
Cancer Cytogenetics
• Chromosome analysis of bone marrow, blood, lymph node
and solid tumor
• FISH for chromosomal abnormalities common in cancers
• FISH for brain cancer
• FISH on parafn-embedded specimens
Constitutional Cytogenetics
• Standard and high-resolution analysis available
• Analysis done on peripherial blood, fbroblasts, amniotic
fuid, chorionic villius samples and other tissue types,
including human stem cells
Flourescence in situ Hybridization (FISH)
• Cancer abnormalities
• Chimerism in transplant patients
• Trisomy screening
• Microdeletion/duplication syndromes
• Identifcation of marker, derivative or structural aberrations
Cell Line Verifcation
• Karyotype analysis
• FISH verifcation
Additional Services
• Research services
• Tissue culture
• Cryopreservation
• Alpha-fetoprotein & acetylcholinesterase
analysis on amniotic fuid samples
Colorado Genetics Laboratory
CANCER SPECIMENS
TEST REQUEST FORM
3055 Roslyn Street, Suite 200
Denver, Colorado 80238
(303) 724-5701
(888) 659-4932 Toll Free
(303) 322-1052 FAX
PLEASE CALL PRIOR TO SENDING SPECIMEN(S)
PATIENT INFORMATION
Colorado Genetics Laboratory
Patient Last Name _______________________________________ First Name ___________________________ Middle Initial _____ Sex: M F
Date of Birth __________________________ Hospital/ID Number ______________________________ INPATIENT OUTPATIENT
REFERRED BY
PHYSICIAN ___________________________________________________
Address __________________________ ___________________________
City ______________________________ State: _______ Zip: ________
Telephone ______________________ Fax ___________________
FACILITY _____________________________________________________
Address __________________________ ___________________________
City ______________________________ State: _______ Zip: ________
Telephone ______________________ Fax ___________________
BILLING
BILL CHARGES TO: Patient Insurance Hospital Physician/Clinic (provide billing information on reverse side of form)
SIGNS, SYMPTOMS, NARRATIVE DIAGNOSIS AND ICD9 CODES
Required for specimen processing (PLEASE DO NOT USE “RULE OUT”)
ICD9 _____
ICD9 _____
ICD9 _____
In addition to the studies requested below, the
Colorado Genetics Laboratory is authorized to
perform FISH (fluorescence in situ hybridization)
if indicated by the patient’s clinical history or
cytogenetic results.
_____________________________________
Physician Signature
SPECIMEN COLLECTION
Date Collected: ___________________ Time: __________ AM PM Amount Collected: ____________________
PATIENT STAMP HERE
PRENATAL & TISSUE SPECIMENS
Gestation by ultrasound on date specimen
collected _________________________
LMP ____________________________
G ___ P ____ SAB ____ TAB ____
Fetal sex (if known): M F
Specimen Type
?Amniotic Fluid
?Chorionic Villus
?Percutaneous umbilical blood
?Products of conception
?Placenta
?Fetal Tissue
?Skin Biopsy
?Other
Studies Requested
?Chromosome analysis
?Trisomy screen by FISH and
chromosome analysis
?Alpha-fetoprotein? Yes No
?Acetylcholinesterase (AchE)
?FISH for:
?Culture and freeze for future studies
?Culture for molecular or biochemical
studies:*
*Please attach “Information for Referral
Specimens” form
?CML
?AML
?ALL
?Myeloma
?Diagnostic
?Myelodysplasia
?B-cell Lymphoma
?T-Cell Lymphoma
?CLL
?Post Transplant
Sex of Donor:
M F
Specimen Type
?Bone marrow aspirate
?Bone marrow core biopsy
?Peripheral blood
?Lymph Tumor
?Solid Tumor:
?Other:
Studies Requested
?Chromosome analysis
Fish Studies for:
?BCR/ABL t(9;22)
?MLL (11q23)
?PML/RARA t(15;17)
?ALL Panel
?AML Panel
?CLL Panel
?MDS Panel
?Myeloma Panel
?Chimerism (for BMT patients)
?Screen for prior abnormal clone
?Other
Additional FISH studies available.
Please call the laboratory.
CONSTITUTIONAL BLOOD SPECIMENS
?Peripheral blood
?Cord blood
?Other:
Studies Requested
?High resolution chromosome analysis
?Routine chromosome analysis
?STAT trisomy screen by FISH and routine
chromosome analysis
(Call before ordering)
?FISH for:
?Chromosomal Microarray (CMA)
?Parental FISH follow-up for abnormal array
?Fragile X Panel
(Includes FMR1 and routine chromosome
analysis)
specify
specify
specify
specify
source
specify
specify
specify
specify
Patient's accession number
Revised July, 2010 Continued on Reverse Side
Disease FISH Probes Included in Panel
Acute Myelogenous Leukemia (AML)
Chronic Lymphocytic Leukemia (CLL) 12, 13q14, TP53, ATM
Chronic Myelogenous Leukemia (CML) BCR/ABL
Diagnostic Acute Lymphoblastic Leukemia (ALL) - Pediatric 4, 10, 17, 21, TEL/AML, BCR/ABL, MLL, p16 deletion
Diagnostic Acute Lymphoblastic Leukemia (ALL) - Adult 4, 10, 17, 21, p16 deletion, BCR/ABL, MLL
Lymphoma - see individual probes below
Multiple Myeloma (MM) 1q21, 11q23, 13q14, TP53, IGH
Reflex for Positive IGH IGH/FGFR3, IGH/CCND1, IGH/MAF
Myelodysplastic Syndrome (MDS) 5/5q31, 7/7q31, 8, 20q12, MLL
Neuroblastoma MYCN, 1p36, ATM, 17qtel
FISH Probe Chromosome(s) Disease
1p36 deletion 1 Neuroblastoma
1p36/19q13 deletion 1, 19 Brain tumors
1q21 enumeration 1 Multiple myeloma
4 enumeration 4 ALL
4q12 (PDGFRA) 4 Hypereosinophilia
5/5q31 enumeration Loss of 5q AML, MDS
7/7q31 enumeration Monosomy 7 AML, MDS
8 enumeration Trisomy 8 AML, MDS
9p21 deletion (p16, CDKN2A) 9 ALL
10 enumeration 10 ALL
12 enumeration Trisomy 12 CLL
13q14 (D13S319) enumeration 13q14.3 CLL, Multiple myeloma
17 enumeration 17 ALL
17qtel enumeration iso 17q Neuroblastoma, brain tumors
20q12 deletion 20 MDS
21 enumeration 21 ALL
ALK 2p23 Lymphoma, ALCL
AML1 (RUNX1) 21q22 ALL, AML
AML1/ETO t(8;21) AML
API2/MALT1 t(11;18) MALT lymphoma
ATM 11q22.3 CLL, Neuroblastoma
BCL3 19q13 Lymphoma
BCL6 3q27 Lymphoma
BCR/ABL t(9;22) ALL, AML, CML
Chimerism XX/XY Post transplant
CBFB 16q22 AML
CHOP (DDIT3) 12q13 Myxoid liposarcoma
C-MYC amplification 8q24 Brain tumors
E2A 19p13 ALL
EGFR enumeration 7p12 Brain tumors
ETV6 (TEL) 12p13 ALL, AML
EVI1 3q26 Myeloid malignancies
EWS 22q12 Ewing sarcoma
FKHR (FOX01A) 13q14 Rhabdomyosarcoma
IGH 14q32 Lymphoma, Myeloma
IGH/BCL2 t(14;18) Follicular lymphoma, DLBCL
Acute Promyelocytic Leukemia (APL)
5/5q31, 7/7q31, 8; AML1/ETO, MLL, CBFB (BCR/ABL on request)
PML/RARA - Reflex to AML Panel for Negative PML/RARA
ONCOLOGY FISH PROBES
Brain Tumors 1p36/19q13 deletion, EGFR, PTEN, amplification C-MYC, MYCN
FISH TEST LIST
Please remember to check off "Chromosome Analysis" on the
Cytogenetics Request form and attach it to this form.
Patient Name:_______________________________________________________________
ONCOLOGY FISH PANELS
Colorado Genetics Laboratory
FISH Probe Chromosome(s) Disease
IGH/CCND1 t(11;14) Mantle cell lymphoma, Multiple myeloma
IGH/CCND3 t(6;14) Multiple myeloma, DLBCL
IGH/FGFR3 t(4;14) Lymphoma, Multiple myeloma
IGH/MAF t(14;16) Multiple myeloma
IGH/MAFB t(14;20) Multiple myeloma
IGH/MALT1 t(14;18) MALT lymphoma
IGH/MYC t(8;14) Burkitt lymphoma, DLBCL
IGK 2p11.2 Immunoglobulin kappa
IGL 22q11 Immunoglobulin lambda
MALT1 18q21 MALT lymphoma
MLL 11q23 ALL, AML, MDS
Monosomy 22 22q Brain tumors, ATRT, Ependymoma, Meningioma
MYB 6q23 ALL
MYC 8q24 Lymphoma, DLBCL
MYCN amplification 2p23-p24 Neuroblastoma
PDGFRB 5q33 Myeloid neoplasm, Eosinophilia
PML/RARA t(15;17) APL
p16 deletion 9p21 ALL
PTEN 10q23 Brain tumors
Post Transplant XX/XY Post transplant chimerism
RB1 13q14 Retinoblastoma
SYT (SS18) 18q11 Synovial sarcoma
TEL/AML t(12;21) ALL
TP53 deletion 17p13.1 CLL, Multiple myeloma
Previous clone Specify:
Enumeration for individual chromosome Specify:
Microdeletion / Duplication Syndrome
1p36 Deletion 1p36
4p16.3 Wolf-Hirschhorn
5p15.2 Cri-du-Chat
5q35 Sotos
7q11.2 Williams
15q11.2 Prader-Willi / Angelman / 15q duplication
17p11.2 Smith Magenis
22q11.2 DiGeorge / VCFS
Xp22.3 Kallmann 1
Xp22.32 Steroid Sulfatase
Identification
Centromere enumeration probes Specify:
Whole chromosome paint probes Specify:
Aneuploid Interphase Screen Chromosomes
Prenatal Trisomy Screen
Postnatal Trisomy Enumeration
Postnatal Gender Determination
Tissue Trisomy Enumeration
CONSTITUTIONAL FISH PROBES
X, SRY
X, Y, 13, 15, 16, 18, 21, 22
X, Y, 13, 18, 21
X, Y, 13, 18, 21
Cytogenetics Request form and attach it to this form.
FISH TEST LIST
Please remember to check off "Chromosome Analysis" on the
Patient Name:_______________________________________________________________
ONCOLOGY FISH PROBES CONTINUED
Colorado Genetics Laboratory
Colorado Health Outcomes Program (COHO)
Contacts:
David West, PhD
Director
Tel: 303-724-1170
[email protected]
Allison Kempe, MD, MPH
Director, Children’s
Outcomes Research
Director, Primary Care
Research Fellowships
Professor, Pediatrics
Tel: 303-724-1176
[email protected]
Kyle Osborn, COHO/COR
Administrator
Tel: 303-724-1177
[email protected]
Lou Moss
Program Assistant/IRB
Coordinator
Tel: 303-724-1171
[email protected]
http://www.uchsc.edu/coho/
The core function and mission of The Colorado Health Outcomes Program (COHO) is to conduct and
evaluate interventions which improve population health and the overall quality of health care. COHO is
committed to expanding partnerships not just with academic researchers at national universities, but also
within community organizations that deliver health care, public and private payers that finance it, and the
many organizations dedicated to developing innovative health care technologies, services, and delivery
systems. The Colorado Health Outcomes Program (COHO) is dedicated to conducting clinical and
systems health services research. Four methodological “core” areas are the focus of the program: 1)
Primary Care Research; 2) Comparative Effectiveness and Safety Research; 3) Systems Redesign of
Healthcare Systems to improve quality and efficiency; and 4) the application of clinical informatics to
improve the quality of care.
The health care system in the United States today faces many difficult questions. What are the best ways
to measure a person's health status and quality of life and to assess the impact of health care on such
outcomes? How should health care delivery be organized to optimize care for individuals with chronic
health conditions? How can disparities in health and health care for vulnerable populations be reduced?
Questions such as these prompted the formation of COHO.
COHO shares its mission, faculty, staff, and offices with the Children's Outcomes Research (COR)
program.
Our investigators currently consult to and collaborate with on a variety of investigators and agencies on
grant and contract-funded projects.
COHO is not a typical technical core. Rather, we are a Center for Health Services Research.
Colorado Multiple Institutional Review
Board (COMIRB) Review Fees
Marie Wade, Office Manager
Phone: 303-724-1053
Fax: 303-724-0990
E-mail: [email protected]
Website:http://comirbweb.uchsc.edu/portal/
Full Board Initial Review
$ 2,000
Full Board Continuing Review $ 1,500
Expedited Initial Review $ 950
Expedited Continuing Review No Charge
Exempt Initial Review No Charge
Exempt Continuing Review N/A
Amendments and Updates No Charge
Western Institutional Review Board
(WIRB) Review Fees
Effective July 1, 2008
Full-Board Initial Review $3,000
Full-Board Annual Continuing Review $1,800
COMIRB
From: Lakin, Alison
Sent: Monday, November 02, 2009 6:12 PM
Unfortunately, due to the transition to a new database, I do not have the capability to provide
some of the data at this time.
Below is my response to the questions asked.
Sorry
Alison
Alison Lakin RN, LL.B, LL.M, Ph.D
a. How is the quality of your measurements evaluated – quality control?
We do internal quality assurance
b. What is the turn-a-round time for the service you provide?
This data is not currently available
c. Who documents the data provided and signs off on the data?
Protocol review is conducted by 5 panels headed by two co-chairs. The co-chairs have
signature authority for approvals. Any reports generated via the COMIRB database are
handled by Greg Olender, IT Manager.
d. Have you had experience providing data for industry?
COMIRB reviews industry sponsored protocols but most of its current volume is review
of grant funded protocols.
e. Do you have a standard operating procedure manual?
COMIRB Policies and Procedures are available on the COMIRB website.
f. How will you track billing and financial aspects of your core?
Marie Wade, Office Manager, is responsible for billing and tracking finances
The Program in Biomolecular Structure
Computational Biology Core
Contact:
Robert Hodges, PhD
303-724-3253
[email protected]
Website:http://biomol.uchsc.edu/
The Program is an interdepartmental graduate training program
offered within the School of Medicine at the University of Colorado at
Denver and Health Sciences Center Fitzsimons campus in Aurora,
Colorado. Student training places a major emphasis on research
experiences, both in lab rotations and thesis projects, and includes a
range of coursework in biochemistry; drug design; pharmacology;
cellular, molecular and structural biology.
The Program encourages students to engage in collaborative projects
and provides shared mentoring that can include faculty from outside
The Program. Such interactions are geared towards fostering
interdisciplinary training.
Faculty research activities cover a range of structural and computational
techniques including NMR Spectroscopy, X-Ray Crystallography,
Mass Spectrometry and Proteomics, Biophysics, and Peptide/Protein
Chemistry that are focused on a diversity of biological targets such as
signaling molecules, transmembrane proteins, RNA, genome
bioinformatics, lipids, and oligosaccharides.
The Program In Biomolecular Structure
University of Colorado Denver
12801 E. 17
th
Avenue, Mail Stop 8101
Aurora, Colorado 80045
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
Jackie Newnam, Administrator and primary contact for information regarding The Program
including graduate studies.
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9118
[email protected]
Core Facilities Contact Information
Biophysics
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
Brooke Hirsch, Facility Manager
Phone: 303-724-3322
Fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
Computational Biology
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
David Farrell, Systems Administrator
Phone: 303-724-3320
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
Fees vary must contact David Farrell
Mass Spectrometry / Proteomics
Dr. Mark Duncan, Director
Phone: 303-724-3343
12801 E. 17
th
Avenue, Mail Stop 8119
[email protected]
Dr. Kirk Hansen, Facility Manager
Phone: 303-724-3325
12801 E. 17
th
Avenue, Mail Stop 8119
[email protected]
Nuclear Magnetic Resonance
Dr. David Jones, Director/Facility Manager
Phone: 303-724-3600
Fax: 303-724-3663
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Dr. Geoffrey Armstrong, Operational Specialist
800/900 MHz NMR
Phone: 303-724-3331
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Peptide/Protein Chemistry
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
Dziuleta Cepeniene, Operations Specialist
Voice: 303-724-3336
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
X-Ray Crystallography
Dr. Mair Churchill, Director
Phone: 303-724-3670
Fax: 303-724-3663
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Sarah Roemer, Facility Manager
Phone: 303-724-3672
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
University of Colorado Cancer Center
Cytogenetics Core
Contacts:
Marileila Varella-Garcia, PhD
Director
[email protected]
303-724-3147
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/cytogenics/index.aspx
FISH
Aneusomies for EGFR (red) and centromere 7 (green) sequences detected in formalin-fixed,
paraffin embedded lung cancer tissue sections
The UCCC Cytogenetics Core Laboratory provides classic and molecular cytogenetics services,
including fluorescence in situ hybridization (FISH). We have experience with commercially
available and researcher-provided probes, such as:
• chromosome enumeration probes
• painting probes
• translocation probes
• single copy or locus-specific probes
• nick-translated DNA fragments
We also provide consulting services and training for non-assisted lab use.
Our Services
Single and dual color fluorescence in situ hybridization (FISH) assays
• Differentiation of mammalian chromosomes or DNA sequences translocated to rodent
chromosomes and monitoring established cell lines using human genomic or Cot-1 DNA
probes.
• Identification of specific aneuploidies in metaphase spreads and interphase nuclei, in
preparations from diffuse or solid tissues using satellite and locus-specific DNA probes.
• Identification of particular human chromosomes or chromosome fragments in complex
rearrangements and/or marker chromosomes using whole chromosome-specific painting
probes (WCP) or a region-specific probe (Partial Chromosome Probes). WCPs are used
also for identification of human chromosomes in hybrid cells.
• DNA clone mapping (phage, cosmid, P1, PAC, BAC, and YAC) on metaphase
chromosomes of human, rat, mouse and hamster cells.
• Investigation of genomic deletion, duplication or amplification in metaphase and in
interphase nuclei in fresh or preserved biological preparations using DNA clones.
• Detection of chromosome translocations in metaphase or interphase cells using probes
encompassing or closely associated with the breakpoints.
Multicolor-FISH assay
• Simultaneous hybridization of several probes to extended chromatin to determine the
orientation and overlap of the tested sequences.
• Analysis of multiple probes in a given cell for more accurate definition of its genomic
status.
Spectral Karyotyping
Spectral karyotype of a cell representative of the small cell lung carcinoma cell line
UMC19.
Comparative Genomic Hybridization (CGH) assay
• Analysis of DNA sequence copy numbers of cultured or uncultured human, mouse and
rat specimens.
• Multicolor Karyotyping using spectral karyotyping in human, mouse and rat specimens
(SKY) and multiplex-FISH (M-FISH) in human specimens.
Unbanded chromosome analysis
• Breakage evaluation.
• Cell proliferation index (mitotic index).
• Ploidy evaluation
Giemsa-trypsin (GTG) banded chromosome analysis
• Karyotype characterization of human, mouse, rat, and hamster specimens or cell lines in
metaphase or prometaphase cells.
• Determination of cell line homogeneity and evolution using metaphase analysis.
• Identification of parental species in hybrid cell lines.
Additional procedures
Tissue culture
Initiation, maintenance, harvest, and freezing of cell cultures for cytogenetic purposes.
Establishment of immortal cell lines from lymphocytes
DNA labeling by nick-translation for FISH assays
Lab staff performs nick translation labeling. DNA fragments may be genomic DNA, cDNA or
vector DNA. Due to sensitivity limitations of our current instrumentation, we need unique
sequence probes larger than 2.5 kb for mapping studies. If the probe is known to be amplified,
we can use probes >1.0 kb.
How to Use This Core Lab
Testing and instrumentation are available by appointment only. Turnaround time is highly
dependent on the specimen or project. Please contact Dr. Varella-Garcia to schedule your project
and discuss turnaround times.
Prices
We offer discounts for University of Colorado Cancer Center members. All prices listed are
estimated based on special conditions. Please contact Dr. Varella-Garcia for specific pricing for
your project.
Test Description
Member
Base
Non-Member
Base
Cell culture and harvesting $89 $165
EBV transformation of lymphocytes $463 $727
Slide making $20 $38
Ploidy Evaluation $97 $173
Classical Karyotyping $444 $797
DNA Cloning $751 $1,229
DNA Labeling $103 $170
FISH assays – probe A (homebrew) $367 $619
FISH assays – probe B (commercial) $356 $624
Multicolor Karyotyping $1,546 $2,248
Comparative Genomic Hybridization $1,088 $1,603
Consulting $174 $233
Prices 07/01/2008-06/30/2009
Cytogenetics Core
From: Garcia, Marileila
Sent: Tuesday, November 03, 2009 9:57 AM
a) How is the quality of your measurements evaluated – quality control?
We follow standard guidelines required by CAP-CLIA and FDA.
b) What is the turn-a-round time for the service you provide?
It is very much depending on the test. Some tests are reported in 3 days, some may take
one month.
c) Who documents the data provided and signs off on the data?
The technologists document the data provided and the reports are signed by the Core
Director.
d) Have you had experience providing data for industry?
Yes, we have many contracts with pharmaceutical and biotech companies in the last 8
years.
e) Do you have a standard operating procedure manual?
Yes, exactly as required by CAP-CLIA and FDA regulation.
f) How will you track billing and financial aspects of your core?
The Cancer Center requires annual cost study, which is submitted and approved by the
University officials. The Core generate an invoice and the Cancer Center Administrative
Office assists with all financial issues.
Developmental Core
Center for Aids Research (CFAR)
Contacts:
Myron Levin, MD,
Core Director
303-724-2451
[email protected]
Linda Van Dyk, Ph.D.
Core Co-Director
303-724-4207
[email protected]
Website:http://www.uchsc.edu/ccfar/cores/development.htm
The primary purpose of the Developmental Core is to allocate resources to augment AIDS
research efforts at component institutions. Emphasis is placed on support for interdisciplinary
projects and infrastructure investments that will have a broad impact on AIDS research
capabilities by recruiting new investigators, providing transitional funding to Junior Faculty, and
facilitating the conduct of pilot studies.
The Developmental Core has three Specific Aims:
1. To make major infrastructure or programmatic investments that will broadly facilitate
interactions, capabilities, and/or efficiencies of the AIDS research community at the
component institutions.
2. To recruit outstanding new investigators with AIDS expertise to the faculties of the
institution from outside institutions or from training programs within the institution.
3. To provide initial funding for pilot and feasibility studies.
These funds might be used by junior investigators, by established investigators to explore novel
areas of AIDS research, or by experienced investigators not previously involved in AIDS
research.
The CFAR Research Development Fund provides support for three types of
projects:
New Initiative Grant
To facilitate the recruitment of new faculty or investment in major new programs or
infrastructure related to HIV research. In the case of new recruitments these grants can be
used as matching funds with other institutional or philanthropic support. Funds may be
used for salary support, supplies, and/or equipment. Preference will be given to proposals
that involve multiple investigators and/or will facilitate new HIV-related research
collaborations among productive groups.
Grants will be at the level of $60,000 for one year with the potential for renewal under
certain circumstances.
Junior Faculty Grant
To facilitate the transition of trainees to faculty status. Funds may be used for salary
supplementation, technical support, and/or supplies.
Grants will be at the level of $50,000 for one year with the potential for a second year
under certain circumstances.
Pilot Project Grant
To support pilot or feasibility projects that will open a new area of investigation in an
HIV-research laboratory or initiate HIV research in additional laboratories. These awards
should be used to generate sufficient preliminary data to enable investigators to acquire
external funding in the future.
Grants will be at the level of $30,000 for one year.
No Fees
The Diabetes and Endocrinology Research Center (DERC) at the University of Colorado Denver
on the Anschutz Campus in Aurora, Colorado brings together the collective experience of basic
and clinical scientists from different faculty and research backgrounds to enhance the
productivity and the quality of diabetes and endocrinology research within the University of
Colorado Denver Health Sciences Center community.
DERC Program Directors:
J ohn Hutton, PhD
Program Director, Barbara Davis Center for Childhood Diabetes, UCD.
Professor, Departments of Pediatrics, Cellular & Structural Biology.
Phone: 303-724-6836
George Eisenbarth, MD, PhD
Program Deputy Director, Barbara Davis Center for Childhood Diabetes, UCD.
Professor, Departments of Pediatrics, Cellular & Structural Biology.
Phone: 303-724-6837
Website:http://www.uchsc.edu/misc/diabetes/DERC/index.htm
UCD DERC Molecular Biology Services
Automated DNA Sequencing
• Dye-terminator sequencing on ABI 3130xl and ABI 3100-Avant capillaries
• Online sample submission and results retrieval
• 24-36 hour turnaround time
- Next business day for samples submitted before 12pm
• See Sample Submission Guidelines for details and requirements
Automated Fragment Analysis
• Microsatellite analysis
• SNP detection
• Determination of STR or VNTR number
Real Time PCR
• Roche LC480 and AB 7000 SDS
• High Resolution Melt Capable
• Genotyping
• Gene Quantification and Expression analysis
in-situ hybridization probe synthesis
• Full scale hybridization from gene of interest selection to imaging and analysis
• Preparative work underway to build probe library for islet related targets (insulin,
glucagon, slc30a8, etc)
• In conjunction with the DERC Histology Core
Basic Molecular Biology Services
• Nucleic acid purification
• Cloning and expression of genes of interest in bacterial systems
• Plasmid DNA preparation (small-large scale)
• Site directed mutagenesis
• Restriction digestion and analysis
• RT-PCR
• PCR and PCR product purification
• Recombinant protein expression and purification
Custom Services
• Please contact [email protected] or [email protected] for
inquiries regarding your project.
The purpose of this website is to provide some basic information about the DERC cores
including contact information and links to on-line services where they are available. If you have
questions about the UCD DERC please contact us (email or phone: 303.724.6836).
Diabetes & Endocrinology Research Center
Molecular Biology Core Facility (DERC MBCF) Price List
DERC Members
Non-DERC or
UCD Affiliate
DNA Sequencing
Data Collection Only $5.10 $6.35
Reaction Plus Data Collection $8.90 $9.90
Fragment Analysis
Genomic DNA Preparation $1.90 $2.30
PCR - ABI True $0.56 $0.67
PCR - Epicentre $1.00 $1.20
SNP Analysis $3.80 $4.55
Injection on 3100 Avant $5.10 $6.10
Analysis $25/hour $35.00/hour
Real Time PCR Machine Usage
Real Time PCR Session $22.00 $24.00
Allelic Discrimination (Pre/Post Read) $10.00 $12.00
Laboratory Services*
Mouse Model Identification (MMI) - per sample $6.25 $7.50
Bulk MMI (20+samples) $5.00 $6.00
Plasmid Maxi Prep (single) $28.15 $33.80
Plasmid Maxi Prep (5+samples) $24.20 $29.00
Plasmid Mini Prep (single) $3.30 $4.00
Plasmid Mini Prep (10+samples) $2.75 $3.30
RNA Isolation - Mini Prep (single) $8.85 $10.60
Cloning/Transformation PCR product $25.00 $30.00
in situ Probe Generation $167 min. $225 min.
*Cost of materials/reagents included
We offer many common molecular biology related laboratory techniques for services.
Please contact us for pricing/quotes for your project!
Manager: Randy Wong, phone: 303.724.6825
Prices current thru J une 2009.
The purpose of this website is to provide some basic information about the DERC cores
including contact information and links to on-line services where they are available. If you have
questions about the UCD DERC please contact us (email or phone: 303.724.6836).
Barbara Davis Center – Page 1 of 7
Diabetes & Endocrinology Research Center (DERC)
Barbara Davis Center for Childhood Diabetes at UCD
From: Powell, Mary, Cc: Hutton, John
Sent: Friday, October 09, 2009 2:09 PM
The Barbara Davis Center (BDC) is the home for the NIH Diabetes Endocrinology Research
Center (DERC) that provides funding for seven distinct cores. These cores provide services to
principal investigators within the BDC researching type 1 or childhood diabetes and other
principal investigators throughout campus wide scientific projects. Core facilities at the BDC are
BioResources (animal and islet), Autoantibody Measurement, Flow Cytometry, Histology and
Molecular/Vector.
In addition, the BDC is the home of the Juvenile Diabetes Research Foundation (JDRF)
Autoimmunity Prevention Center. Another of the facilities funded by the JDRF Center grant
provides Lymphocyte Analysis core.
Responses to your queries are below and identified by each core.
Each core has described their response to question f). A general statement applies to all. The
core operates as a service center with an auxiliary university account and the UCD Finance
Office approves charges on an annual basis. Requests are submitted online and monthly billing
is performed through the same portal to preapproved account holders and speed types.
BioResources Core (Animal and Islet Preparation)
The core focuses on animal models of autoimmune diabetes (particularly the NOD mouse) and
derived strains eg. NOD Scid, NOD Rag -/-, NOD Ins 1 -/-, NOD Ins 2 -/-.
a) How is the quality of your measurements evaluated – quality control?
Animal: Basic evaluation of diabetes such as glucose tolerance testing and disease monitoring is
performed a Veterinary Technologist with 20+ years experience. She performs all the hands-on
animal work that allows us to offer a high standard of care and competence, and there is
continuous researcher feedback for assessing the quality and timeliness of the work performed.
The Animal Core work is done in the University’s AALAC-certified Center for Comparative
Medicine, and thus we must operate at a high standard commensurate with their rules and
regulations.
Islet: Each new lot of digestive enzyme is tested for optimal concentration and pancreas
digestion time, and the islets produced are functionally tested by transplantation into diabetic
mice. Additionally, there is continuous researcher feedback of islet viability and quality.
b) What is the turn-a-round time for the service you provide?
Animal: Animal procedures are normally scheduled a week in advance.
Maintenance of researchers’ breeding colonies is an ongoing process.
Islet: Islet preparations are normally booked about one week in advance.
Barbara Davis Center – Page 2 of 7
c) Who documents the data provided and signs off on the data?
Animal: The BDC Animal Core Vet. Tech. performs all animal procedures, breeding colony
maintenance, and maintains all appropriate records. The core manager oversees all animal core
work.
Islet: The core manager maintains a notebook, detailing each islet harvest, which is monitored by
the core director.
d) Have you had experience providing data for industry?
No, for both animal and islet services.
e) Do you have a standard operating procedure manual?
Yes, for animals and both mouse and rat islet harvesting.
f) How will you track billing and financial aspects of your core?
Animal: The Animal Core produces a comprehensive annual cost analysis, which must be
evaluated and approved by the University’s finance department. The Vet. Tech. records and
collates all animal procedure and breeding colony maintenance charges. From this information,
the core manager generates monthly invoices, and the BDC administrative staff reallocates the
charges to the appropriate speed types.
Islet: The Islet Core produces a comprehensive annual cost analysis, which must be evaluated
and approved by the University’s finance department. The core manager records and collates all
islet harvesting data. From this information, he generates monthly invoices, and the BDC
administrative staff reallocates the charges to the appropriate speed type.
Autoantibody Measurement Core
The core performs standardized measurements of circulating autoantibodies including insulin
AA, 1A2A, GADA, ZnT8A, 2104A, TPO A, TG 2A.
a) How is the quality of your measurements evaluated – quality control?
CLIA inspection by state. Internal quality control of assays with standard samples with results
within set ranges and Shewhart plots. External quality control where existing, in particular CDC
and Immunology of Diabetes Society coded workshops (DASP). External quality control UCLA
for molecular HLA typing. Internal: Shewart Plot for each assay is plotted all time. External:
DASP autoantibody workshop organized by CDC and IDS every 18 months. Blinded split
duplicate programs by each NIH project we involved.
b) What is the turn-a-round time for the service you provide?
Less than one week. Routinely one week, maximum two weeks.
Barbara Davis Center – Page 3 of 7
c) Who documents the data provided and signs off on the data?
Liping Yu and Roberto Gianani and for specific research projects George Eisenbarth
Liping Yu documents all the data and signs off the report and George Eisenbarth double checks
the data and sign off all consent forms.
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Yes, we have SOP for each autoantibody assay.
f) How will you track billing and financial aspects of your core?
Auxiliary University account established and Cost Center analysis.
Liping Yu and Kathy Barriga report the numbers of assays to Luciana Smith every month.
Luciana generates bill to each internal speed type and keep the records.
Flow Cytometry Core
The BDC core maintains and operates two flow cytometers used principally for research studies
of autoimmunity in humans and animal models.
a) How is the quality of your measurements evaluated – quality control?
The core’s two cytometers are maintained on Preventive Maintenance/service contracts from the
manufacturer. The core manager runs daily QC/calibration programs on both instruments.
b) What is the turn-a-round time for the service you provide?
Open blocks of times are usually available to reserve for the following day, although booking
more is advance is prudent. Use of both cytometers is by an on-line reservation system, with
BDC researchers having first priority.
c) Who documents the data provided and signs off on the data?
The researchers and their staffs run their own samples and collect/collate their own data.
Technical assistance/training for core users is available from the core Monday – Friday, 8AM to
5PM.
d) Have you had experience providing data for industry?
No.
e) Do you have a standard operating procedure manual?
Barbara Davis Center – Page 4 of 7
Yes, for both cytometers.
f) How will you track billing and financial aspects of your core?
The Cytometry Core produces a comprehensive annual cost analysis, which must be evaluated
and approved by the University’s finance department. Researchers record their usage and
provide an appropriate speed type on line (dnaLIMS program). From this information, the core
manager generates monthly invoices, and the BDC administrative staff reallocates the charges.
Histology Core
The core performs standard histopathological analyses based on light microscopy and
immunohistochemistry.
a) How is the quality of your measurements evaluated – quality control?
The quality of our data is measured by using control tissues to ensure that proper staining has
occurred. Stains and alcohol solutions are replaced on a regular basis to ensure that stains are of
the highest quality.
b) What is the turn-a-round time for the service you provide?
The average turn-a-round time for the service that we provide is about 2-3 days.
c) Who documents the data provided and signs off on the data?
Researchers and their staff provide and sign off on the data from our service.
d) Have you had experience providing data for industry?
No.
e) Do you have a standard operating procedure manual?
The histology core has a standard operating procedure manual that is stored in the facility. It
contains the protocols for all of the staining/embedding that the core provides and is updated as
new procedures and stains are added. Additionally we have operating manuals on hand for the
Leica tissue processor, microtome, and cryotome.
f) How will you track billing and financial aspects of your core?
Billing for the core is tracked online using the dnaTools web site. Customers place their order via
the website and upon submitting their order they are quoted the price. Monthly accounting
reports are created the first of the month and are submitted for billing. The histology core keeps a
copy of these records in the core.
Lymphocyte Analysis Core
Barbara Davis Center – Page 5 of 7
This core supported by the JDRF Center grant provides high-quality services for lymphocyte
subset purification and phenotypic and functional analyses. Lymphocytes are a fundamental
requirement for a wide variety of studies addressing the role of T and B cells in pathogenesis of
type 1 diabetes.
a) How is the quality of your measurements evaluated – quality control?
ELISPOT BioReader
In addition to the routine maintenance service performed as part of the service contract with the
Biosys ELISPOT Reader, Core personnel run reference plates twice a month for instrument
calibration to insure accurate readings.
AutoMacs Cell Sorter
1) To ensure maximum performance of the AutoMACS Separator over time, technical service is
provided by Miltenyi Inc. The service contract includes technical support and annual preventive
maintenance such as thorough cleaning, replacing o-rings, tubing, valves, and syringes.
2) AutoMACS columns are replaced every two weeks.
3) Routine clean programs – see SOP.
4) SAFE Program - The SAFE Clean Program (programmed into the AutoMACS by Miltenyi)
should is performed on the AutoMACS sorter at least once per week or after 2.4E+09 cells have
been passed through a single sorting column, whichever occurs first.
Bioplex
Instrument calibration is done monthly using a kit containing beads to standardize daily signal
output and ensure unit-to unit reproducibility of the reader. Instrument validation is performed
prior to analysis run, using a kit containing beads to validate the operational specifications of the
reader, including accuracy, linearity, dynamic range, slope, fluidics, and optical alignment.
b) What is the turn-a-round time for the service you provide?
Depending on the work load between 4-7 days
c) Who documents the data provided and signs off on the data?
The PRA documents the data and the Core’s director signs off on the data
d) Have you had experience providing data for industry?
No.
e) Do you have a standard operating procedure manual?
Yes.
f) How will you track billing and financial aspects of your core?
At this point we are not charging for our service and will adopt the standard systems in place for
the DERC and UCD Finance department.
Barbara Davis Center – Page 6 of 7
Molecular/Vector Core
This core is a centralized resource for automated DNA sequencing, genotyping, fragment
analysis, quantitative PCR, production of recombinant adenoviruses, and provision of certified
specific reagents.
a) How is the quality of your measurements evaluated – quality control?
Molecular: The MBCF’s two DNA sequencing instruments are maintained on service contracts
from the manufacturer. Inclusive in the service contracts are bi-annual instrument maintenance,
spectral calibration, and cleaning. Positive control standards are run with each reaction set, which
are run twice daily. Additionally, our LIMS system and instrument manufacturer software
analysis program provides universal quality scoring.
Vector: What quality control. The quality control of the vector core most often comes from
titer’s generated with the final product and a specific Supernatant Rescue assay. Additional
assays can be ordered to analyze whether the virus does what it was designed to do such as
Western blotting or PCR analysis.
b) What is the turn-a-round time for the service you provide?
Molecular: For DNA sequencing, the MBCF provides results within 24-36 hours after sample
submission. For genotyping services, the MBCF strives to provide results within 3-5 days.
Vector: The turn-a-round time depends on the specific service requested and ranges from about 3
days to 6 weeks. Due to the past customer level, most requests can be started immediately.
c) Who documents the data provided and signs off on the data?
Molecular: The MBCF provides data archival/retrieval through a LIMS (Laboratory Information
Management System), which is housed on an internal server. For all other services,
documentation is recorded by all staff for all techniques performed, similar to a laboratory
notebook documentation. All procedures are documented and disseminated to all recipients of
services.
Vector: The sole employee, vector core manager, documents all data produced from the work
done in the core.
d) Have you had experience providing data for industry?
Molecular: Yes, the MBCF currently services at least four external Non-University entities.
Vector: No
e) Do you have a standard operating procedure manual?
Molecular: Yes the MBCF maintains an internal standard operating procedure manual. These
SOPs apply mainly to routine high-throughput services. For more variable services (custom
projects), the MBCF utilize generally accepted/published methodology.
Barbara Davis Center – Page 7 of 7
Vector: Yes, we have a standard operating procedure for most of the procedures we use to
produce Adenovirus.
f) How will you track billing and financial aspects of your core?
Molecular: Monthly invoicing is created by the MBCF Core Manager with service orders
recorded online through the LIMS system and direct service requests. The MBCF produces a
comprehensive annual cost study (evaluated and approved through the UCD finance department)
that determines unit costs for all products and services. All invoices are emailed to each user.
Summary invoicing is sent to our Administrative Core where all charges are reallocated to each
requestor’s Speed Type.
Vector: The vector core tracks all billing and financial aspects with the use of spreadsheets that
have been designed for filling in monthly accounting.
DNA Diagnostic Laboratory
Introduction
The UCD DNA Diagnostic Laboratory at the University of Colorado Denver is a clinical
molecular genetics laboratory offering full service nucleic acid-based testing. Established as a
national and regional resource for the medical and genetics communities, the laboratory performs
testing for a variety of genetic diseases utilizing state of the art techniques.
Clinical and Laboratory Staff
Elaine B. Spector, PhD
Director, DNA Diagnostic Laboratory
303-724-3801
[email protected]
Website:http://www.uchsc.edu/dnalab/
Accreditation
The laboratory is licensed by the College of American Pathologists (#211828-31) and
acknowledged by the Clinical Laboratories Improvement Act (#06D0644348). The laboratory
voluntarily participates in quality assurance programs.
University of Colorado DNA Diagnostic Laboratory: Testshttp://www.uchsc.edu/dnalab/tests.html 7/11/2007
UCDHSC DNA Diagnostic Laboratory
We offer the following tests:
Ashkenazi Jewish Panels: FGFR3, Fibroblast Growth Factor Receptor 3
Ashkenazi Panel 1 Achondroplasia
Tay Sachs Disease (Hexosaminidase A Deficiency) Hypochondroplasia
Canavan Disease Thanatophoric Dysplasia, Types I and II
Fanconi Anemia (FANCC-Related) Nonsyndromic Craniosynostosis Syndromes
Familial Dysautonomia Muenke Syndrome
Ashkenazi Panel 2 Crouzon Syndrome with Acanthosis Nigricans
Niemann-Pick, Type A/ B (Sphingomyelinase Deficiency) Hereditary Hemochromatosis
Mucolipidosis, Type IV Limb / Heart Disorders
Bloom Syndrome Holt-Oram Syndrome, TBX5 – sequence * SOON
Glycogen Storage Disease, Type Ia (Von Gierke Dis.) Duane Radial Ray Syndrome, SALL4 – sequence * NEW
Ashkenazi Panel 3
Townes-Brock Syndrome, SALL1 – sequence * SOON
Gaucher Disease Liver Disease, UGT1A1 * NEW
CFTR-Related Disorders (41 mutations) Crigler-Najjar Syndrome, Gilbert Syndrome
Cystic Fibrosis Hyperbilirubinemia, Transient Familial
CBAVD (Congenital Bilateral Absence of Vas Deferens) Chemotherapy Dosage Test * SOON
Cardiomyopathy Disorders Metabolic Disorders
Danon Disease (Glycogen Storage IIB) * NEW ANT, Antiquitin – Pyridoxine-Responsive Neonatal Seizures * NEW
Lamin A/C (LMNA) GA I, Glutaric Acidemia Type 1 – Sequence GCD
LMNA-Related Cardiomyopathy GA II (MADD) – Sequence ETFDH/ ETF-QO * NEW
Emery-Dreifuss Muscular Dystrophy, Autosomal GA II (MADD) – Sequence ETFA and ETFB * NEW
Limb-Girdle Muscular Dystrophy (LGMD), Type 1B Homocystinuria due to CBS Deficiency * NEW
Charcot-Marie-Tooth Neuropathy, Type 2B1 LCHAD, Long Chain 3-Hydroxy-Acyl-CoA Dehydrogenase Def. –
Hutchinson-Gilford Progeria Syndrome Common Mutation
Mandibuloacral Dysplasia MCAD, Medium Chain Acyl-CoA Dehydrogenase Deficiency –
Clotting Disorders Common Mutation
Factor V Leiden Thrombophilia MCAD, Full Sequence * SOON
Prothrombin G20210 Thrombophilia (Factor II) NKH, Non-Ketotic Hyperglycinemia – Sequence AMT, GLDC
MTHFR, A233V: C677T (Thermolabile Variant) NKH, Non-Ketotic Hyperglycinemia – Sequence GCSH
MTHFR, E429A: A1298C * NEW Propionic Acidemia due to PCCA or PCCB Deficiency * NEW
Warfarin Dosage Test * NEW VLCAD, Very Long Chain Acyl-CoA Dehydrogenase Def. * NEW
DNA Isolation MCC, Maternal Cell Contamination Study
Deafness / Nonsyndromic Hearing Loss Pigmentation Disorders
Connexin 26, GJ B2-Related DFNB 1 HPS, Hermansky-Pudlak Syndrome, Type 1
Connexin 30, GJ B6-Related DFNB 1 * NEW OCA1, Oculo-Cutaneous Albinism, Type 1a/ 1b * NEW
FMR-1
OCA2, Oculo-Cutaneous Albinism, Type 2 * NEW
Fragile X Syndrome WT-1 Related Disorders – sequence * NEW
FXTAS: Adult-Onset Tremor Ataxia Syndrome Denys-Drash Syndrome, Isolated Diffuse Mesangial Sclerosis,
POF: Premature Ovarian Failure Familial Wilms Tumor, Frasier Syndrome
Please contact the laboratory for prices: 303-724-3801
Send samples with Consent Form and Request Form, to shipping address: RC-1 North, Rm P18-4404J, 12800 E. 19th Ave, Aurora, CO 80045
Mailing address: UCDHSC DNA Diagnostic Laboratory, Mail Stop 8313, PO Box 6511, Aurora, CO 80045
University of Colorado (Old name: UCHSC DNA Diagnostic Laboratory)
UCD DNA Diagnostic Laboratory: Tests Offered
?? Each Sample Needs a Completed Request Form AND Consent Form AND Fax Form, and This Checklist ??
Lab director: [email protected]; 303-724-3801 Mailing address for correspondence: Mail Stop 8313, PO Box 6511, Aurora, CO 80045
Genetic counselor: [email protected]; 303-724-1572 Shipping address for samples: 12800 E. 19th Ave, Rm P18-4404J, Aurora, CO 80045
www.uchsc.edu/DNALab, Fax: 303-724-3802 1 of 3 3/11/2009
Test # (5% prepay discount for all testing; parents free for some.) Prices CPT Codes
1 DNA Isolation $75 1 x 83891; 1 x 83912
2 Shipping: $50 plus all shipping costs $50 +
3 Carrier test (for many disorders listed): 2 known mutations NEW REDUCED PRICE $250 1 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 1 x 83912
4 Carrier test (for many disorders listed): 1 known mutation $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
5 Prenatal test (for many disorders listed): 2 known mutations $800 2 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 2 x 83912
6 Prenatal test (for many disorders listed): 1 known mutation $500 2 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 2 x 83912
7 MCC, Maternal Cell Contamination Study (for all prenatal testing) $200 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
Ashkenazi Panels + Cystic Fibrosis
8 Ashk 1 + Ashk 2 + Ashk 3 + CF $525 1 x 83891; 4 x 83894; 4 x 83898; 2 x 83896; 2 x 83900; 80 x 83901; 4 x 83912
9 Ashkenazi Panel 1: Tay Sachs; Canavan; Fanconi; Familial Dysautonomia $200 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
10 Ashkenazi Panel 2: Niemann-Pick; Mucolipidosis; Bloom; Glycogen Storage Dis. Ia $200 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
11 Ashkenazi Panel 2, ordered with other ASHK $100 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
12 Ashkenazi Panel 3: Gaucher Disease $200 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
13 Ashkenazi Panel 3, ordered with other ASHK $100 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
100 Ashkenazi Panel 4: MSUD, Maple Syrup Urine Disease – COMING SOON (Test is in development)
101 Ashkenazi Panel 4, ordered with other ASHK – COMING SOON (Test is in development)
14 Cystic Fibrosis, CFTR-Related Disorders $250 1 x 83891; 2 x 83896; 2 x 83900; 80 x 83901; 1 x 83912
15 Cystic Fibrosis, CFTR-Related Disorders, ordered with ASHK panel(s) $125 1 x 83891; 2 x 83896; 2 x 83900; 80 x 83901; 1 x 83912
Cardiomyopathy Disorders
16 ARVD comprehensive, Panels A+B ordered together $2,000 1 x 83891; 106 x 83894; 106 x 83898; 106 x 83904; 4 x 83912
17 ARVD Panel A: ARVD9, PKP2 $1,400 1 x 83891; 34 x 83894; 34 x 83898; 34 x 83904; 1 x 83912
18 ARVD Panel B, ARVD8+10+11, ordered together $1,400 1 x 83891; 72 x 83894; 72 x 83898; 72 x 83904; 3 x 83912
19 ARVD8, DSP, ordered alone $525 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
20 ARVD10, DSG2, ordered alone $1,000 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
21 ARVD11, DSC2, ordered alone $1,060 1 x 83891; 32 x 83894; 32 x 83898; 32 x 83904; 1 x 83912
22 Danon Disease (LAMP2, Glycogen Storage IIB) $650 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
23
Lamin A/C (LMNA): LMNA-Related Dilated Cardiomyopathy; Autosomal Emery-Dreifuss
Muscular Dystrophy; Limb-Girdle Muscular Dystr. 1B; Familial Partial Lipodystrophy Dunnigan
type; Charcot-Marie-Tooth 2B1; Hutchinson-Gilford Progeria; Mandibuloacral Dysplasia
$750 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
Clotting Disorders
24 FV, Factor V (five) Leiden Thrombophilia $150 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83908; 1 x 83912
25 MTHFR-AV, A233V: C677T (Thermolabile Variant) $175 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83898; 2 x 83908; 1 x 83912
26 MTHFR-EA, E429A: A1298C $75 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83898; 2 x 83908; 1 x 83912
27 PT, Prothrombin G20210 Thrombophilia (Factor II, FII or F2) $125 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83908; 1 x 83912
28 Warfarin Dosage Test-Discontinued $325
Deafness / Hearing Loss
29 Connexin 26, GJB2-Related DFNB1, sequence $450 1 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 1 x 83912
30 Connexin 30, GJB6-Related DFNB1, common deletion $350 1 x 83891; 3 x 83894; 3 x 83898; 1 x 83912
31 Pendred Syndrome, SLC26A4 $1,100 1 x 83891; 36 x 83894; 36 x 83898; 36 x 83904; 1 x 83912
32 Waardenburg Comprehensive: all 4 genes ordered together $2,400 1 x 83891; 68 x 83894; 68 x 83898; 68 x 83904; 4 x 83912
University of Colorado (Old name: UCHSC DNA Diagnostic Laboratory)
UCD DNA Diagnostic Laboratory: Tests Offered
?? Each Sample Needs a Completed Request Form AND Consent Form AND Fax Form, and This Checklist ??
Lab director: [email protected]; 303-724-3801 Mailing address for correspondence: Mail Stop 8313, PO Box 6511, Aurora, CO 80045
Genetic counselor: [email protected]; 303-724-1572 Shipping address for samples: 12800 E. 19th Ave, Rm P18-4404J, Aurora, CO 80045
www.uchsc.edu/DNALab, Fax: 303-724-3802 2 of 3 3/11/2009
Test # (5% prepay discount for all testing; parents free for some.) Prices CPT Codes
33 Waardenburg syndrome 1, 3, CDHS: PAX3, ordered alone $650 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
34 Waardenburg syndrome 2, Tietz: MITF, ordered alone $1,000 1 x 83891; 30 x 83894; 30 x 83898; 30 x 83904; 1 x 83912
35 Waardenburg syndrome 4: SOX10, ordered alone $400 1 x 83891; 6 x 83894; 6 x 83898; 6 x 83904; 1 x 83912
36 Waardenburg-Shah syndrome, EDNRB, ordered alone $600 1 x 83891; 14 x 83894; 14 x 83898; 14 x 83904; 1 x 83912
Disorders of Sex Development
37 AIS Panel (Androgen Insensitivity Syndrome): AR+SRY+WT1 ordered together $1,500 1 x 83891; 42 x 83894; 42 x 83898; 42 x 83904; 3 x 83912
38 AR: Androgen Receptor, sequence $1,000 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
39 SRY: XY Gonadal Dysgenesis, Y-linked $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
40 WT1-Related Disorders: Denys-Drash; Frasier; Wilms Tumor; Nephrotic Syndrome $750 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
FGFR3, Fibroblast Growth Factor Receptor 3
41 Achondroplasia; Hypochondroplasia $400 1 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 1 x 83912
42 Thanatophoric Dysplasia, Types I and II $400 1 x 83891; 10 x 83894; 10 x 83898; 10 x 83904; 1 x 83912
43 Muenke Syndrome (Exon 7) $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
44 Crouzon Syndrome with Acanthosis Nigricans (Exon 10) $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
45 Saddan (Exon 15) $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
46
Fragile X, FMR-1: Fragile X Syndrome; FXTAS: Adult-Onset Tremor Ataxia
Syndrome; POF: Premature Ovarian Failure
$300
1 x 83891; 2 x 83892; 4 x 83894; 1 x 83896; 1 x 83897;
4 x 83898; 4 x 83904; 1 x 83912
Iron Storage Disorders
47 Hereditary Hemochromatosis $150 1 x 83891; 3 x 83892; 3 x 83894; 4 x 83898; 1 x 83912
Limb / Heart Disorders
48 SALL1, Townes-Brock Syndrome $950 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
49 SALL4, Duane Radial Ray Syndrome $950 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
50 TBX5, Holt-Oram Syndrome $950 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
Liver Disorders
51 UGT1A1: Gilbert Syndr.; Transient Familial Hyperbilirubinemia; Ristocetin Chemo Dosage Test $300 1 x 83891; 1 x 83893; 4 x 83896; 4 x 83898; 4 x 83904; 1 x 83912
Metabolic Disorders
52 3MCC Panel, 3-Methylcrotonyl-CoA Carboxylase Def.: 3MCC A+B ordered together $1,500 1 x 83891; 34 x 83894; 34 x 83898; 34 x 83904; 2 x 83912
53 3MCC-A (3MCCC1), ordered alone $900 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
54 3MCC-B (3MCCC2), ordered alone $800 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
55 ANT, Antiquitin, Pyridoxine-Dependent Neonatal Seizures, ALDH7A1 $1,500 1 x 83891; 34 x 83894; 34 x 83898; 34 x 83904; 1 x 83912
56 GA I, Glutaric Acidemia Type 1, GCD $525 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
57 GA II comprehensive, Glutaric Acidemia Type II, all three genes $2,400 1 x 83891; 54 x 83894; 54 x 83898; 54 x 83904; 3 x 83912
58 GA II (MADD), ETFDH (also known as ETF-QO) $1,000 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
59 GA II (MADD), ETFA $850 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
60 GA II (MADD), ETFB $550 1 x 83891; 12 x 83894; 12 x 83898; 12 x 83904; 1 x 83912
61 HCS, Holocarboxylase Synthetase Deficiency $725 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
62 Homocystinuria due to CBS Deficiency $1,200 1 x 83891; 30 x 83894; 30 x 83898; 30 x 83904; 1 x 83912
63 LCHAD, Long Chain 3-Hydroxy Acyl-CoA Dehydrogenase Deficiency, common mut. $250 1 x 83891; 1 x 83892; 1 x 83894; 2 x 83898; 1 x 83912
University of Colorado (Old name: UCHSC DNA Diagnostic Laboratory)
UCD DNA Diagnostic Laboratory: Tests Offered
?? Each Sample Needs a Completed Request Form AND Consent Form AND Fax Form, and This Checklist ??
Lab director: [email protected]; 303-724-3801 Mailing address for correspondence: Mail Stop 8313, PO Box 6511, Aurora, CO 80045
Genetic counselor: [email protected]; 303-724-1572 Shipping address for samples: 12800 E. 19th Ave, Rm P18-4404J, Aurora, CO 80045
www.uchsc.edu/DNALab, Fax: 303-724-3802 3 of 3 3/11/2009
Test # (5% prepay discount for all testing; parents free for some.) Prices CPT Codes
64 MCAD, Medium Chain Acyl-CoA Dehydrogenase Deficiency, common mutation $250 1 x 83891; 2 x 83898; 2 x 83904; 1 x 83912
65 MCAD, Medium Chain Acyl-CoA Dehydrogenase Deficiency, full sequence $1,000 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
66 MMA, Methylmalonic Acidemia, Panel 1: MUT + A + B $1,500 1 x 83891; 52 x 83894; 52 x 83898; 52 x 83904; 3 x 83912
67 Methylmalonic Acidemia, MMA-MUT, ordered alone $960 1 x 83891; 24 x 83894; 24 x 83898; 24 x 83904; 1 x 83912
68 Methylmalonic Acidemia, MMA-A, ordered alone $480 1 x 83891; 12 x 83894; 12 x 83898; 12 x 83904; 1 x 83912
69 Methylmalonic Acidemia, MMA-B, ordered alone $640 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
70 MMA, Methylmalonic Acidemia, Panel 2: C + E $500 1 x 83891; 14 x 83894; 14 x 83898; 14 x 83904; 2 x 83912
71 Methylmalonic Acidemia, MMA-CHC, ordered alone $320 1 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 1 x 83912
72 Methylmalonic Acidemia, MCEE, ordered alone $240 1 x 83891; 6 x 83894; 6 x 83898; 6 x 83904; 1 x 83912
73 NKH Tier 1, Non-Ketotic Hyperglycinemia, AMT + GLDC $2,400 1 x 83891; 60 x 83894; 60 x 83898; 60 x 83904; 2 x 83912
74 NKH, only AMT $800 1 x 83891; 12 x 83894; 12 x 83898; 12 x 83904; 1 x 83912
75 NKH, only GLDC $1,600 1 x 83891; 48 x 83894; 48 x 83898; 48 x 83904; 1 x 83912
76 NKH Tier 2, Non-Ketotic Hyperglycinemia, GCSH $400 1 x 83891; 10 x 83894; 10 x 83898; 10 x 83904; 1 x 83912
77 Propionic Acidemia A+B $1,800 1 x 83891; 76 x 83894; 76 x 83898; 76 x 83904; 2 x 83912
78 Propionic Acidemia due to PCCA Deficiency $1,100 1 x 83891; 48 x 83894; 48 x 83898; 48 x 83904; 1 x 83912
79 Propionic Acidemia due to PCCB Deficiency $700 1 x 83891; 28 x 83894; 28 x 83898; 28 x 83904; 1 x 83912
80 SPR, Sepiapterin Reductase Deficiency $400 1 x 83891; 6 x 83894; 6 x 83898; 6 x 83904; 1 x 83912
81 Trimethylaminuria, TMAU (coming soon, not available now) $500 1 x 83891; 14 x 83894; 14 x 83898; 14 x 83904; 1 x 83912
82 VLCAD, Very Long Chain Acyl-CoA Dehydrogenase Deficiency, ACADVL $725 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
Pigmentation Disorders
83 HPS1, Hermansky-Pudlak Syndrome Type 1, common mutation only $250 1 x 83891; 1 x 83894; 2 x 83898; 1 x 83912
84 HPS package, sequence HPS1+HPS4 $2,500 1 x 83891; 56 x 83894; 56 x 83898; 56 x 83904; 2 x 83912
85 HPS1, Hermansky-Pudlak Syndrome Type 1, sequence $1,700 1 x 83891; 28 x 83894; 28 x 83898; 28 x 83904; 1 x 83912
86 HPS4, Hermansky-Pudlak Syndrome Type 4, sequence $1,700 1 x 83891; 28 x 83894; 28 x 83898; 28 x 83904; 1 x 83912
Albinism Panel: max price for all OCA1-4 + OA testing needed by patient $2,500 It varies
87 OCA1, Oculo-Cutaneous Albinism, Type 1a/1b, TYR sequence $1,000 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
88 OCA2, Oculo-Cutaneous Albinism, Type 2, P-gene sequence $1,500 1 x 83891; 46 x 83894; 46 x 83898; 46 x 83904; 1 x 83912
89 OCA2, Oculo-Cutaneous Albinism, Type 2, P-gene deletion $350 1 x 83891; 2 x 83894; 4 x 83898; 1 x 83912
90 OCA3, Oculo-Cutaneous Albinism, Type 3, TYRP1 sequence $1,000 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
91 OCA4, Oculo-Cutaneous Albinism, Type 4, MATP sequence $1,000 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
92 OA1, X-linked Ocular Albinism, GPR143 sequence $800 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
Aicardi-Goutieres Syndrome
93 AGS Comprehensive: Aicardi-Goutieres Syndrome (all 4 genes ordered together) $1,650 1 x 83891; 50 x 83894; 50 x 83898; 50 x 83904; 4 x 83912
94 AGS Tier 1, AGS 1,5+2: TREX1 + RNASEH2B together (65% of mutations) $900 1 x 83891; 26 x 83894; 26 x 83898; 26 x 83904; 2 x 83912
95 AGS Tier 2, AGS 3+4: RNASEH2C + RNASEH2A ordered together $900 1 x 83891; 24 x 83894; 24 x 83898; 24 x 83904; 2 x 83912
96 AGS Type 1,5: TREX1-Related Aicardi-Goutieres Syndrome, ordered alone $450 1 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 1 x 83912
97 AGS2, RNASEH2B-Related, Type 2, ordered alone $650 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
98 AGS3, RNASEH2C-Related, Type 3, ordered alone $500 1 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 1 x 83912
99 AGS4, RNASEH2A-Related, Type 4, ordered alone $600 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
DNA SEQUENCING SERVICES
Contacts:
Chr istopher Korch, Efang Li,
Todd Pitts, Har r y Dr abkin
303-724-3167
303-724-3889
DNA.Cor [email protected]
Web Site:http://loki.uchsc.edu/
1. Overview of DNA Sequencing Services
2. Premium Full-Service Standard Single-Pass DNA Sequencing
3. Normal Mid-Level Standard Single-Pass DNA Sequencing
4. High Through-put Mid-Level Single-Pass DNA Sequencing
Budget Single-shot DNA Sequencing
1. Overview of DNA Sequencing Services
The primary function of the CU-Cancer Center DNA Sequencing Core is to sequence DNA
samples brought to us as purified DNA. We can also purify DNA from bacterial colonies for
sequencing. However, we highly recommend that the customer confirm that the E. coli
transformant does in fact bear the correct plasmid before submitting it for DNA purification and
sequencing.
We offer several levels of sequencing service - from our Premium Full-Service Single-Pass
Sequencing to budget "Single-Shot" sequencing, where the customer performs the sequencing
reaction themselves and submits the reaction products ready for electrophoresis on one of our
automated sequencers. The Core's two capillary ABI fluorescent sequencing instruments can
provide between 650 and 950 bp of reliable DNA sequence per AmpliTaq FS cycle sequencing
reaction with dRhodamine and BigDye labelled dye-terminators.
Sequencing results will only be delivered electronically as follows: customers will receive an
email informing them that their results are ready. In the message, there will be a link to our
website from where the results can be downloaded, using the customer's name and password.
The data will be available on the server for one month from date of posting; afterwards
customers will need to contact the Core directly for the data. We will no longer print
electropherograms of sequencing results.
On this website customers will have access to the text files (.seq), electropherogram files (.ab1),
and .pdf files of the electropherograms. The electropherogram (.ab1) files will be editable, but
the .pdf files will not. Viewing the .ab1 files you will need to download either Editview (for
MACs) or Chromas (for PCs). Both are free of charge and available at the following websites:
Editview:http://www.appliedbiosystems.com/support/software/dnaseq/installs.cfm
Chromas:http://www.technelysium.com.au/chromas.html
Xplorer Lite:http://www.dnatools.com/download.html
2. Premium Full-Service Standard Single-Pass DNA Sequencing
This is the highest level of sequencing service, which includes performance and processing of
the sequencing reaction, loading the products on a sequencing instrument, and preparing and
troubleshooting the results for the customer. The DNA samples should be quantified by the
customer using agarose gel electrophoresis and be submitted to the Core at the following
concentrations:
Premium Service DNA and Primer Concentrations
Type of DNA
DNA Concentration
(nanograms / microliter)
Primer Concentration
(micromolar)
Plasmid DNA
150. 5.
Uncloned PCR Product
15. 5.
DNA restriction fragment
15. 5.
Lambda, PAC, BAC, Cosmid
DNA 500.
100.
The DNA and primers should be submitted in 1.5-1.7 mL microfuge tubes and the labels on the
tubes must be exactly as that submitted through the on-line ordering system. To estimate the
concentration and purity (i.e., presence of RNA and genomic DNA) of your DNA samples, we
recommend that you electrophorese your samples on an agarose gel and compare the intensity of
the ethidium bromide bands of your DNA sample against that of the bands present in a ladder of
mass standards. Three commercially available mass standards that can be used are: PGC
Scientifics Gene Choice DNA Ladder I (Cat. No. 62-6108-00), which we sell and you thereby
avoid paying shipping costs. New England Biolabs (NEB) also have a 1KB Ladder (Cat. No.
N32325), which is available in the NEB freezer in the UCHSC School of Medicine Room 5626.
Inter-Mountain Scientific Company (ISC Bioexpress) sells the Gene Mate Quanti-Maker 1 kb
Ladder (Cat. No. C-5087-200), which is very similar to the mass ladder from PGC Scientifics.
When it comes to DNA concentration, more is not always better. Too much DNA or too
concentrated primer solutions can give results with high background or appear to be a mixture of
sequences. We will assume the concentration of your sample is the one appropriate for your
samples (see above table) and will run the reactions accordingly. If the reaction fails because of
a possible error on the part of Core personnel, the reaction will be repeated at no extra charge.
We can provide several standard sequencing primers (M13 Forward, M13 Reverse, SP6
promoter, T3 promoter, T7 promoter primer, and T7 terminator, see section below for primer
sequences) at no additional cost to the customer. We also have the primer T7neo, which is
specific for the mammalian expression vectors derived from the pCIneo and pSI vectors. The
customer may also bring their own primer for sequencing their DNA samples. We can sequence
different types of DNAs: plasmids, PCR fragments, restriction fragments, cosmid, PAC, and
lambda phage. The Core will provide the customer with the sequencing results as an electronic
copy of the text file, and a printout of the electropherogram.
3. Normal Mid-Level Standard Single-Pass DNA Sequencing
For EACH reaction, the customer should mix the below specified amounts of DNA and the
desired primer made up in a total volume of 17.0 microliters using either water or 10 mM Tris-
HCl (pH 8) in a labelled 1.5 -1,7 mL microcentrifuge tube (Please note tube size!).
Mid-Level Service DNA and Primer Quantities
Type of DNA DNA Quantity (nanograms) Primer Quantity (picomoles)
Plasmid DNA
1250 10
Uncloned PCR Product
50 10
DNA restriction fragment
50 10
Lambda, PAC, BAC, Cosmid
DNA
3000 100
Do not use TE, because the EDTA will inhibit the reaction. The Core does not supply any
primers for this level of service. Instructions for labelling the tubes are found below and on the
order form specific for this service. The Core will add an aliquot of this mixture to a tube
containing the sequencing reagents, perform and process the cycle-sequencing reactions, load the
samples on a gel, and provide the customer with the sequencing results as described above. Only
failures clearly due to an error of the sequencers will be repeated.
4. High Throughput Mid-Level Single-Pass DNA Sequencing
These options include running and analysis of sequencing reactions and emailing of electronic
copies of the data. The customer mixes specific amounts of DNA and primer (see below) and we
do the rest. No repeats unless due to Core error. Turn-around time approximately 1-2 working
days.
In order to offer these inexpensive sequencing options, we must specify how the samples are
brought to the Core. The samples must be a minimum of 47 samples and pre-loaded in an
Applied Biosystems MicroAmp Optical 96-well Reaction plate (Part Number N801-0560 which
can be purchased through the ABI Freezer Program in the DNA Core; currently $40.70 per box
of 10 plates). The wells must be covered with either strips of 8 caps (ABI part # N801-0535
currently $55.50 for 300 strips of 8 caps) or with optical adhesive cover sheets (AB part #
4311971; currently $122.00 for package of 100 cover sheets). Each of the wells must contain one
sample of DNA mixed with a single primer in the amounts below, depending on the type of
DNA. The last well in the batch ( H12) should be left empty for the addition of a control
template provided by the Sequencing Core. The DNAs and primers must be dissolved in water.
We suggest quantifying the DNAs using a mass ladder as described above.
High-Through-put Mid-Level Service DNA and Primer Quantities
Type of DNA DNA Quantity
(nanograms)
Primer Quantity
(picomoles)
Total Volume
(microliters)
Plasmid (3 - 20 kb)
150 5 10
PCR Fragment (Purified,
i.e., not cloned
15 5 10
DNA Restriction
Fragment (Purified, i.e.,
not cloned
15 5 10
BAC (bacterial artificial
chromosome)
600 100 10
Lambda phage DNA,
Cosmid DNA (> 30 kb)
600 100 10
We suggest that DNAs with unusual features that can make them difficult to sequence (e.g., very
GC rich regions, known hairpins structures) be submitted for Premium Full Service Sequencing
instead of attempting to sequence them by any of the Mid-Level DNA sequencing services and
that the customer inform the Core personnel of these potential problems.
Budget Single-shot DNA Sequencing
The customer performs the sequencing reactions with either of the ABI dye-terminator cycle
sequencing ready reaction kits: the dRhodamine (ABI part number 403044 or 403045) or
BigDye dye-terminator kit (ABI part number 4303149 or 4303150). The customer must
perform and process the cycle-sequencing reactions per instructions from ABI and from the
Core. Instructions for labelling the tubes are on the order form specific for this service. Core
personnel will electrophorese the reaction products on on the appropriate automated DNA
sequencing instrument and provide the customer with the sequencing results as described above.
Results will only be repeated if due to a failure of the automated sequencers.
Please specify on the order form which ABI sequencing chemistry kit was used!!
DNA SEQUENCING & ANALYSIS CORE PRICES
FOR SERVICES
Effecti ve July 1, 2005
Price List For Cancer Center Members Only
DNA Sequencing
Premium Full Service Single-Pass Sequencing Reaction
Core quantifies DNA and performs sequencing reaction. Use of standard
sequencing primers included: M13 Forward, M13 Reverse, SP6, T7, T7-neo, and
T3. Repeats included, if fault due to Core
$ 12.50
Normal Mid-Level Single-Pass Sequencing Reaction
Customer mixes DNA and desired primers at specified DNA
and primer concentrations. Core does not provide any sequencing
primers. Core performs sequencing reaction. No repeats.
$ 9.00
High Through-put Mid-Level Single-Pass Sequencing Reaction
Batches of 48+ Samples (price per sample)
$ 8.00
Budget Single-shot Sequencing
The Core runs customer's processed sequencing reaction on its automated
sequencers. No repeats.
$ 4.00
DNA Profiling - Identification of Cell Lines
PCR Amplification and Fragment Analysis $ 40.00
Template Preparation
Plasmid Minipreps (from colonies or liquid cultures)
High Copy Number Plasmids
Low - Medium Copy Number Plasmids
$ 15.00
$ 20.00
Purification of PCR Products from Reaction Mixtures $ 10.00
Semiautomatic, High-Throughput Plasmid Minipreps
Price per 96 cultures
$500.00
Quantification of Templates of Unknown Concentration $ 5.00
Miscellaneous Services (e.g., dilution of primer) $ 5.00
Hybridization Filters
High Density Hybridization Filters for Screening DNA Libraries
2 copies
3-7 copies
$180.00
$200.00
DNA Analysis Available on request.
Please call for quotation.
Additional Services
Available on request. Please call for quotation for Primer Walking, Large-scale Preps of
Sequence Quality Plasmid DNA, Preparation of Lambda or Cosmid DNA Templates,
Construction and Screening of DNA Libraries (In vitro Transposon Libraries in Plasmids
and Cosmids), Preparation of Sequence Submissions.
DNA SEQUENCING & ANALYSIS CORE PRICES
FOR SERVICES
Effecti ve July 1, 2005
Price List For Academic and Non-Profit Institutions
DNA Sequencing
Premium Full Service Single-Pass Sequencing Reaction
Core quantifies DNA and performs sequencing reaction. Use of standard
sequencing primers included: M13 Forward, M13 Reverse, SP6, T7, T7-neo, and
T3. Repeats included, if fault due to Core
$ 15.00
Normal Mid-Level Single-Pass Sequencing Reaction
Customer mixes DNA and desired primers at specified DNA
and primer concentrations. Core does not provide any sequencing
primers. Core performs sequencing reaction. No repeats.
$ 11.00
High Through-put Mid-Level Single-Pass Sequencing Reaction
See brochure or separate description for details on sample preparation for this
procedure.
Batches of 47+ Samples (price per sample)
$ 9.00
Budget Single-shot Sequencing
The Core runs customer's processed sequencing reaction on its automated
sequencers. No repeats.
$ 4.50
DNA Profiling - Identification of Cell Lines
PCR Amplification and Fragment Analysis $ 50.00
Template Preparation
Plasmid Minipreps (from colonies or liquid cultures) $ 15.00
High Copy Number Plasmids
Low-Medium Copy Number Plasmids
$ 20.00
Purification of PCR Products from Reaction Mixtures $ 10.00
Semiautomatic, High-Throughput Plasmid Minipreps
Price per 96 cultures
$500.00
Quantification of Templates of Unknown Concentration $ 5.00
Miscellaneous Services (e.g., dilution of primer) $ 5.00
Hybridization Filters
High Density Hybridization Filters for Screening DNA Libraries
2 copies
3-7 copies
$180.00
$200.00
DNA Analysis Available on request.
Please call for quotation.
Additional Services
Available on request. Please call for quotation for Primer Walking, Large-scale Preps of
Sequence Quality Plasmid DNA, Preparation of Lambda or Cosmid DNA Templates,
Construction and Screening of DNA Libraries (In vitro Transposon Libraries in Plasmids
and Cosmids), Preparation of Sequence Submissions.
DNA SEQUENCING & ANALYSIS CORE PRICES
FOR SERVICES
Effecti ve July 1, 2005
Price List For Industrial and For-Profit Customers
DNA Sequencing
Premium Full Service Single-Pass Sequencing Reaction
Core quantifies DNA and performs sequencing reaction. Use of standard
sequencing primers included: M13 Forward, M13 Reverse, SP6, T7, T7-neo, and
T3. Repeats included, if fault due to Core
$ 16.00
Normal Mid-Level Single-Pass Sequencing Reaction
Customer mixes DNA and desired primers at specified DNA
and primer concentrations. Core does not provide any sequencing
primers. Core performs sequencing reaction. No repeats.
$ 12.00
High Through-put Mid-Level Single-Pass Sequencing Reaction
Batches of 48-Samples (price per sample)
$ 10.00
Budget Single-shot Sequencing
The Core runs customer's processed sequencing reaction on its automated
sequencers. No repeats.
$ 6.00
DNA Profiling - Identification of Cell Lines
PCR Amplification and Fragment Analysis $ 60.00
Template Preparation
Plasmid Minipreps (from colonies or liquid cultures) $ 22.00
$ 27.00
High Copy Number Plasmids
Low Medium Copy Number Plasmids
Purification of PCR Products from Reaction Mixtures $ 15.00
Semiautomatic, High-Throughput Plasmid Minipreps
Price per 96 cultures
$600.00
Quantification of Templates of Unknown Concentration $ 5.00
Miscellaneous Services (e.g., dilution of primer) $ 5.00
Hybridization Filters
High Density Hybridization Filters for Screening DNA Libraries
2 copies
3-7 copies
$270.00
$300.00
DNA Analysis Available on request.
Please call for quotation.
Additional Services
Available on request. Please call for quotation for Primer Walking, Large-scale Preps of
Sequence Quality Plasmid DNA, Preparation of Lambda or Cosmid DNA Templates,
Construction and Screening of DNA Libraries (In vitro Transposon Libraries in Plasmids
and Cosmids), Preparation of Sequence Submissions.
The Evaluation Center
Contact:
Bonnie Walters
Director
The Evaluation Center
School of Education and Human Development
University of Colorado Denver
Campus Box 106; P.O. Box 173364
Denver, CO 80217-3364
303-315-4967
General Email: [email protected]
http://www.ucdenver.edu/academics/colleges/SchoolOfEducation/CentersPartnerships/Evaluation/Pages/E
valuation.aspx
Vision:
Powered by a commitment to cutting edge evaluation methodologies, we strive to make program
evaluation a widely accepted and valued practice.
Mission:
As a collaborative enterprise, it is our mission to use rigorous, innovative evaluation processes to inform
and promote evidence-based programs, practices and policies in schools, institutions of higher education,
health care and in our communities.
Goals:
•
To promote the use of evaluation by diverse stakeholders;
•
To help institutions and organizations become effective consumers of evaluation data;
•
To provide a setting where Ph.D. and master's degree students can further develop quantitative
and qualitative evaluation expertise by working on real life evaluation projects; and
•
To become a resource for informing health, education, and social policiesAll trademarks are
About Us
The Evaluation Center is a distinct division of the university whose purpose is to promote
evidence-based practices and policies through inquiry-based evaluation processes to non-profit
agencies. The Evaluation Center provides credible, scholarly, and objective formative and
summative evaluation. Our staff has experience in providing large-scale evaluation services
having worked with projects funded by the National Science Foundation, the University
Corporation for Atmospheric Research, the Danforth Foundation, the National Education
Association, and the US Department of Education.
Resources
Collaborative Process Initiation Flowchart
Frequently Asked Questions
Useful Links to Other Sites
•
Digital Resources for Evaluators
Links to online evaluation tools, texts, and other resources.
•
The Online Evaluation Research Library
This site, funded by the National Science Foundation, provides evaluation plans, instruments, and
reports for NSF projects that can be used as examples by Principal Investigators, project evaluators, and
others outside the NSF community as they design proposals and projects.
•
Research Methods Knowledge Base
This page is an introduction to basic ideas, types, and questions about evaluation.
•
Resources for Methods in Evaluation and Social Research
This page lists FREE resources for methods in program evaluation and social research. The focus is on
"how-to" do evaluation research and the methods used: surveys, focus groups, sampling, interviews, and
other methods.
Flow Cytometry and Cell Sorting Facility
Contacts:
Brent Palmer, PhD
Director
303-724-7203
[email protected]
Website:http://www.uchsc.edu/clinimmune/flowcytometry/index.htm
General Information about Flow Cytometry
Flow cytometry is a multi faceted technique for characterizing and delineating cell populations
via size, shape, surface and intracellular protein expression, which yields valuable information
on both phenotype and cell expression. Flow cytometry is unique in its ability to rapidly analyze
and sort thousands of cells per second while simultaneously providing data on distinctive cell
populqations resolved at the single cell level. Flow cytometry can be used as a tool to identify
novel cell populations based on the expression of cell surface markers through intracellular
staining. It can also be used to examine antigen specific T cells, gene expression, or qualify the
proliferative capacity of different cell populations. In addition it is a technique that can be
performed using any cell sample suspension, e.g., blood cells, collagen digested or disaggregated
tissue (e.g. lung, liver, and spleens cells), stem cells and cultured cells.
The BD FACSAria is a cell sorter that is capable of rapid, simultaneous purification of
phenotypically distinct populations of cells. Up to four different cell populations can be purified
simultaneously from the same sample.
The Immunohistopathology Unit provides CFAR members with the following tools and services:
• Cryostat for cutting frozen infectious tissue for HIV-1-related research
• Leica DMR – Light microscope capable of color imaging and associated with
quantitative image analysis software
• Leica DM5000B – Fluorescent microscope capable of imaging fluorescently stained
specimens (4 colors)
• Immunostaining and assay development including software programming for image
analysis, for HIV-1-related projects
• Identification of HIV-1-producing cells by in situ hybridization
• Technical expertise in design and implementation of immunohistochemical or
immunofluorescent staining studies
• Training in immunostaining techniques and use of microscopy equipment and software
Please note our services, equipment and pricing below:
CFAR
Member Rate
Non-CFAR
Member Rate
Non-Academic
Industry Rate
CELL Analysis
FACScan (1-3
colors)**
$35 $40 $60
FACSCalibar (1-4
colors)**
$40 $50 $75
LSR II (1-13
colors)**
$55 $80 $100
FACSAria (1-13
colors)
$77 $99 $125
Cell Sorting
FACSAria (1-13
colors)*
$99 $125 $150
Data Analysis
FlowJO, Diva, Cell
Quest
Free Free Free
Training and
Consultation
Free Free Free
* The price for cell sorting (FACSAria) includes technician time.
* Please add $40/hour to the price of the FACScan, FACSCalibur and LSR II if the samples are
run by Flow Lab personnel.
The facility's technical director, Brent Palmer Ph.D., and staff help design experiments, develop
and implement new applications as well as collaborate scientifically with users. The staff provide
full service flow cytometry assistance, including sample preparation, staining, and data
acquisition and analysis. We currently perform immunophenotyping for a number of clinical
trials, including CD4/CD8 immunophenotyping for the Adult Clinical Trials Group (ACTG).
Please contact Brent Palmer PhD ([email protected]) if you have additional questions
about our services.
Flow Cytometry & Immunology Core
From: Palmer, Brent
Sent: Thursday, October 08, 2009 9:32 AM
a) How is the quality of your measurements evaluated – quality control?
Our flow cytometry laboratory follows CLEA guild lines and is certified by the College of American Pathologist
(CAP). Everyday our flow cytometers are QC’ed using standard bead-based methods.
b) What is the turn-a-round time for the service you provide?
We have online scheduling for the use of our flow cytometer (potentially immediate access) and all of the clinical
tests we provide have 24 hour or less turn around time.
c) Who documents the data provided and signs off on the data?
All clinical flow cytometry tests are CAP certified and all tests are signed off by the technical director (Brent
Palmer) of the lab.
d) Have you had experience providing data for industry?
We have provided service to multiple biotech companies in the Denver-Boulder area
e) Do you have a standard operating procedure manual?
Yes
f) How will you track billing and financial aspects of your core?
Billing is carefully tracked by our personal and billing is done by sending invoices to all user. Lab Manager
(Prosoft) data-base is use to track clinical samples and flow cytometer usage is determined by tracking log on and
log off time on the flow cytometers. Flow cytometry billing is done in 15 minutes increments. Billing is done
monthly.
Flow Cytometry Services at the
University of Colorado Cancer Center
Contacts:
Christopher J. Hogan, PhD
Director
303-724-3145
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/flowcytometry/index.aspx
The Flow Cytometry Core at the University of Colorado Cancer Center offers services to
Cancer Center members, Charles C. Gates Regenerative Medicine and Stem Cell Biology
Program members, academic non-members and private industry researchers. CC and RMSCB
Members receive scheduling priority and a discounted rate for services. Learn more about
becoming a UCCC member or a RMSCB member .
Our experienced staff can analyze your samples for you or train you to run the analysis
equipment for all services except cell sorting. Core staff performs all cell sorting.
Flow Cytometry Analysis Services
We have three main analyzers, each best for different types of analysis. You may use the
machines yourself or ask us to analyze your samples for you.
Becton Dickinson FACSCalibur
• 2 lasers: 488 and 635
• 4 color analysis
• Suggested fluors: FITC , PE , PECy7, APC
Beckman Coulter FC500
• High through-put
• 2 lasers: 488 and 635
• 5 color analysis
• Suggested fluors: FITC , PE , PE-Texas Red, APC, PECy7, PI
Cyan
• Analysis rate of 50,000 events/second
• 100 million event data files
• New 40mW red diode laser for enhanced APC and APC-Cy7 detection
• 9-color analysis
• 9 colors
Cell Sorting Services
We have two cell sorting machines with different capabilities. Core staff performs all cell sorts.
Moflo
• 3 lasers: 488, 635 and tunable Krypton
• Many laser lines for optimizing fluorescent protein detection
• Plate sorting
• 7 color capability
Moflo XDP
• Optimized for rare events
• Plate sorting
• 4 lasers: UV, 405, 488, 635
• 9 color capability
• Sort rate of 70,000 events per second
• 5 decade data resolution
• Plate sorting for any size plate
• 4-way sorting
Luminex Multiplex Bead Assays
This analysis measures cytokines, chemokines, phosphoproteins and apoptosis markers.
Also available
• ViCell Cell Counter
• Victor Multilabel Counter (self-service only in RC-1 South, Room 4215)
• Cytospin microscope slide centrifuge
Prices
Service Description
Cancer
Center
Member Rate
Stem Cell
Member
Rate
Non Cancer
Center
Member Rate
Stem Cell Non
Cancer
Center Rate
Commercial
Rate
Research Flow
Analyzers
$78 $66 $229 $216 $251
Research Flow
Analyzers - Self-
Run/Consult
$51 $39 $99 $87 $109
Research Flow Sorts $122 $99 $242 $219 $267
Wallac Plate Reader $17 $17 $57 $57 $63
Vicell Cell Counter $2.66 $2.66 $3.56 $3.56 $3.91
• Prices effective July 1, 2008-June 30, 2009
Flow Cytometry & Immunology Core (UCCC)
From: Hogan, Chris
Sent: Monday, November 09, 2009 5:01 PM
a) How is the quality of your measurements evaluated – quality control?
Instrument quality control is performed daily to verify alignment and sensitivity.
b) What is the turn-a-round time for the service you provide?
Turn-a-round t ime probably doesn’t really apply, but scheduling l ead t ime does.
Time is u sually a vailable o n th e a nalyzers within 1 -2 da ys a nd l ead t ime f or
scheduling the sorters is 3-4 days.
c) Who documents the data provided and signs off on the data?
We have a staff of three, all of whom are highly experienced in Flow Cytometry
and have at l east 10 years of experience. All of the staff participates i n national
and international flow cytometry training workshops and conferences.
d) Have you had experience providing data for industry?
Yes, several private industry organizations routinely use our services.
e) Do you have a standard operating procedure manual?
We have standard operating procedure manuals for each instrument that relate to
instrument maintenance and operation. The staff consults on a n i ndividual basis
with i nvestigators c oncerning t he pr oper c ontrols a nd s pecimen pr eparation f or
their individual assays.
f) How will you track billing and financial aspects of your core?
Flow Cytometry services ar e ch arged o n a t ime-used b asis. E ach i nstrument
automatically l ogs t he t ime u sed f or ea ch i nvestigator. Invoices ar e p repared
monthly f or t he pr evious m onth’s c harges. A cost s tudy i s p erformed yearly
through t he U niversity finance de partment t o e nsure t hat pr icing i s f air a nd
reasonable.
University of Colorado Cancer Center
Gene Expression, Microarray and PCR Core
Contacts:
Mark Geraci, MD
Core Director
[email protected]
303-315-0398
Bifeng Gao, PhD
Microarray Core Manager
[email protected]
303-724-3367
Bryan Haugen, MD
Core Co-Director
PCR Director
[email protected]
303-724-3921
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/gene-
expression/index.aspx
HNSCC and NSCLC cell lines with similar
gefitinib response sort together.
The Gene Expression Core is dedicated to providing state-of-the-art facilities and technical support and
services for analysis of gene expression, which will allow UCCC members to be on the cutting edge of
cancer research.
The Gene Expression Core is comprised of:
• Microarray Core
• PCR Core
Core Objectives
• Analyze gene expression using both pre-made and custom designed oligonucleotide arrays
• Facilitate gene discovery
• Accurately quantitate gene expression using real time PCR and GenomeLab GeXP technology
• Provide support for data analysis and bioinformatics by our data mining tool and our data
analysis capabilities
• Remain committed to using a variety of approaches for expression analysis
• Provide consultation and educational services to help those members with limited knowledge
on microarray technology and to bring the Core customers up to date as technology advances
The Gene Expression Core was established in response to the technological advances in gene array, as
well as the demand for high throughput expression analysis and genomic investigation to investigate
pathogenesis, therapeutics, genetic susceptibility and gene discovery in cancer research. The informatics
aspect is of paramount importance, and five distinct analysis programs, as well as a network, are used to
store, share and analyze the data.
To date, the Core is one of the highest volume Affymetrix microarray facilities in academia in the
country, having performed more than 10,900 microarrays including test arrays over seven years for
nearly 250 investigators. On average, 85% of the users are UCCC members.
Contacts:
Mark W. Geraci, M.D.
Director
[email protected]
Office: 303-724-6040
Bifeng Gao, PhD
Assistant Professor
Core Manager
303-724-6048
[email protected]
Website:http://microarray.uchsc.edu/index.php
Microarray Core
The Microarray Core Facility at University Of Colorado Health Sciences Center (UCHSC) is an
advanced, state-of-the-art Microarray Technology Center providing crucial research support for
investigators interested in using Affymetrix GeneChips®, CombiMatrix CustomArray™ Chips or the
Nanogen NanoChip®. We also host rtPCR with the Bio-Rad iCycler. Our team is dedicated to
providing high-quality microarray laboratory instruction, service, and consultation to the research and
clinical community affiliated with UCHSC and other research institutions in the region.
Affymetrix Nanogen CombiMatrix iCycler Agilent
Nucleic Acid Isolation Call or Email Dr. Gao
The quality of the nucleic acid is essential to the overall success of the
microarray analysis. Since the most appropriate protocol for the isolation of
RNA or DNA is source dependent, we recommend using a protocol that has
been established for the tissues or cells being used. In the absence of an
established protocol, we recommend using one of the commercially available
kits designed for nucleic acid isolation.
Nucleic acid analysis via the Agilent Bioanalyzer 2100. Price
The 2100 bioanalyzer is Agilent's highly successful microfluidics-based
platform for the analysis of DNA, RNA, proteins and cells. As the first
commercial, analytical instrument based on lab-on-a-chip technology the
Agilent 2100 bioanalyzer has proven to be an excellent alternative to messy
and labor-intensive gel electrophoresis techniques; delivering fast,
automated, high quality digital data instead of the subjective, time-consuming
results associated with gels.
The process only takes 35 ~ 40 minutes for 12 samples: Load samples, run
chip, view output.
Nucleid acid analysis and concentration determination via the
NanoDrop® ND-1000.
Free for
Array Customers
The NanoDrop® ND-1000 UV-Vis Spectrophotometer enables highly
accurate analyses of extremely small samples with remarkable
reproducibility. The patented sample retention system eliminates the need for
cuvettes and capillaries which decreases the measurement cycle time. The
ND-1000 is designed for 1-2 ul undiluted samples.
RNA Sample Labeling Price
• 1 to 5 µg of total RNA required for Affymetrix labeling protocol
• 5 to 10 µg of total RNA required for ENZO Biosciences labeling
protocol
• 1st and 2nd strand cDNA synthesis from total RNA
• Generation of biotin-labeled cRNA
• Quantification and quality check
• cRNA fragmentation
Small Amount RNA Sample Labeling (5-200ng of total RNA is
required)
Price
• Total RNA quality assessment
• 1st and 2nd strand cDNA synthesis from total RNA
• in vitro transcription (IVT)
• Second round 1st and 2nd strand cDNA synthesis
• IVT with biotin
• Quantification and quality check
• cRNA fragmentation
Genomic DNA Sample Labeling for Genotyping Call or Email Dr. Gao
• 0.25 µg of genomic DNA is required
• Restriction digestion of DNA
• Cleanup, and QC for the restriction digest
• Ligation
• PCR
• Fragmentation
• End-labeling
GeneChip® Processing Price
• Samples are loaded on to an expression or mapping array and
hybridized overnight.
• The samples are removed to microfuge tubes,
• The arrays are then processed through the GeneChip® Fluidics
Station 450.
• Each array is then scanned on the Affymetrix GeneChip® Scanner
3000.
Combimatrix CustomArray™ Chips Call or Email Dr. Gao
CombiMatrix Corporation's CustomArray™ is a high quality, completely
customizable array format that provides a cost effective and timely solution
for microarray users. Oligonucleotide probes can be defined and designed by
the user and supported by the open source CombiMatrix probe design
system at no additional cost. CustomArray™ uses a specially modified
"CMOS" semi-conductor to direct the molecular assembly of a specific
sequence of DNA bases in response to a digital command. The 12,000
feature CustomArray™ chip available in 1 × 3 inch format to fit most spotted
microarray scanners.
SNP / STR Detection via Nanogen NanoChip® MBW Call or Email Dr. Gao
The NanoChip® Molecular Biology Workstation is an automated multi-purpose
instrument that facilitates detection of known sequences, such as in the
analysis of Single Nucleotide Polymorphisms (SNPs) and Short Tandem
Repeats (STRs) using the NanoChip® Electronic Microarray. The unique,
open-architecture design permits us to define, select and build our own test
panels or use predefined analyte specific reagent packs (ASR's).
Data analysis service Call or Email Dr. Gao
Basic Data Analysis: the core will run a pairwise comparision analysis (e.g.,
control vs. experimental) using Affymetrix GCOS data analysis software.
Extended Data Analysis: the core analyst will provide an indepth analysis of
multivariate experiment data (e.g., 3 or more treatments, time-course
experiment, etc.).
Pricing
Core lab service cost
Affymetrix GeneChip® price list attached for UCHSC
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
GeneChip® Arrays & Reagents
GeneChip ® arrays are analysed with GeneChip ® instruments and software systems only
Expression Anal ysis
Human Arrays
Part Product Name Contents Per Array Total Price
900366 GeneChip® Human Genome U133A Array contains 5 arrays $1,875 $375
900367 GeneChip® Human Genome U133A Array contains 30 arrays $11,250 $375
900470 GeneChip® Human Genome U133 Plus 2.0 contains 2 arrays $850 $425
900466 GeneChip® Human Genome U133 Plus 2.0 contains 6 arrays $2,550 $425
900467 GeneChip® Human Genome U133 Plus 2.0 contains 30 arrays $12,750 $425
900471 GeneChip® Human Genome U133A 2.0 contains 2 arrays $550 $275
900468 GeneChip® Human Genome U133A 2.0 contains 6 arrays $1,650 $275
900469 GeneChip® Human Genome U133A 2.0 contains 30 arrays $8,250 $275
900368 GeneChip® Human Genome U133B Array contains 5 arrays $1,875 $375
900369 GeneChip® Human Genome U133B Array contains 30 arrays $11,250 $375
900370 GeneChip® Human Genome U133 Set contains 5 U133A and 5 U133B human arrays $3,750 $375
900444 GeneChip® Human Genome U133 Set contains 30 U133A and 30 U133B human arrays $21,000 $350
900377 GeneChip® Human Genome Focus Array contains 5 arrays $1,000 $200
900376 GeneChip® Human Genome Focus Array contains 30 arrays $6,000 $200
900649 GeneChip® Human Exon 1.0 ST Array contains 2 arrays $1,050 $525
900650 GeneChip® Human Exon 1.0 ST Array contains 6 arrays $3,150 $525
900651 GeneChip® Human Exon 1.0 ST Array contains 30 arrays $15,750 $525
900653 GeneChip® Human Exon 1.0 ST Array Training Kit each $9,050
900654 GeneChip® Human Exon 1.0 ST Array Starter Pack each $28,700
Rat Arrays
900404 GeneChip® Rat Expression Array 230A contains 5 arrays $1,750 $350
900405 GeneChip® Rat Expression Array 230A contains 30 arrays $10,500 $350
900505 GeneChip® Rat Genome 230 2.0 Array contains 2 arrays $800 $400
900506 GeneChip® Rat Genome 230 2.0 Array contains 6 arrays $2,400 $400
900507 GeneChip® Rat Genome 230 2.0 Array contains 30 arrays $12,000 $400
900406 GeneChip® Rat Expression Array 230B contains 5 arrays $1,750 $350
900407 GeneChip® Rat Expression Array 230B contains 30 arrays $10,500 $350
900408 GeneChip® Rat Expression Set 230 contains 5 230A and 5 rat 230B arrays $3,500 $350
900442 GeneChip® Rat Expression Set 230 contains 30 230A and 30 rat 230B arrays $19,500 $325
Mouse Arrays
900412 GeneChip® Mouse Expression Array 430A contains 5 arrays $1,875 $375
900413 GeneChip® Mouse Expression Array 430A contains 30 arrays $11,250 $375
900495 GeneChip® Mouse Genome 430 2.0 contains 2 arrays $850 $425
900496 GeneChip® Mouse Genome 430 2.0 contains 6 arrays $2,550 $425
900497 GeneChip® Mouse Genome 430 2.0 contains 30 arrays $12,750 $425
900498 GeneChip® Mouse Genome 430A 2.0 contains 2 arrays $550 $275
900499 GeneChip® Mouse Genome 430A 2.0 contains 6 arrays $1,650 $275
900500 GeneChip® Mouse Genome 430A 2.0 contains 30 arrays $8,250 $275
900414 GeneChip® Mouse Expression Array 430B contains 5 arrays $1,875 $375
900415 GeneChip® Mouse Expression Array 430B contains 30 arrays $11,250 $375
900416 GeneChip® Mouse Expression Set 430 contains 5 430A and 5 430B mouse arrays $3,750 $375
900443 GeneChip® Mouse Expression Set 430 contains 30 430A and 30 430B mouse arrays $21,000 $350
Arabidopsis Arrays
900385 GeneChip® Arabidopsis ATH1 Genome Array contains 5 arrays $1,500 $300
900386 GeneChip® Arabidopsis ATH1 Genome Array contains 30 arrays $9,000 $300
Bovine Arrays
900561 GeneChip® Bovine Genome Array contains 2 arrays $550 $275
900562 GeneChip® Bovine Genome Array contains 6 arrays $1,650 $275
900563 GeneChip® Bovine Genome Array contains 30 arrays $8,250 $275
Canine Arrays
900725 GeneChip® Canine Genome 2.0 Array contains 2 arrays $800 $400
900726 GeneChip® Canine Genome 2.0 Array contains 6 arrays $2,400 $400
900727 GeneChip® Canine Genome 2.0 Array contains 30 arrays $12,000 $400
900489 GeneChip® Canine Genome Array contains 5 arrays $1,375 $275
900490 GeneChip® Canine Genome Array contains 30 arrays $8,250 $275
C. elegans Arrays
900383 GeneChip® C. elegans Genome Array contains 5 arrays $1,500 $300
900384 GeneChip® C. elegans Genome Array contains 30 arrays $9,000 $300
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
Chicken Arrays
Part Product Name Contents Per Array Total Price
900590 GeneChip® Chicken Genome Array contains 2 arrays $800 $400
900591 GeneChip® Chicken Genome Array contains 6 arrays $2,400 $400
900592 GeneChip® Chicken Genome Array contains 30 arrays $12,000 $400
Drosophila Arrays
900531 GeneChip® Drosophila Genome 2.0 Array contains 2 arrays $550 $275
900532 GeneChip® Drosophila Genome 2.0 Array contains 6 arrays $1,650 $275
900533 GeneChip® Drosophila Genome 2.0 Array contains 30 arrays $8,250 $275
900335 GeneChip® Drosophila Genome Array contains 5 arrays $1,500 $300
900336 GeneChip® Drosophila Genome Array contains 30 arrays $9,000 $300
E. coli Arrays
900550 GeneChip® E. coli Genome 2.0 Array contains 2 arrays $350 $175
900551 GeneChip® E. coli Genome 2.0 Array contains 6 arrays $1,050 $175
900552 GeneChip® E. coli Genome 2.0 Array contains 30 arrays $5,250 $175
900381 GeneChip® E. coli Antisense Genome Array contains 5 arrays $1,500 $300
900382 GeneChip® E. coli Antisense Genome Array contains 30 arrays $9,000 $300
Maize Arrays
900614 GeneChip® Maize Genome Array contains 2 arrays $550 $275
900615 GeneChip® Maize Genome Array contains 6 arrays $1,650 $275
900616 GeneChip® Maize Genome Array contains 30 arrays $8,250 $275
Medicago Arrays
900734 GeneChip® Medicago Genome Array contains 2 arrays $850 $425
900735 GeneChip® Medicago Genome Array contains 6 arrays $2,550 $425
900736 GeneChip® Medicago Genome Array contains 30 arrays $12,750 $425
P. aeruginosa Arrays
900339 GeneChip® P. aeruginosa Genome Array contains 5 arrays $1,500 $300
900340 GeneChip® P. aeruginosa Genome Array contains 30 arrays $9,000 $300
Plasmodium/Anopheles Arrays
900511 GeneChip® Plasmodium/Anopheles Genome Array contains 2 arrays $600 $300
900512 GeneChip® Plasmodium/Anopheles Genome Array contains 6 arrays $1,800 $300
Poplar Arrays
900728 GeneChip® Poplar Genome Array contains 2 arrays $850 $425
900729 GeneChip® Poplar Genome Array contains 6 arrays $2,550 $425
900730 GeneChip® Poplar Genome Array contains 30 arrays $12,750 $425
Porcine Arrays
900623 GeneChip® Porcine Genome Array contains 2 arrays $550 $275
900624 GeneChip® Porcine Genome Array contains 6 arrays $1,650 $275
900625 GeneChip® Porcine Genome Array contains 30 arrays $8,250 $275
Rhesus Macaque Arrays
900655 GeneChip® Rhesus Macaque Genome Array contains 2 arrays $850 $425
900656 GeneChip® Rhesus Macaque Genome Array contains 6 arrays $2,550 $425
900657 GeneChip® Rhesus Macaque Genome Array contains 30 arrays $12,750 $425
Rice Arrays
900599 GeneChip® Rice Genome Array contains 2 arrays $850 $425
900600 GeneChip® Rice Genome Array contains 6 arrays $2,550 $425
900601 GeneChip® Rice Genome Array contains 30 arrays $12,750 $425
Soy Arrays
900525 GeneChip® Soy Genome Array contains 2 arrays $850 $425
900526 GeneChip® Soy Genome Array contains 6 arrays $2,550 $425
Sugar Cane Arrays
900626 GeneChip® Sugar Cane Genome Array contains 2 arrays $350 $175
900627 GeneChip® Sugar Cane Genome Array contains 6 arrays $1,050 $175
900628 GeneChip® Sugar Cane Genome Array contains 30 arrays $5,250 $175
Test Arrays
900341 GeneChip® Test3 Array contains 5 arrays $500 $100
900342 GeneChip® Test3 Array contains 30 arrays $3,000 $100
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
Tomato Arrays
Part Product Name Contents Per Array Total Price
900737 GeneChip® Tomato Genome Array contains 2 arrays $350 $175
900738 GeneChip® Tomato Genome Array contains 6 arrays $1,050 $175
900739 GeneChip® Tomato Genome Array contains 30 arrays $5,250 $175
V. vinifera Arrays
900509 GeneChip® V. vinifera Genome Array contains 2 arrays $550 $275
900510 GeneChip® V. vinifera Genome Array contains 6 arrays $1,650 $275
Wheat Arrays
900558 GeneChip® Wheat Genome Array contains 2 arrays $850 $425
900559 GeneChip® Wheat Genome Array contains 6 arrays $2,550 $425
900560 GeneChip® Wheat Genome Array contains 30 arrays $12,750 $425
Xenopus Arrays
900491 GeneChip® Xenopus Genome Array contains 5 arrays $1,500 $300
900492 GeneChip® Xenopus Genome Array contains 30 arrays $9,000 $300
Yeast Arrays
900553 GeneChip® Yeast Genome 2.0 Array contains 2 arrays $350 $175
900554 GeneChip® Yeast Genome 2.0 Array contains 6 arrays $1,050 $175
900555 GeneChip® Yeast Genome 2.0 Array contains 30 arrays $5,250 $175
900256 GeneChip® Yeast Genome S98 Array contains 5 arrays $1,500 $300
900285 GeneChip® Yeast Genome S98 Array contains 30 arrays $9,000 $300
Zebrafish Arrays
900487 GeneChip® Zebrafish Genome Array contains 5 arrays $1,500 $300
900488 GeneChip® Zebrafish Genome Array contains 30 arrays $9,000 $300
Made-to-Order: Select Custom Expression Arrays
900513 GeneChip® B.subtilis Genome Array contains 6 arrays $1,800 $300
900514 GeneChip® S.aureus Genome Array contains 6 arrays $1,650 $275
900515 GeneChip® Barley Genome Array contains 6 arrays $1,800 $300
900516 GeneChip® Human X3P Array contains 6 arrays $2,550 $425
Made-to-Order Array Program
Part Product Name Number of Arrays Per Array Price
510429 GeneChip® Arabidopsis Genome Array (previous generation) 40 +/- 5 arrays $300
510051 GeneChip® E. coli Genome Array (Sense) 40 +/- 5 arrays $300
510332 GeneChip® Human Cancer G110 Array 90 +/- 5 arrays $300
510137 GeneChip® HuGeneFL Array 40 +/- 5 arrays $375
510559 GeneChip® Human Genome U95Av2 Array 40 +/- 5 arrays $375
510462 GeneChip® Human Genome U95B Array 40 +/- 5 arrays $375
510463 GeneChip® Human Genome U95C Array 40 +/- 5 arrays $375
510464 GeneChip® Human Genome U95D Array 40 +/- 5 arrays $375
510465 GeneChip® Human Genome U95E Array 40 +/- 5 arrays $375
510243 GeneChip® Mu11KsubA Genome Array 40 +/- 5 arrays $375
510244 GeneChip® Mu11KsubB Genome Array 40 +/- 5 arrays $375
510318 GeneChip® Tag 3 Probe Array 90 +/- 5 arrays $300
510424 GeneChip® Rat Neurobiology U34 Array 160 +/- 5 arrays $250
510330 GeneChip® Rat Toxicology U34 Array 160 +/- 5 arrays $250
510338 GeneChip® Rat Genome U34A Array 40 +/- 5 arrays $350
510339 GeneChip® Rat Genome U34B Array 40 +/- 5 arrays $350
510340 GeneChip® Rat Genome U34C Array 40 +/- 5 arrays $350
510568 GeneChip® Murine Genome U74Av2 Array 40 +/- 5 arrays $375
510570 GeneChip® Murine Genome U74Bv2 Array 40 +/- 5 arrays $375
510571 GeneChip® Murine Genome U74Cv2 Array 40 +/- 5 arrays $375
GeneChip® Custom Expressi on™ Array Design 100-2187
Part Product Name Number of Arrays Total Price
000356 CustomExpress Design Fee for 90 array order 90 +/- 5 arrays $10,000
000357 CustomExpress Design Fee for 180 array order 180 +/- 10 arrays $7,500
000358 CustomExpress Design Fee for 360 array order 360 +/- 15 arrays $5,000
000359 CustomExpress Design Fee for 540 or greater array order 540 +/- 20 arrays $0
000390 CustomExpress Array - 11um features each $150
000455 Custom Tiling Array - 11um features each $125
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
GeneChip® Custom Expressi on™ Array Design 100-3660
Part Product Name Number of Arrays Total Price
000321 CustomExpress Design Fee for 90 array order 90 +/- 5 arrays $20,000
000322 CustomExpress Design Fee for 180 array order 180 +/- 10 arrays $15,000
000323 CustomExpress Design Fee for 360 array order 360 +/- 15 arrays $10,000
000324 CustomExpress Design Fee for 540 or greater array order 540 +/- 20 arrays $0
000391 CustomExpress Array - 11um features each $230
000454 Custom Tiling Array - 11um features each $200
GeneChip® Custom Expressi on™ Array Design 49-5241
Part Product Name Number of Arrays Total Price
000372 CustomExpress Design Fee for 40 array order 40 +/- 5 arrays $40,000
000373 CustomExpress Design Fee for 80 array order 80 +/- 10 arrays $30,000
000374 CustomExpress Design Fee for 160 array order 160 +/- 15 arrays $20,000
000375 CustomExpress Design Fee for 240 or greater array order 240 +/- 20 arrays $10,000
000395 CustomExpress Array - 11um features each $345
000453 Custom Tiling Array - 11um features each $300
GeneChip® Custom Expressi on™ Array Design 49-7875
Part Product Name Number of Arrays Total Price
000364 CustomExpress Design Fee for 40 array order 40 +/- 5 arrays $50,000
000365 CustomExpress Design Fee for 80 array order 80 +/- 10 arrays $40,000
000366 CustomExpress Design Fee for 160 array order 160 +/- 15 arrays $30,000
000367 CustomExpress Design Fee for 240 or greater array order 240 +/- 20 arrays $20,000
000396 CustomExpress Array - 11um features each $375
000452 Custom Tiling Array - 11um features each $325
GeneChip® Custom Expressi on™ Array Design 400
Part Product Name Number of Arrays Total Price
000407 CustomExpress Design Fee for 380 array order 380 +/- 5 arrays $110,000
000408 CustomExpress Design Fee for 760 array order 760 +/- 10 arrays $105,000
000409 CustomExpress Design Fee for 1520 array order 1520 +/- 15 arrays $95,000
000410 CustomExpress Design Fee for 2280 or greater array order 2280 +/- 20 arrays $85,000
000393 CustomExpress Array - 11um features each $150
000451 Custom Tiling Array - 11um features each $125
GeneChip® Custom Expressi on™ Array Design 169
Part Product Name Number of Arrays Total Price
000415 CustomExpress Design Fee for 155 array order 155 +/- 5 arrays $120,000
000416 CustomExpress Design Fee for 310 array order 310 +/- 10 arrays $115,000
000417 CustomExpress Design Fee for 620 array order 620 +/- 15 arrays $100,000
000418 CustomExpress Design Fee for 930 or greater array order 930 +/- 20 arrays $90,000
000392 CustomExpress Array - 11um features each $175
000450 Custom Tiling Array - 11um features each $150
GeneChip® Custom Expressi on™ Array Design 100
Part Product Name Number of Arrays Total Price
000411 CustomExpress Design Fee for 90 array order 90 +/- 5 arrays $130,000
000412 CustomExpress Design Fee for 180 array order 180 +/- 10 arrays $120,000
000413 CustomExpress Design Fee for 360 array order 360 +/- 15 arrays $105,000
000414 CustomExpress Design Fee for 540 or greater array order 540 +/- 20 arrays $90,000
000397 CustomExpress Array - 11um features each $275
000449 Custom Tiling Array - 11um features each $225
GeneChip® Custom Expressi on™ Array Design 64
Part Product Name Number of Arrays Total Price
000403 CustomExpress Design Fee for 55 array order 55 +/- 5 arrays $140,000
000404 CustomExpress Design Fee for 110 array order 110 +/- 10 arrays $125,000
000405 CustomExpress Design Fee for 220 array order 220 +/- 15 arrays $110,000
000406 CustomExpress Design Fee for 330 or greater array order 330 +/- 20 arrays $95,000
000389 CustomExpress Array - 11um features each $400
000448 Custom Tiling Array - 11um features each $350
GeneChip® Custom Expressi on™ Array Design 49
Part Product Name Number of Arrays Total Price
000399 CustomExpress Design Fee for 40 array order 40 +/- 5 arrays $150,000
000400 CustomExpress Design Fee for 80 array order 80 +/- 10 arrays $135,000
000401 CustomExpress Design Fee for 160 array order 160 +/- 15 arrays $115,000
000402 CustomExpress Design Fee for 240 or greater array order 240 +/- 20 arrays $95,000
000394 CustomExpress Array - 11um features each $425
000447 Custom Tiling Array - 11um features each $375
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
NimbleExpress Arrays
511298 NimbleExpress Array each $650
000469 NimbleExpress Design Fee $2,500
Expression Anal ysis Reagents
Part Product Name Contents Total Price
900542 GeneChip® DNA Labeling Reagent, 7.5 mM sufficient for 30 reactions $300
900585 GeneChip® Blood RNA Concentration Kit sufficient for 30 reactions $120
900586 GeneChip® Globin-Reduction RNA Controls sufficient for 12 reactions $120
900433 GeneChip® Eukaryotic Poly-A RNA Control Kit sufficient for approx. 100 reactions $300
900371 GeneChip® Sample Cleanup Module sufficient for 30 reactions $225
900375 GeneChip® T7-Oligo(dT) Promoter Primer Kit sufficient for 150 reactions $975
900301 Control Oligo B2, 3nM (also included in 900454 and 900457) sufficient for 30 reactions $75
900449 IVT Labeling Kit sufficient for 30 reactions $1,440
900547 IVT cRNA Cleanup Kit sufficient for 30 reactions $120
900431 One-Cycle cDNA Synthesis Kit sufficient for 30 reactions $1,650
900432 Two-Cycle cDNA Synthesis Kit sufficient for 30 reactions $2,400
900686 GeneChip® HT One-Cycle Target Labeling and Control Kit sufficient for 96 reactions $10,120
900687 GeneChip® HT One-Cycle cDNA Synthesis Kit sufficient for 96 reactions $5,280
900688 GeneChip® HT IVT Labeling Kit sufficient for 96 reactions $4,610
900493 GeneChip® Expression 3' Amplification One-Cycle Target Labeling and
Control Reagents
$3,300
900494 GeneChip® Expression 3' Amplification Two-Cycle Target Labeling and
Control Reagents
$4,145
900454 GeneChip® Expression 3' Amplification Reagents - Hybridization
Controls
sufficient for 30 reactions $300
900457 GeneChip® Expression 3' Amplification Reagents - Hybridization
Controls
sufficient for 150 reactions $1,350
900720 GeneChip® Hybridization Wash and Stain Kit sufficient for 30 reactions $625
900721 Stand-alone Wash Buffer A $105
900722 Stand-alone Wash Buffer B $75
Expression Anal ysis WT Reagents
900652 WT Target Labeling and Control Reagents sufficient for 30 reactions $3,900
900673 WT cDNA Synthesis and Amplification Kit sufficient for 30 reactions $1,650
900671 WT Terminal Labeling Kit sufficient for 30 reactions $1,950
900812 WT Double-Stranded DNA Terminal Labeling Kit sufficient for 30 reactions $950
900813 WT Double-Stranded cDNA Synthesis Kit sufficient for 30 reactions $1,900
900672 WT cDNA Synthesis and Amplification Kit sufficient for 10 reactions $580
900670 WT Terminal Labeling Kit sufficient for 10 reactions $685
900811 WT Amplified Double-Stranded cDNA Synthesis Kit sufficient for 10 reactions $2,100
Expression Anal ysis Accessories
900223 Expression Analysis Technical Manual $65
DNA Analysis
GeneChip® Human Mapping 10 K System
Part Product Name Contents Per Array Total Price
900540 GeneChip® Human Mapping 10K 2.0 Xba Array contains 30 arrays $5,550 $185
900446 GeneChip® Human Mapping 10K Xba 131 Array contains 30 arrays $10,500 $350
900441 GeneChip® Human Mapping 10K 2.0 Xba Assay Kit sufficient for 30 reactions $1,500
900534 Affymetrix PCR Primer 001 sufficient for 100 reactions $100
900548 GeneChip® Human Mapping 10K 2.0 Training Kit $2,900
000386 GeneChip® Human Mapping 10K Training $2,500
GeneChip® Human Mapping 100K System
900518 GeneChip® Human Mapping 50K Xba Array contains 30 arrays $6,300 $210
900523 GeneChip® Human Mapping 50K Hind Array contains 30 arrays $6,300 $210
900520 GeneChip® Human Mapping 50K Xba Assay Kit sufficient for 30 reactions $1,500
900521 GeneChip® Human Mapping 50K Hind Assay Kit sufficient for 30 reactions $1,500
900549 GeneChip® Human Mapping 50K Xba Training Kit $3,800
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
GeneChip® Human Mappi ng 500K System
Part Product Name Contents Per Array Total Price
900768 GeneChip® Human Mapping 250K Nsp Array contains 30 arrays $14,100 $470
900770 GeneChip® Human Mapping 250K Sty Array contains 30 arrays $14,100 $470
520330 GeneChip® Human Mapping 250K Nsp Array min. 200 array order, each $470
520331 GeneChip® Human Mapping 250K Sty Array min. 200 array order, each $470
900765 GeneChip® Human Mapping 250K Sty Assay Kit sufficient for 30 reactions $1,650
900766 GeneChip® Human Mapping 250K Nsp Assay Kit sufficient for 30 reactions $1,650
900753 GeneChip® Human Mapping 250K Nsp Assay Kit sufficient for 100 reactions $5,500
900754 GeneChip® Human Mapping 250K Sty Assay Kit sufficient for 100 reactions $5,500
900786 GeneChip® Mapping 500K Nsp Training Kit $4,800
GeneChip® CustomSeq™ Resequencing Arrays
Part Product Name Contents Total Price
000527 CustomSeq Resequencing 50kb Array Design Fee for 1 wafer order 155 arrays $10,000
000528 CustomSeq Resequencing 50kb Array Design Fee for 2 wafer order 310 arrays $7,500
000529 CustomSeq Resequencing 50kb Array Design Fee for 4 wafer order 620 arrays $4,500
000530 CustomSeq Resequencing 50kb Array Design Fee for 6 wafer order 930 arrays $0
511445 CustomSeq Resequencing 50KB Array (1st Lot) each $150
000505 CustomSeq Resequencing 100kb Array Design Fee for 1 wafer order 90 arrays $15,000
000506 CustomSeq Resequencing 100kb Array Design Fee for 2 wafers order 180 arrays $10,000
000507 CustomSeq Resequencing 100kb Array Design Fee for 4 wafers order 270 arrays $5,000
000508 CustomSeq Resequencing 100kb Array Design Fee for 6 wafers order 540 arrays $0
511336 CustomSeq Resequencing 100KB Array (1st Lot) each $225
000509 CustomSeq Resequencing 300kb Array Design Fee for 1 wafer order 45 arrays $20,000
000510 CustomSeq Resequencing 300kb Array Design Fee for 2 wafers order 90 arrays $15,000
000511 CustomSeq Resequencing 300kb Array Design Fee for 4 wafers order 180 arrays $10,000
000512 CustomSeq Resequencing 300kb Array Design Fee for 6 wafers order 270 arrays $0
511337 CustomSeq Resequencing 300KB Array (1st Lot) each $325
900447 GeneChip® Resequencing Reagent Kit sufficient for 30 reactions $850
520016 GeneChip® SARS Resequencing Array each $300
511300 GeneChip® Mitochondrial Resequencing 2.0 Array each $150
Instrument and Software Systems
GeneChip® Instrument Systems
High Throughput Scanner
00-0172 GeneChip® HT Scanner $325,000
Complete Instrument System
Part Product Name Contents Total Price
00-0185 GCS 3000 MegAllele System, NA $279,000
00-0212 GeneChip® Scanner 3000 7G System, NA $199,000
00-0217 GCS 3000 7G w/Workstation and AutoLoader, NA $219,000
00-0162 GeneChip® Array Station, NA $250,000
Scanner System wi th Workstation
00-0211 GeneChip® Scanner 3000 7G w/Workstation $146,000
00-0214 GA2500 to GCS3000 7G Upgrade $120,000
00-0215 GCS 3000 7G w/Workstation and AutoLoader $165,000
GeneChip® System Components
00-0183 GCS 3000 MegAllele Genotyping 7G Upgrade $75,000
00-0205 GCS 3000 7G Field Upgrade $10,000
00-0206 GCS 3000 7G MegAllele Genotyping 4C Upgrade $65,000
00-0210 GeneChip® Scanner 3000 7G $140,000
00-0223 GCS 3000 MegAllele Genotyping Upgrade for S/N ?547 $65,000
QC Toolbox
00-0225 QC Toolbox Software Kit, Version 2 $2,500
Node System
00-0104 GCS 3000 Node U.S./Canada $69,000
Fluidics Station 450
00-0079 Fluidics Station 450 $55,500
00-0081 Fluidics Station 450 Upgrade U.S./Canada $20,000
Hybridization Oven 640
800138 Hybridization Oven 640 (110V) $7,500
800139 Hybridization Oven 640 (220V) $7,500
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
Probe Array Cartri dge Carriers
Part Product Name Contents Total Price
90-0356 GeneChip® Probe Array Cartridge Carriers Red (qty 2) $69
90-0357 GeneChip® Probe Array Cartridge Carriers Green (qty 2) $69
90-0358 GeneChip® Probe Array Cartridge Carriers Purple (qty 2) $69
90-0359 GeneChip® Probe Array Cartridge Carriers White (qty 2) $69
AutoLoader
Part Product Name Total Price
00-0179 2D Handheld Barcode Reader $975
00-0093 External Barcode Reader Holder $275
00-0094 AutoLoader Carousel $975
00-0111 Uninterruptible Power Supply, NA $2,900
00-0129 AutoLoader Upgr w/EBR-GCS 3000 S/N 502 $25,000
00-0090 AutoLoader Upgrade with EBR & Holder $25,000
Affymetrix® Software Solutions
Software Solutions
Acquisition and Analysis
Part Product Name Description Total Price
690025 Microarray Suite-Software License (5.1) 1 seat, perpetual license $4,200
690037 Full Application Package annual licenses $4,000
690038 Genotyping Application Package annual licenses $2,000
690039 Expression Application Package annual licenses $2,200
00-0126 Full Application Package with Computer annual licenses $8,000
00-0127 Genotyping Application Package with Computer annual licenses $6,000
00-0128 Expression Application Package with Computer annual licenses $6,200
Management Storage Soluti ons
690035 GeneChip® Operating Software Server Basic Package annual licenses $45,000
800143 LIMS Server Hardware Standard $32,000
900328 MicroDB™ Software 1 seat, perpetual license $5,600
Data Mining Soluti ons
690043 Data Mining Tool 3.1 (GCOS) annual license $2,200
690045 Data Mining Tool 3.1 (GCOS) 1 seat, perpetual license $5,600
690004 Data Mining Tool 3.0 (MAS) 1 seat, perpetual license $5,600
External Developer Program
Part Product Name Description Total Price
690050 Commercial Software Developer's Kit geographic license annual subscription $10,000
690033 GCOS Development Server Software geographic license annual subscription $9,800
690034 GCOS Development Client Software $1,000
000349 Software Consulting Services per hour $300
000350 Software Training per hour $300
Software Manual s
700293 Microarray Suite User's Guide $65
700338 LIMS Installation and Administration Guide $65
700339 LIMS User's Guide $65
700233 Data Mining Tool User's Guide $65
700480 MicroDB User's Guide $50
Software Combi nation Packages
Software Combi nation Packages
Desktop Packages
00-0180 Dual Processor Instrument Control Workstation with GCOS $6,500
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
PCR core facility
Contacts:
Mark Geraci, MD
Core Director
[email protected]
303-315-0398
Bryan Haugen, MD
Core Co-Director
PCR Director
[email protected]
303-724-3921
Umarani Pugazhenthi
Core Manager
Phone: 303-724 -3965
[email protected]
How to use our core facility……
1. Send the mRNA sequence for the target of interest, marking the exon borders
(if known) to [email protected] via email.
2. We will design the primers/probe and send you the optimal set for real time PCR. You then blast the
probe sequence for specificity.
4. We will place the order and notify you by email when it is received (approximately 7~10 days from
ABI). Pl will provide the speed type for charging.
5. You will need to provide one of the following in order to optimize the primers/probe and to set up a
standard curve for your assay:
a) Quantitated riboprobe (absolute standard)
b) RNA from source with known expression of gene (relative standard)
c) DNA (absolute PCR standard)
6. When your test samples (RNA in water ~ 1 ug/ul) are ready, contact Uma @ 303-724 3965 to set up a
date and time for sample drop off.
7. The results of your experiment include the following: Plots showing the amplification of target and
normalizing genes, the standard curve and quantities of target genes normalized to control genes.
8. Please send a copy of your publications for our record.
Pricing :
Effective 07-01-2008
Cancer Center Non member
Member Pricing Pricing
RNA Duplicate $13 $17
DNA Duplicate $ 9 $13
rRNA Control $17 $23
Standard Curve $110 $174
Optimization $123 $ 205
Plate Run $ 91 $170
RNA Extraction-5 samples $157 $284
RNA Extraction-10 samples $188 $341
RNA Extraction-15 samples $218 $396
RNA Extraction-20 samples $248 $ 452
Gene Expression, Microarray & PCR (UCCC)
From: Geraci, Mark
Sent: Monday, November 02, 2009 11:02 AM
a) How is the quality of your measurements evaluated – quality control?
Standard “best Practices for Microarray” criteria
b) What is the turn-a-round time for the service you provide?
About one week, depending on the project size
c) Who documents the data provided and signs off on the data?
Core Manager, Dr. Bifeng Gao
d) Have you had experience providing data for industry?
Yes, extensive
e) Do you have a standard operating procedure manual?
Yes
f) How will you track billing and financial aspects of your core?
Cancer Center support
Gene-Targeting/Viral Vector Core
Contact:
Mark Dell'Acqua, PhD
Core Director
[email protected]
http://www.uchsc.edu/neuroscience/Program/cores.htm
This core has two components:
1. Generation of Gene-Targeted/Transgenic Mouse Constructs (Mark Dell'Acqua, Core B
Director; Brain Parr, Coordinator; Wallace Chick; Research Associate). Neuroscience
Program members interested in generating transgenic, knock-out and knock-in mice
should contact Mark Dell'Acqua. Due to the highly specialized nature of the work only a
small number of gene-targeted/transgenic mouse projects will be under taken at any given
time. Selection of these projects will be based on proposals from investigators that will be
evaluated by the Core B advisory panel (Wallace Chick, Brian Parr, Trevor Williams,
Mark Dell'Acqua, and Diego Restrepo). Please contact Core B director Mark Dell'Acqua
for more details.
2. Generation of Viral Vectors for Infection of Neurons/Glia (Jerry Schaack, Coordinator).
This aspect of the core is open for business. Individuals should contact Jerry (Jerry
Schaack).
This core is not open to the general university community at this time (it is open only
Neuroscience Program members on a case-by-case basis). This core provides very specialized,
low throughput, time intensive services on a project-by-project basis so the questions in the
questionnaire are not really applicable. Nonetheless, here is the link to our website:
Grants & Contracts
Contacts:
General Information please call 303-724-0900
Pamela J. Jones Ph.D., Director
303-724-0096
Contracts/Policy
Christine Ahearn, JD
Assistant Director
303-724-0245
[email protected]
PreAward/IS
Jennifer Silverthorne, MPA
Assistant Director
303-724-0093
[email protected]
PostAward/Accounting
Pam Vincent, BS
Assistant Director
303-724-0019
[email protected]
Website:http://www.uchsc.edu/ogc/index.php
About Grants and Contracts
Mission
The mission of Grants and Contracts (G&C) is to provide service to principal investigators and
administrators, for the purpose of obtaining and administering extramural funds in compliance
with University and sponsor guidelines.
Services
Grants and Contracts assists University of Colorado Denver faculty in their efforts to secure
external support for their instructional, research, public service, and scholarly activities. This
includes:
a. budget development;
b. grant application and contract proposal review;
c. contract proposal development, negotiation, and acceptance;
d. subrecipient agreement development, negotiation, and acceptance; and
e. providing advice on sponsor and University requirements.
Grants and Contracts is also responsible after award for compliance with non-technical sponsor
requirements which include:
a. financial reporting and standard invoicing (e.g. does not include non-governmental
clinical trial invoicing which is done by academic departments);
b. providing advice on sponsor and University requirements;
c. acting as a liaison with sponsor contract/financial representatives;
d. managing cash; and
e. acting as a liaison for audits of sponsored activity.
OGC also has responsibility for various systems required by the federal government, for
providing management reports, and for keeping abreast of major grant/contract regulations
changes.
No fees
Can charge for these fees
1. Invoicing contracts
2. Contract Negotiations
3. Training
4. Info Ed
5. All business operations for research administration
6. Research Services
Grants & Contracts
From: J ones, Pamela J
Sent: Friday, November 06, 2009 2:48 PM
a) How is the quality of your measurements evaluated – quality control?
OGC has operating standards that are monitored for all aspects of the three core areas.
These operating standards incorporate general operations standards, General Accounting
Standards Board requirements, National Research Compliance Standards and internal
control/ procedural standards.
b) What is the turn-a-round time for the service you provide?
Turn-Around times are established by type of service, institutional requirements or
business standards
General Operational Service Standards for OGC include but are not limited to:
Proposal Review – paper – 5 days electronic – 12 days
Contract Negotiation – primary and subs – depending upon complexity – 6-8 weeks is the
average
Project Set-Up – average is 5-10 business days after receipt of award unless there are
problems with the award
On-time FSR submissions
c) Who documents the data provided and signs off on the data?
Director, Assistant Directors and Managers
d) Have you had experience providing data for industry?
Yes – to the compliance and sponsor industries
e) Do you have a standard operating procedure manual?
Yes – see website
f) How will you track billing and financial aspects of your core?
OGC is funded via Fund 10 and F&A from sponsored projects – we do not bill for our
services.
High-Throughput Genome Sequencer
Contact:
David Pollock, PhD
Department of Biochemistry & Molecular Genetics
Mail Stop 8101
Research Complex 1 South
12801 17th Ave., Room #10111
PO Box 6508
Aurora, CO 80045
[email protected]
http://www.evolutionarygenomics.com/CCG/CCG.html
The Lab:
Protein sequence, structure, and functional evolution; Evolutionary genomics; Adaptive co
evolution and ancestral reconstruction; Evolution of mitochondrial genomes; Evolutionary
theory; Testing evolutionary predictions through mutagenesis and directed evolution
Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories by
A. P. Jason de Koning, Wanjun Gu and David D. Pollock, Molecular Biology and Evolution
(available online September 2009). Complex models, way fast. Check it out.
New:
We have developed a code package called PLEX (Phylogenetics, Likelihood, Evolution, and
compleXity), written by Jason de Koning, Wanjun Gu, and David Pollock. The approach is
described in the above paper. Code is under continued development, with versions available
upon request.
Evidence for an ancient adaptive episode of convergent molecular evolution, Todd A. Castoe, A.
P. Jason de Koning, Hyun-Min Kim, Wanjun Gua, Brice P. Noonan, Gavin Naylor, Zhi J. Jiang,
Christopher L. Parkinson and David D. Pollock, PNAS, 2009
See PNAS commentary by Scott Edwards, "Natural Selection and Phylogenetic Analysis"
(May/June 2009).
Convergence/Divergence code from Castoe et al 2009 for use with codeml
See addendum/commentary by Castoe, de Koning, and Pollock (preprint available upon request)
We're looking for postdoc applicants for computational biology fellowships working on protein
evolution (Pollock) or transcription factor binging site (TFBS) evolution (Pollock and Kechris).
Please contact David Pollock for details. This is an ongoing search for excellent candidates.
List of Services & Fees:
In house pricing for a full plate of FLX or Titanium sequencing costs $10,000. Please contact us
for additional services and pricing.
High-Throughput Sequencing Core
From: Pollock, David
Sent: Monday, October 12, 2009 9:13 AM
Information for Dick Traystman r.e. High-Throughput Sequencing Core (HTSC run by
the Consortium for Comparative Genomics within the UCCC DNA Sequencing Core)
a) How is the quality of your measurements evaluated – quality control?
All sequencing runs include an internal set of quality control sequences which are
evaluated in each run. Also, the sequencing output (number, length, and sequence
quality scores) of the empirical data provide a measure of the quality of each
sequencing run
b) What is the turn-a-round time for the service you provide?
The turn-a-round time for a sample submitted according to the requirements
outlined in the HTSC core guidelines and sequenced on a full plate of Titanium or
FLX, with no major problems arising, is 2-3 weeks. If a shotgun library is needed,
an additional week should be added to the turn-a-round time. If sequencing is
requested on a smaller scale, i.e. 1/8 plate, ¼ plate or ½ plate, the timing will
depend not only on the sample submitted but also the rest of the samples that are
needed to fill the plate. Any delays in filling the plate translate to delays in
sequencing. We plan according to the samples that are being submitted and delays
due to unfilled plates should be low.
c) Who documents the data provided and signs off on the data?
The HTSC saves all sequencing data from the 454 sequencing process. The data
files are labeled, and sent to HTSC users. An internal record is kept of each
sample sequenced, the date the data is sent to the customer, invoicing and
payment details, and the name and storage location of the data file.
d) Have you had experience providing data for industry?
Yes, we have provided sequencing services to industrial organizations.
e) Do you have a standard operating procedure manual?
We follow the Roche GS FLX & Roche GS FLX Titanium Sequencing Method
Manuals. If library creation is needed, follow the GS FLX Shotgun DNA Library
Preparation Method Manual or the GS FLX Titanium 20kb and 8kb Span Paired
End Library Preparation Method Manual.
f) How will you track billing and financial aspects of your core?
We have a dedicated accountant from the University of Colorado Cancer Center
who tracks the spending, billing and revenue for the HTSC. We have contact with
him, and are updated regularly on the financial status of our facility. In addition to
this, we keep our own internal records of all financially related aspects of the
HTSC.
List of Services & Fees:
In house pricing for a full plate of FLX or Titanium sequencing costs $10,000.
Please contact us for additional services and pricing.
Website:http://www.evolutionarygenomics.com/CCG/CCG.html
HLA (Histocompatibility) Testing and
Umbilical Cord Blood Bank
ClinImmune Labs and the University of Colorado Cord Blood Bank
ClinImmune Labs, located i n t he B ioscience P ark C enter ne xt t o t he U niversity o f C olorado
Anschutz M edical C ampus i n A urora, C olorado, i s a hi ghly efficient a cademic bus iness t hat
integrates th e h ighest quality la boratory s ervices a nd p roducts w ith its s cholarly mis sion to
contribute t o t he s cience o f an d education ab out s tem cel l t herapy. Our co mpany v iews a v ery
important c omponent of i ts bus iness a s c onsultative. O ur s taff p rovides e ducation and t echnical
advice t o t he r esearch a nd m edical c ommunity on s tem c ell processing a nd s torage,
histocompatibility analysis and sequencing issues.
As an acad emic-based bi otechnology c ompany, ClinImmune Labs is c ommitted to p roviding th e
highest quality s ervice t o our clinical customers bot h i n Denver and t hroughout t he world, t o our
research faculty at the University of Colorado Anschutz and Boulder campuses, stem cell biologists
throughout the U.S, and to the biotechnology companies that reside in the Rocky Mountains.
ClinImmune Labs is accredited by the American Society for Histocompatibility and Immunogenetics
(ASHI), th e College o f American P athologists ( CAP), th e Clinical Laboratory Improvement Act
(CLIA), t he Foundation f or Accreditation of Cellular Therapy ( FACT), and t he AABB ( American
Associations of B lood B anks). A num ber of t he s taff a re bo ard-certified c onsultants in
histocompatibility, diagnostic immunology, allergy and asthma, and pulmonary medicine.
A. Histocompatibility and Immunogenetics Laboratory
Contacts for information or price quotes:
HLA Testing is available for:
• Epitope analysis as part of population studies
• Genetic HLA Disease Association
• Immunotherapy, including vaccine
development
• HPC Transplant
• Pharmacogenetics
Michael Aubrey, MS, CHS
303-724-1313
[email protected]
Linda Cagle, CLDir, CHS
303-724-1315
[email protected]
Brian M. Freed, PhD
Executive Director
[email protected]
Clinically Approved Assays:
• HLA-A, B, Cw, DRB, DQ, DPB1 loci
? Low to high resolution Class I and Class II testing for HLA-A, B, Cw, DRB1,
DRB3/4/5,
DQB1, DPB1
? Low resolution testing for DQA1
? Serological and HLA-A,B testing
• Cylex Immune Function Test, IMMUKNOW®
• HLA Antibody Detection
? Panel Reactive Antibody (PRA)
? Luminex HLA Class I, Class II, and MICA Antibody screen
? Luminex PRA, including HLA Specificity Analysis
? Luminex single antigen beads for allele level Class I, Class II, and MICA antibodies
? Titration/Quantitation studies for transplant immunotherapy protocols
? Flow cross matching for transplant compatibility
? Platelet support panels to assess allo-reactive HLA antibodies and HLA-A,B typing
for selection of matched platelets
Services Provided:
• Initial consultations provided for test selection, cost effectiveness, sample and turn-around
time requirements
• Customized requisitions and clear, concise reports; electronic data transfer
• Additional test interpretation consults upon request
• Analysis of HLA allele frequency
B. University of Colorado Cord Blood Bank
Contact for information or price quotes:
Sabine Stockinger
303-724-1247
[email protected]
The University of Colorado Cord Blood Bank (UCCBB), a major component of ClinImmune Labs,
has a t en year hi story of collecting, processing, banking and distributing umbilical cord bl ood f or
human t ransplantation. UCCBB has c onsented ove r 10,700 w omen a nd ba nked ove r 6,700 c ord
blood units, of which over 500 have been transplanted at 95 different transplant centers in the United
States and abroad. UCCBB is a major provider of Hispanic cord blood units to patients in the United
States, Mexico, Central and South America. UCCBB is a member of t he National Marrow Donor
Program and i s accr edited b y AABB. HRSA awarded UCCBB one o f s ix c ord bl ood c ollection
contracts i n 2006. UCCBB also pr ovides c ord b lood t o s tem c ell i nvestigators i n Michigan, New
York, Tennessee, Washington and Colorado.
Histocompatibility and Umbilical Cord Blood Bank: ClinImmune Labs
and the University of Colorado Cord Blood Bank
Executive Director: Brian M. Freed, Ph.D.
a)
ClinImmune Labs i s a ccredited by t he American Society f or Histocompatibility a nd I mmunogenetics
(ASHI), the College of American Pathologists (CAP), the Clinical Laboratory Improvement Act (CLIA),
the AABB ( American Associations of Blood Banks), and the Foundation for Accreditation of Cellular
Therapy (FACT). All of t hese a ccreditation or ganizations ha ve s trict g uidelines that g overn qu ality
control. ClinImmune Labs requires that each of its programs undergo both internal and external audits on
a regular schedule, including the validation that all reagents and equipment meet strict IQ, OQ and PQ
requirements prior to their use. Testing methodologies and staff are proficiency tested under CAP, SCT,
UCLA an d ASHI. All l aboratory st aff retains cu rrent co mpetency an d cer tifications with o n-going
continuing education.
How is the quality of your measurements evaluated – quality control:
b)
ClinImmune Labs prides itself on c lient satisfaction and meeting t he needs of University of Colorado
clients as well as clients from area wide hospitals, hospitals outside of Colorado, and private industry.
Our turn-a-round times range from 3 to 14 days, depending on the services requested, and are mutually
agreed upon with the clients in our service agreements. Flexible pricing exists for research projects that
are not urgent.
What is the turn-a-round time for the service you provide?
c)
As per our detailed SOPs and depending on the laboratory service required, our medical and laboratory
directors, laboratory supervisors and managers, and quality assurance staff review specific types of data
and at least two reviews are required for sign-off prior to reporting.
Who documents the data provided and signs off on the data?
d)
ClinImmune Labs has a n umber of r esearcher clients f rom i ndustry who r eceive l aboratory ser vices,
cord blood products and electronically transmitted data from us.
Have you had experience providing data for industry?
e)
ClinImmune maintains a detailed quality management pl an and SOP manuals t hat outline GLP, GTP,
and GMP under FDA /CLIA regulatory compliance.
Do you have a standard operating procedure manual?
f)
ClinImmune Labs has a billing staff that tracks the billing of all tests, customizes billing templates, and
develops electronic reports for clients as mutually agreed upon in the service agreement.
How will you track billing and financial aspects of your core?
Histology Core
Contact:
Roberto Gianani, MD
Histology Core Director
Diabetes & Endocrinology Research Center
at the Barbara Davis Center for Childhood Diabetes
303-724-6824
[email protected]
http://www.uchsc.edu/misc/diabetes/DERC/histology.htm
Histology Core
Routine histological services in tissue fixation, processing, sectioning, and staining with
histochemical dyes and immunochemical reagents. Provision of slide and tissue banks of
commonly used tissues or animal models e.g. developmental or NOD disease progression.
Epifluorescence microscopy for acquisition of images and performance of morphometric
analyses.
Confocal microscopy for use by investigators interested in high-resolution fluorescence
microscopy and live cell imaging requiring the use of FRAP and FRET analyses.
In-situ hybridization analyses that include all elements from acquisition and amplification of the
gene of interest, probe synthesis, optimization of hybridization conditions, and performance of
multigene analyses on a moderate scale.
Higher-level microscopy including access to instrumentation and services in Laser Capture
Microscopy, 2-photon confocal microscopy, spinning disk confocal microscopy, Total Internal
Reflectance microscopy, conventional, and immunoelectron microscopy.
Training of fellows and students in morphological and morphometric techniques and
consultation in specific areas including microdissection and single cell microinjection, low-level
computer programming.
Core Personnel
Roberto Gianani, MD (Director) is Assistant Professor, Department of Pathology. Dr. Gianani
is Investigator at the Barbara Davis Center for Childhood Diabetes, UCHSC.
Informatics Core University of Colorado Cancer Center
Contacts:
Jessica Bondy, MHA
Director
303-724-4353
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/informatics/index.aspx
Mission
To increase the efficiency of conducting clinical/ translational trials by insuring the accessibility,
integrity, and security of research databases.
The University of Colorado Cancer Center Informatics Core, located on the 6th Floor of
Building 500 on the Anschutz Medical Campus in Aurora, was established to work with
researchers and clinicians to design, implement and maintain information technology
applications that support the Cancer Center research enterprise.
• We build databases and integrate them with dynamic websites or client/server front ends
• We provide workstation support and network and server administration
We have developed applications in the areas of clinical trials registration, specimen tracking,
clinical trials pathology and prevention and control. In addition, we have developed databases
containing clinical data (prognostic clinical factors, therapies, toxicities, response to treatment
and outcomes) for the Lung SPORE and for breast cancer.
Informatics Core Services
Researchers who have informatics projects have a choice of funding part of an FTE or
purchasing services on an hourly basis. When the informatics project is substantial and planned,
funding part of an FTE is the preferred approach, since projects funded under FTEs will be given
higher priority. When the project is small or unanticipated, the hourly charge back is appropriate.
We offer members discounted hourly rates.
We offer the following services
1. Network administration / workstation support: web-, database-, file- and print server
administration, including backups, access, and security. Workstation configuration and
maintenance.
2. Website development: analysis and development of dynamic or static websites
3. Database design and development: analysis and development of table structures for
appropriate security and performance.
4. Data quality assurance: loading and querying databases to ensure timely and proper data
collection.
5. Report development: analysis and development of static or parameterized reports.
How to order services
To order services, you will need to consult with either the Core Director or Core Manager by
telephone or email. See the contact panel on the right for phone and email information.
Prices
The cost for core services is based time spent, either as part of an FTE or as an hourly fee. For an
estimate of the time your project is likely to require, contact the Core Manager (See the contact
panel on the right for phone and email information).
Service Member
Non-
Member
Application Development & Support $84 $97
Network Administration & Workstation Support:
Complete administration of file and print servers
(backups, access, security). Ensures that workstations
are configured for user's needs.
$67 $78
Prices valid July 1, 2008-June 30, 2009
Informatics Core (UCCC)
From: Bondy, J essica
Sent: Thursday, October 01, 2009 5:09 PM
a) How is the quality of your measurements evaluated – quality control?
N/A
b) What is the turn-a-round time for the service you provide?
N/A
c) Who documents the data provided and signs off on the data?
N/A
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
We write SOPs for the applications we develop.
We don’t really have an SOP for our own work.
f) How will you track billing and financial aspects of your core?
Much of our work is done on an FTE basis. Only about 7% of our budget
comes through our service center. This work is billed hourly. We use a time
tracking system that was developed by the CSPH’s DISC (Development
Informatics Service Center) for the CBC (Colorado Biostats Consortium).
Website (includes services):http://www.uccc.info/for-healthcare-
professional/cancer-center/cores/informatics/index.aspx
Fees:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/informatics/prices.aspx
Institutional Animal Care and Use Committee
(IACUC)
Contacts:
Mark Douse, PhD
303-724-1057
[email protected]
Website:http://www.uchsc.edu/animal/iacuc_index.htm
IACUC
The Institutional Animal Care and Use Committee (IACUC), mandated
by the Health Research Extension Act (HREA) of 1985 and the Animal
Welfare Act (AWA), is responsible for the oversight and evaluation of
the Institution's animal care and use program, procedures and facilities,
ensuring that they are consistent with the recommendations in the
Guide for the Care and Use of Laboratory Animals, Animal Welfare
Regulations and PHS Policy.
The IACUC is an Institutional level committee, the direct representative
of the Chancellor of the University of Colorado Denver and comprises
veterinarian, scientist and non-scientist members, as well as at least
one member who represents the general community interests in the
proper care and treatment of animals, and, is not affiliated in any way
with the Institution other than as a member of the Committee.
AAALAC Accreditation File Number:
00235 (re-approved 10/26/2006)
PHS Animal Assurance of Compliance
#A 3269-01 (expires 07/31/2011)
USDA License:
#84-R-0059 (expires 11/07/2010)
IACUC
From: Douse, Mark
Sent: Monday, November 02, 2009 4:35 PM
Questions:
a) How is the quality of your measurements evaluated – quality control?
Response: The UC Denver Institutional Animal Care and Use Committee
(IACUC) adheres to all federal laws, regulations, and guidelines established by
government and professional groups to protect research animals. The federal law
(Animal Welfare Act) is enforced by the USDA, who performs unannounced site
visits of our Animal Program once or twice a year. We are also voluntarily
accredited by the Association for the Assessment and Accreditation of Laboratory
Animal Care, International. This international oversight body provides an
additional review of our entire Animal Program and holds UC Denver to a higher
standard than is required by the rigorous governmental laws and regulations.
AAALAC performs a site visit of our Animal Program once every three years.
This site visit is very extensive and intensive and is performed by four
professionals over a four day time period. Finally, there are a number of
interested Investigators who do not hesitate in providing feedback on quality
control.
b) What is the turn-a-round time for the service you provide?
Response: The IACUC meets once per month for review of new protocols; the
average turnaround time for final IACUC approval is 40 days and includes
IACUC and Investigator response time. An IACUC sub-committee meets once
every two weeks to review amendments to an existing IACUC approved protocol;
the typical turnaround time is 2 to 3 weeks.
c) Who documents the data provided and signs off on the data?
Response: Director, IACUC Office; IACUC Co-Chairs; Vice Chancellor for
Research
d) Have you had experience providing data for industry?
Response: Yes
e) Do you have a standard operating procedure manual?
Response: Yes
f) How will you track billing and financial aspects of your core?
Response: We do not currently bill for our services. Per Diem and all other
charges are billed through the Office for Laboratory Animal Resources (OLAR).
Interdisciplinary Transcranial Magnetic Stimulation (TMS)
Director: Benzi Kluger, MD
Preferred contact: email
[email protected]
Services:
Review of proposals using TMS, assistance with preparation of IRB materials for TMS projects,
training in the use of TMS and stereotactically guided TMS, performance of TMS on human
subjects for research and therapeutic purposes.
Fees:
TMS conducted on human subjects will be $200/hour for internal users and $400/hour for
investigators outside of the University of Colorado. Other services and discounts for collection of
pilot data or junior investigators may be discussed with Dr. Kluger and the steering committee.
Interdisciplinary Trancranial Magnetic Stimulation
From: Kluger, Benzi M
Sent: Monday, November 09, 2009 1:49 PM
a) How is the quality of your measurements evaluated – quality control?
Transcranial magnetic stimulation (TMS) stimulates and modulates cortical activity. This is
most easily measured by examining motor response to motor cortex stimulation with EMG.
Motor thresholds and motor evoked potentials are routinely performed even when the focus
of TMS is a non-motor region to ensure adequate stimulation.
b) What is the turn-a-round time for the service you provide?
For studies or indications with IRB approvals TMS can be provided within a few weeks.
EMG data for motor studies can be provided within a week of TMS sessions.
c) Who documents the data provided and signs off on the data?
Dr. Benzi Kluger, Director of the Interdisciplinary TMS Laboratory, will review all
protocols prior to TMS, as well as data collection procedures with the PI of the study and
TMS technician. TMS technicians will provide and document data. In cases of inconsistent
data, Dr. Kluger will review the results and records of TMS sessions.
d) Have you had experience providing data for industry?
No, but we are willing to provide TMS services to industry including measures of cortical
excitability, Trancranial direct current stimulation (tDCS) and repetitive TMS treatments.
e) Do you have a standard operating procedure manual?
Yes, but only for depression treatments and current TMS studies. Operating procedures
will be written up on an as needed basis for other protocols.
f) How will you track billing and financial aspects of your core?
The TMS laboratory has its own cost center in the Department of Neurology which can
track billing and sources of funding.
Laboratory Science Core
Contacts:
Elizabeth Connick, M.D.
Director
[email protected]
303-724-4930
Website:http://www.uchsc.edu/ccfar/cores/immunology.htm
The mission of the Colorado CFAR Laboratory Science Core is to provide state-of-the-art tools,
technical support, and training in laboratory-based techniques as well as to identify unmet needs and
fill gaps in laboratory services for D-CFAR members and other investigators to support and promote
research on pathogenesis, treatment, and prevention of HIV-1 infection and its complications.
More information on the Flow Cytometry Unit and an Immunohistopatholgy Unit
can be found by clicking on the links.
Laser Capture Shared Core Service
Contacts:
Wilbur Franklin, MD, PhD
Director
[email protected]
303-724-3080
Jennifer Richer, PhD
Co-Director
[email protected]
303-724-3735
M. Scott Lucia, MD
Co-Director
[email protected]
303-724-3470
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/pathology/laser-
capture/index.aspx
What is Laser Capture Microdissection (LCM)?
Laser capture microdissection (LCM) is technique for obtaining pure cells from specific tissue
sections. A machine uses a laser beam to activate a special transfer film. The film bonds to cells
that have been identified and targeted by microscopy.
Laser capture microdissection (LCM) is a technique that allows pathologists to lift specifically
targeted cells from a section of cell tissue, leaving behind unwanted cells that could contaminate
the molecular purity of subsequent analysis. This technology, which was developed in the late
1990s at NIH in collaboration with bioengineering and cancer pathology groups, is precise,
accurate and automated.
LCM uses a special laser and film, which absorbs the laser energy and leaves the
macromolecules undamaged. Starting tissue can be fixed, embedded in paraffin or frozen.
Why Use LCM in Gene Expression Studies?
To reveal accurate, cell-type specific expression profiles that otherwise might be obscured in
mixed cell samples.
Technology isolates homogeneous populations of cells from tissue sections
• Cells can be collected based on morphologic or immunohistologic features
• Machine can recognize color (stains) or fluorescence
• Cells are harvested for DNA, RNA or Protein analysis
AutoPix LCM Machine
The AutoPix allows you to select all cells or areas to be captured automatically, instead of
manual firing.
• You can train the machine to recognize cells based on morphology or
immunohistochemical or fluorescent staining. We can also store customized recognition
programs.
• The machine's optical upgrade provides improved visualization of non-cover-slipped
tissue sections, allowing for better cell-type recognition.
• You can focus the laser to capture single cells, or use a broader area to capture cell
clusters.
• We provide technical assistance and reagents for dealing with LCM-captured material for
subsequent molecular analysis.
Laser Capture Prices
The Laser Capture Core offers discounted prices to University of Colorado Cancer Center
Members. Non-members can also use the facilities.
Pricing Structure for Cancer Center Members
Member
Price
Non-Member
Price
Service Description
1 Initial Introduction/consultation ($0) $294
2
LCM initial training session on slides of investigator
(feasibility/pilot experiments)
$222 $394
3 Machine Usage LCM $107 $228
4 H & E Staining Frozen $19 $54
4a H & E Staining FFPE $28 $62
5 RNA Isolation $7 $77
6 RNA Amplification Real Time PCR $159 $896
7 Burn CD $1 $1
8 Paraffin Embedded - Amplification $287 $1,025
9 Paraffin Embedded - QC $72 $177
10 Nanochip $21 $56
11 Picochip $23 $57
12 Turbo Labeling $69 $208
13 Paradise WT $51 $329
14 Paradise qrt PCR $205 $735
Prices effective 7/1/08 thru 6/30/09
Laser Capture Shared Core Service
From: Franklin, Wilbur
Sent: Friday, November 20, 2009 6:41 AM
a) How is the quality of your measurements evaluated - quality control?
The answer to this question depends on what is being evaluated. The Pathology Core is
responsible for processing tissues and the endpoint of this tissue processing is frequently
an excellent histologic preparation. Every sample that is prepared by the laboratory for
clinical work and most of the samples that are used for research are evaluated by a
certified pathologist, and the quality of the preparation is commented upon. These
records are open for inspection by CAP inspectors, who regularly recertify the laboratory.
b) What is the turn-a-round time for the service you provide?
This again depends on which service is involved. The animal tissues that we process
generally are not an emergency and so those are queued, and depending on the workload
in the Pathology Core, the queue may be a few days to a few weeks. Also, tissue
microarrays depending on the number of tissues being evaluated may require 2 or 3
weeks. On the other hand, we operate a molecular service that can generate mutational
results with a turn-around-time of 48-72 hours, and as part of the lab, a CALGB protocol
requires predictive testing for KRAS to be completed within 72 hours of receipt of the
specimen.
c) Who documents the data provided and signs off on the data?
For CLIA certified testing, all reports are signed by the Director. For research in the
Core Laboratory, tissues are returned to the investigator, and investigators are responsible
for interpreting their own histologic data.
d) Have you had experience providing data for industry?
The laboratory is responsible for validating methods and biomarkers for the FDA, and is
submitting data as part of a corporate initiative to obtain FDA approval for certain tests.
The answer to this question is yes.
e) Do you have a standard operating procedure manual?
We have standard operating procedures for all components of the core laboratories and
these are available on request. In fact, the Principal Investigator was responsible for the
preparation of a National Manual of Operations for the NCI Cooperative Group Banking
Committee. This document is also available in the Core.
f) How will you track billing and financial aspects of your core?
This depends on which part of the core is being queried. For the Cancer Center
Pathology Core, the PRA responsible for histology in that core tracks services and
expenses. For the SPORE, services are covered in the grant and again, the annual
progress reports document the output of the laboratory as well as more detailed
accounting through our finance administrators. Finally, the Southwest Oncology Group
Solid Tumor Bank is tracked in real time on a web site that maintains an inventory of
specimens accessioned into the core. We also track usage of the specimens and scientific
productivity through an inventory of published reports.
Light Microscopy
Contacts:
Steven Fadul
PRA
303-724-4508
[email protected]
Website:http://www.uchsc.edu/lightmicroscopy/
Bill Betz
Director
303-724-4502
[email protected]
General: Researchers are trained to use the microscopes
and image acquisition software themselves, with staff
assistance when necessary to ensure collection of high
quality images. Data can then be processed off-line for
export into the required format.
New Users: You will need to be trained to use the
microscope(s) and related instruments. You also must
create an account for charges. Contact Steve Fadul at the
facility to make arrangements.
Voice: (303) 724-4508. Email: [email protected]
Trained Users: Use the on-line Booking Page to sign up.
Special Needs
? Need a hefty block of time for your project?
We can help, especially after NIH grant deadlines
(March, July, and November are best).
? Need speci al equipment, like patch clamp,
bath perfusion, stage warmer? We can help with
these things, too.
Please acknowledge the facility appropriately in
publications, and notify us. When we apply for
equipment grants, we need to demonstrate the
usefulness of the facility.
General: We offer different kinds of pricing
(contact us for details). The simplest is by-the-
hour billing. We are especially interested in
working with grant applicants to have support
funds requested on grant applications for projects
that will involve this facility.
Our aim is to train users to be as independent as
possible in using the instruments.
Cancellation policy: Reservations cancelled less
than 24 hours in advance will be billed unless
someone else signs up.
The facility is open to researchers outside UCD
by special arrangement.
Introductory
Rates
? Zeiss 510 NLO confocal microscope: $35/hr
? Other microscopes: $25/hr
? Fuji Pictography prints: see the Manager for
assistance
? These rates are subj ect to change
Light Microscopy
From: Betz, Bill
Sent: Monday, November 02, 2009 10:55 AM
a) How is the quality of your measurements evaluated – quality control?
Feedback from users, regular meetings between director and staff
b) What is the turn-a-round time for the service you provide?
Usually immediate access to microscopes
c) Who documents the data provided and signs off on the data
Not sure what you mean- the users are trained to use the microscopes, and take their data
with them.
d) Have you had experience providing data for industry?
Very little
e) Do you have a standard operating procedure manual?
Web site
f) How will you track billing and financial aspects of your core?
The staff provides regular updates on all billing, machine use, etc.
Machi ne Shop
Contacts:
Ulli Bayer, PhD
Director
303-724-3610
[email protected]
Michael Hall, PhD
303-724-1335
[email protected]http://www.uchsc.edu/neuroscience/Program/cores.htm
The Neuroscience core machine shop is located in room NG003 on the ground floor of Building
500 (northwest corner) at the Fitzsimons campus of UCD/HSC. The shop's equipment and staff
are there to meet the custom machining needs of the faculty, staff and students of the
Neuroscience program and the university research community.
The shop machinery includes:
• 2 manual milling machines with 9" x 42" tables
(1 with digital readout)
• 1 CNC milling machine (full 3-axis automation)
• 2 precision lathes
• 1 surface grinder
• 1 wood/metal-cutting band saw
• 1 table saw
• 1 chop saw
• 2 grinding machines
• 1 drill press
• 1 6" belt sander
• 1 52" shear
• extensive tooling & precision measuring devices
The shop stocks a modest amount of material (acrylic and other
plastics, aluminum, brass, hardware) so most projects can be
completed using material on-hand.
The shop is staffed by one machinist 24 hours/week although
there are currently no routine hours of operation. Contact
Michael Hall at 303-724-1335 or, preferably, by e-mail at
[email protected] to discuss a project, to arrange a
meeting or with questions
Billing is based upon an hourly shop rate plus material cost and charges are levied against a
university speed-type account. At present there is no mechanism for billing outside of the
university system.
Shop services: custom design and production of equipment for scientific experimentation. The
shop is equipped with machining equipment to produce equipment made from plastics,
aluminum, steel or stainless steel.
Fees: The shop rate is $75.09/hour for design and machining services. Material costs are
additional.
Machine Shop
Ulli Bayer, PhD
From: Hall, Michael
Sent: Thursday, October 08, 2009 9: 16 AM
a) How is the quality of your measurements evaluated – quality control?
The machine shop produces products that adhere to the specifications of the design that is
dictated by the end-user/investigator. The requirements may be very exacting (0.0005”)
or less strict. Products are made to the users’ requirements, if known, or they may be
determined as the design is created in conjunction with shop staff. The end-user of the
product must be satisfied with the product they receive or it will be modified or made
again.
b) What is the turn-a-round time for the service you provide?
Turn-around-time is dictated by the complexity of the project requested and the current
work load in the shop. Work is generally dealt with on a first-come-first served basis,
however, the shop staff does strive to meet the requirements of the person requesting the
work and occasionally is able to accelerate the completion of a particular project. Please
provide as much advanced notice of your needed-by date as possible.
c) Who documents the data provided and signs off on the data?
The shop machinist sees that all requirements for product precision are met.
d) Have you had experience providing data for industry?
Not to date, all projects have been at the request of University investigators.
e) Do you have a standard operating procedure manual?
No. The use of shop machinery is restricted to individuals trained in their use.
f) How will you track billing and financial aspects of your core?
Billing is based upon an hourly shop rate plus material cost. This is recorded by the
machinist and charges are levied against a university speed-type number. At present there
is no mechanism for billing outside of the university system.
Shop services: custom design and production of equipment for scientific experimentation.
The shop is equipped with machining equipment to produce equipment made from
plastics, aluminum, steel or stainless steel. Please see the website for a listing of shop
machinery.
Fees: The shop rate is $75.09/hour for design and machining services. Material costs are
additional.
URL:http://www.uchsc.edu/neuroscience/Program/cores.htm - core D is the machine core.
[Department of Anesthesiology Clinical Research and Development]
Contacts:
Uwe Christians
University of Colorado Denver
Bioscience East, Suite 100
1999 North Fitzsimons Parkway
Aurora, Colorado 80045-7503
Phone: 720 961 4489 (direct)
303 724 5670 (office)
Fax: 303 724 5662
[email protected]
Website:http://www.uchsc.edu/bioanalytics/
The CNRU Mass Spectrometry Core is not an institutional core, but is jointly managed by the Clinical
Nutrition Research Unit (Director: Dr. J.O. Hill) and the Department of Anesthesiology, Clinical Research
& Development. The CNRU Mass Spectrometry Core’s mission is to provide a state-of-the-art laboratory
facility, expertise in mass spectrometry technologies and assays as well as to provide education, training
and consulting to investigators with projects relevant to the field of nutrition. As exemplified over the last
years, the Core has continued to develop diagnostic tools to predict disease and monitor the progress and
treatment of disease. In addition, we have provided comprehensive instruction for interested CNRU
investigators in order to increase their proficiency in our highly complex technologies and
instrumentation.
The Core has been, is and will be specifically involved in:
A. measuring enrichments in biomolecules used to follow metabolism and to determine substrate
turnover rates
B. gas isotope ratio determinations for total energy expenditure (TEE) and total body water (TBW)
C. gas isotope ratio determinations for substrate oxidation
D. biochemical profiling (metabolomics) using magnetic resonance spectroscopy and mass
spectrometry
E. proteomic profiling (proteomics) and mass spectrometry-based quantification of proteins
F. quantitative mass spectrometry of small molecules (drugs and endogenous compounds) and
hormones
G. drug metabolism studies
H. pharmacokinetics
In addition to the quantification of small molecule drugs, the CNRU Mass Spectrometry Core offers a
range of assays for targeted and non-targeted analysis of molecular markers and drug metabolism
services. The available assays and strategies are listed in Appendices I (endogenous compounds and
molecular markers) and II (drug metabolism).
The CNRU Mass Spectrometry Core has the track record, experience and infrastructure to assist basic
science departments to bring drug candidates into clinical development and to serve as a resource for
patient research in clinical departments, to serve as a resource for the pharmaceutical industry and to
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Mass Spectrometry Core (CNRU)
function as a interface between the University of Colorado Denver and Colorado biotech industry. The
CNRU Mass Spectrometry Core has experience with all stages of drug development including direct FDA
interactions. This core is a unique facility since it combines quantitative mass spectrometry (drugs, drug
metabolites, other small molecules and large molecules, endogenous compounds), metabolic and protein
profiling technologies under one roof and thus is capable of complex projects ranging from
pharmacokinetics to the development and qualification of molecular markers and novel diagnostic tools.
Core structure:
Regulatory Compliance
The Mass Spectrometry Core is 21 CFR part 58 compliant (FDA good laboratory practice) and is audited
on a regular basis by industry sponsors. The Principal Investigator’s laboratory is also accredited by the
College of American Pathologists (CAP, LAP#7176093, AU-ID: 1374604, last audit November 2008).
Dr. J elena Klawitter (Quality Assurance Officer) assists the Core Director in achieving and maintaining
GLP compliance and CAP accreditation. Drs. Klawitter and Christians were also awarded a Master in
Research Quality Assurance by the British Association of Research Quality Assurance.
Instrumentation
The following resources are currently available:
- 1 GC/MS (Agilent 5973N MS and 6890 GC) equipped with an 7683 autosampler
Uwe Christians, MD, PhD, MRQA
Core Director
Karen J onscher, PhD
Associate Director
CNRU Executive Committee
J essica Collins
Research Manager
Mary O’Connell
Grants and Account Manager
J aimie Henthorn
Laboratory Operations Assistant
Quantitative Mass Spectrometry
Drug metabolism
Keith Hoffman, B.Sc.
Biochemical Profiling
Metabolomics, GC-MS
Touraj Shokati, PhD
Isotope Ratio MS
Kent Hansen, PhD
Proteomics
Karen J onscher, PhD
Biostatistics
Zung Vu Tran, PhD
J eff Consoer, M.Sc.
Quality Assurance Unit
J elena Klawitter, PhD, MRQA
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- 1 preparative HPLC (Agilent series 1100 with diode array detector)
- 1 LC/LC-MS system (Agilent series 1100 Agilent modules with mass selective detector including
the capability of MS-guided fraction collection)
- 1 LC/LC-MS-iontrap (Agilent series 1100 HPLC modules, Agilent MSD-Trap ion trap mass
spectrometer)
- 1 Nano-LC-MS/ion trap, Agilent 1100 series LC/MSD Ultra ion trap mass spectrometer, includes
Agilent 1100 series nanoflow LC and nanospray ion source and software
- 1 HPLC Chip/AP-MALDI MS, Agilent 1100 LC/MSD Ultra ion trap mass spectrometer, includes
HPLC Chip and AP-MALDI ion source and software
- Spectrum Mill software for protein identification
- 1 Electrospray-time-of-flight (TOF) (Agilent) including Agilent 1100 series LC system, dual
spray electrospray source for reference mass correction and TOF-centric software, Chip interface,
GeneSpring MS software and Metlin database
- 1 UPLC-MS system (Micromass)
- 1 LC-MS/MS system (Thermo Quattro Ultra)
- 3 LC/LC-MS/MS system (Agilent series 1100 HPLC components and Sciex API4000 triple and
API 5000 quadrupole mass spectrometer)
- Complete two-dimensional gel electrophoresis system including IPGPhor, EttanDalt6, and all
accessories for large format gels (Amersham /GE Healthcare), and BioRad Criterion system for
small format gels and western blotting, Typhoon laser scanner, and DeCyder and Imagemaster
2D software.
- Thermo Fischer Exactive orbitrap
- Thermo Electron DELTA V advantage mass spectrometer with autosampler, an HD collector,
dual inlet system, and an H/device for reduction of H
2
O to H
2
Facility Users
The experience of the faculty and staff in quantitative mass spectrometry, labeled tracer studies, biochemical
(metabolomics) and protein profiling (proteomics) is not only a resource for analytical services but also for
new technology development, training, education, strategic research planning and support in grant writing
and publication. Although CNRU investigators are given priority, the CNRU Mass Spectrometry Core is
open to all investigators. In fact, the Core receives samples from all over the United States and has
numerous global collaboration partners.
Scheduling
When possible, the Core Director will accommodate users’ requests for specific time slots. Priority will
be given to NIH-supported CNRU investigators engaged in biomedical research, CNRU seed grant
awardees and CNRU investigators generating preliminary data for NIH grant applications. Lowest
priority will be given to industry-sponsored projects. Any minor scheduling conflicts will be handled by
the Core Director in close collaboration with the affected users. Larger issues will be discussed with the
Core Director in collaboration with the CNRU Director and CNRU Executive Committee to ensure a
balanced decision.
Policies and Access
Since July 2005, the CNRU Mass Spectrometry Core is organized as a Service Center. Service Centers are
“at cost” and must adhere to strict regulations that determine how funds are used and how user fees are
determined. User fees are based on 12-month cost studies conducted and reviewed by University of
Colorado. Service Center fees and spending are audited on a 12-month basis.
Users primarily contact the CNRU Mass Spectrometry Core Director. The reasons for contact can be, but
are not limited to, the following:
- to initiate a collaboration involving the use of the CNRU Mass Spectrometry Core for a research
project.
- to request time on instruments
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- to request assistance in study design; often prior to grant submissions
- to be trained on instrument(s) and in technologies available through the CNRU Mass
Spectrometry Core
- to solve logistic, technical, post-processing or data management issues
Rates
Please refer to the CNRU Mass Spectrometry Core Pricing Structure in Appendix III.
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Appendix I
Available Assays for Endogenous Compounds and Molecular Markers
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CNRU MASS SPECTROMETRY
CORE
Summary of Molecular Marker
Assays and Resources
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Page 2
Table of Contents
Assays and Analytical Strategies
3
1. LC-MS/MS Quantification of Endogenous Compounds 4
2. Amino Acids 5
3. High-Energy Phosphates (LC-MS) 7
4. Fatty Acid Profiling (GC-MS) 8
5. Metabolic Profiling (GC-MS and LC-MS) 9
6. Metabolic Profiling (
1
H-NMR) 10
7. High-Energy Phosphates (
31
P-NMR) 12
8. Lipid Patterns (
1
H-NMR) 13
9.
13
C-Labeled Tracers (
13
C-NMR) 14
10. Isotope Ratio Mass Spectrometry and Measurement of Isotope
Enrichment using GC-MS
15
11. Non-targeted Proteomics 16
12. Targeted Quantification of Proteins 17
page
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Page 3
Assays and Analytical Strategies
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Page 4
1. LC-MS/MS Quantification of Endogenous Compounds
Free Isoprostanes
Method: LC/LC-MS/MS
Status: fully validated
Matrices: human plasma, human urine, rat plasma and urine, tissue (partially validated)
Reference: Haschke M, Zhang YL, Kahle C, Klawitter J , Korecka M, Shaw LM, Christians U.
Quantification of 15-F2t-isoprostane in human urine and plasma using high-
performance liquid chromatography – atmospheric pressure chemical ionization-
tandem mass spectrometry. Clin Chem 2007; 53:489-497.
Total Isoprostanes
Method: LC/LC-MS/MS
Status: partially validated
Matrices: human plasma, human urine, rat plasma and urine
Reference: N/A. Modification of the free isoprostane assay including release of bound
isoprostanes using KOH and extraction with affinity columns.
Vitamin D Profiling
VitD2, VitD3, 25(OH)VitD2, 25(OH)VitD3, 1(OH)VitD3, 1,25(OH)
2
VitD2 and 1, 25(OH)
2
VitD3
Method: LC/LC-MS/MS
Status: partially validated
Matrices: human plasma
Reference: ASMS presentation, publication in preparation
Steroid Hormones
Testosterone (total and free), estrogen (total)
Method: LC/LC-MS/MS
Status: partially validated
Matrices: human plasma
Reference: publication in preparation
In preparation:
Endothelin, angiotensin, aldosterone, ADMA
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Page 5
2. Amino Acids
Method: LC-time-of-flight MS
Status: fully validated
Matrices: human plasma
Reference: Armstrong M, J onscher K, Reisdorph NA. Analysis of 25 underivatized amino
acids in human plasma using ion-pairing reversed-phase liquid
chromatography/time-of-flight mass spectrometry. Rapid Commun Mass
Spectrom. 2007;21(16):2717-26.
Analytes:
Compound
Molecular
formula
Exact
mass
[M+H]
Extracted
ion
window
Low cal
std
(nM/mL)
High
cal std
(nM/mL)
S/N ratio
(pM
injected) IS used for quantitation
Taurine C2H7NO3S 126.0224 126.00-
126.04
1.56 400 851
(125)
Glutamine-d5
Aspartic acid C4H7NO4 134.0453 134.01-
134.05
1.56 400 52.5
(125)
Glutamic acid-d3
Hydroxyproline C5H9NO3 132.0660 132.03-
132.07
1.56 400 1750
(125)
Glutamine-d5
Serine C3H7NO3 106.0504 106.02-
106.06
1.56 400 267
(125)
Glutamic acid-d3
Glycine C2H5NO2 76.0398 76.01-
76.05
25 3200 22.3
(3125)
Glutamic acid-d3
Glutamine-d5
*
C5H5D5N2O3 152.1000 152.05-
152.15
NA NA 637
(1000)
NA
Glutamine C5H10N2O3 146.0769 147.04-
147.08
25 3200 1450
(3125)
Glutamine-d5
Asparagine C4H8N2O3 133.0613 133.03-
133.07
1.56 400 94.9
(125)
Glutamine-d5
Threonine C4H9NO3 120.0660 120.03-
120.07
1.56 400 315
(125)
Glutamic acid-d3
Glutamic acid-
d3
*
C5H6D3NO4 151.1000 151.05-
151.15
NA NA 15.2
(1000)
NA
Glutamic acid C5H9NO4 148.0609 148.03-
148.07
12.5 1600 714
(1562)
Glutamic acid-d3
Alanine C3H7N02 90.0555 90.02-
90.06
12.5 1600 345
(125)
Leucine-d10
(Cysteine)2 C6H12N2O4S2 241.0316 241.01-
241.05
1.56 400 1160
(125)
Methionine-d3
Citrulline C6H13N3O3 176.1035 176.01-
176.05
1.56 400 383
(125)
Glutamine-d5
Proline C5H9NO2 116.0711 116.04-
116.08
1.56 400 355
(125)
Glutamine-d5
Gly-Gln
*
C7H13N3O4 204.2000 204.10-
204.30
NA NA 2560
(1000)
NA
Ala-Gln C8H15N3O4 218.1140 218.08-
218.12
1.56 400 508
(125)
Gly-Gln
Valine C5H11NO2 118.0868 118.05-
118.09
1.56 400 163
(125)
Leucine-d10
Methionine-d3
*
C5H8D3NO2S 153.1000 153.05-
153.15
NA NA 1810
(1000)
NA
Methionine C5H11NO2S 150.0588 150.03-
150.07
1.56 400 737
(125)
Methionine-d3
Tyrosine C9H11NO3 182.0817 182.05- 1.56 400 722 Leucine-d10
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Page 6
182.09 (125)
Isoleucine C6H13NO2 132.1024 132.08-
132.12
1.56 400 340
(125)
Leucine-d10
Leucine-d10
*
C6H3D10NO2 142.2000 142.00-
142.30
NA NA 1450
(1000)
NA
Leucine C6H13NO2 132.1024 132.08-
132.12
1.56 400 228
(125)
Leucine-d10
Phenylalanine C9H11NO2 166.0868 166.06-
166.10
1.56 400 1010
(125)
Leucine-d10
Histidine C6H9N3O2 156.0773 156.05-
156.08
1.56 400 1090
(125)
Tryptophan-d5
Tryptophan C11H12N2O2 205.0977 205.08-
205.12
1.56 400 383
(125)
Tryptophan-d5
Tryptophan-
d5
*
C11H7D5N2O2 210.1000 210.00-
210.30
NA NA 1110
(1000)
NA
Arginine C6H14N4O2 175.1195 175.09-
175.13
1.56 400 1700
(125)
Tryptophan-d5
Ornithine C5H12N2O2 133.0977 133.08-
133.12
1.56 400 544
(125)
Tryptophan-d5
Lysine C6H14N2O2 147.1133 147.09-
147.13
1.56 400 448
(125)
Tryptophan-d5
*
Internal standard.
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3. High Energy Phosphates (LC-MS)
Method: LC-MS
Status: fully validated
Matrices: Tissues
Reference: Klawitter J , Schmitz V, Klawitter J , Leibfritz D, Christians U. Development and
validation of an assay for the quantification of 11 nucleotides using LC/LC-
electrospray ionization-MS. Anal Biochem. 2007 J un 15;365(2):230-9.
Analytes:
AMP (m/z=346)
ADP (m/z=426)
ATP (m/z=506)
GDP (m/z=442)
GTP (m/z=522)
UDP (m/z=403)
UTP (m/z=483)
CDP (m/z=402)
CTP (m/z=482)
NAD
+
(m/z=662)
FAD (m/z=784)
internal standard 6-aminohexyl-ADP (m/z=525).
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4. Fatty Acid Profiling (GC-MS)
Method: GC-MS
Status: partially validated
Matrices: human and rat plasma and tissues
Reference: N/A
Analytes:
C12
C14
C16
C18
C20
C22
C24
C14:1
C16:1
C18:1
C22:1
C18:2
C18:3
C20:4
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5. Metabolic Profiling (GC-MS and LC-MS)
Method: GC-MS
Status: partially validated
Matrices: human and rat plasma, urine and tissues
Reference: N/A
Analytes:
3OH-butyrate
Acetic acid
Alanine
Aminomalonate
Creatinine
Galactonic acid
Glucitol
Glucoronic acid
Glutamine
Glycine
Hippurate
Histidine
Indolacetate
Isocitrate
Isovalerate
Lactic acid
Oxalate
Proline
Pseudouridine
Pyruvic acid
Ribose
Serine
Succinate
Threonine
Tyrosine
Uric acid
Valine
Xylitol
Please note that only the major metabolites are listed. Typically, more than 100 metabolites can be
detected within one GC-MS run, allowing either for quantitation or emi-quantitative comparison.
In addition, LC-TOF and LC-MS-TOF assays are set up and available. Metabolites can be identified
using the METLIN database. However, it must be noted that due to the inherent problem of ion
suppression in the electrospray source use of this data for semi-quantitative comparison may be
limited.
CNRU Mass Spectrometry Core
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Page 10
6. Metabolic Profiling (
1
H NMR)
Method: proton nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: human and rat plasma, urine and tissues
Reference: N/A
Analytes:
No. metabolite 1H
[ppm]
13C
[ppm]
blood urine
1 leucine 0.94 22 ? ?
2 leucine 0.96 23 ? ?
3 valine 0.97 18 ?
4 isoleucine 1.00 16 ? ?
5 valine 1.03 19 ?
6 (isobutyrate / 3oxo-isovalerate) 1.13 23.1 (?)
7 3-hydroxybutyrate 1.19 23 ?
8 threonine 1.29 20.5 ?
9 lactate 1.32 21.3 ? ?
10 lysine 1.43 + 1.47 22.8 ?
11 alanine 1.46 17.5 ? ?
12 arginine 1.67 25.3 ?
13 leucine 1.68 25.0 ? ?
14 leucine 1.69 41.0 ?
15 leucine 1.69 40.2 ?
16 lysine 1.70 27.6 ?
17 2-hydroxyglutarate 1.83 31.9 ?
18 lysine 1.87 31.5 ?
19 arginine 1.87 29.3 ?
20 2-hydroxyglutarate 1.98 31.5 ?
21 acetate 2.02 23.4 ? ?
22 glutamate 2.08 28.3 ?
23 glutamine 2.12 28 ?
24 hydroxyglutarate 2.26 34.3 ?
25 glutamate 2.32 34.7 ?
26 succinate 2.43 34 ?
27 glutamine 2.44 32.1 ?
28 2-oxoglutarate 2.45 31.5 ?
29 glutathione (Glu) both froms 2.49 32.7 ?
30 citrate 2.56 46.2 ?
31 dimethylamine 2.70 35.7 ?
32 citrate 2.71 46.2 ?
33 trimethylamine 2.87 45.7 ?
34 GSSG (Cys) oxidized 2.95 39.9 ?
35 2-oxoglutarate 2.97 36.8 ?
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Page 11
No. metabolite 1H
[ppm]
13C
[ppm]
blood urine
36 lysine 3.01 40.3 ?
37 creatine 3.02 38.3 ? ?
38 creatinine 3.04 31.4 ? ?
39 R-N
+
-(CH
3
)
3 several signals
3.18 - 3.27 53.1 - 55.5 ? (?)
40 taurine 3.20 49.9 ? ?
41 ?-glucose C2 3.23 75.3 ? ?
42 arginine 3.23 41.7 ?
43 trimethylamine N-oxide 3.25 60.8 ? ? 3.3
ppm
44 phenylalanine 3.28 36.9 ?
45 GSSG (Cys) oxidized 3.30 39.8 ?
46 taurine 3.32 36.8 ? ?
47 ?, ?-glucose C4 3.40 70.8 ? ?
48 ?-glucose C3/C5 3.48 77.1 ? ?
49 ? -glucose C2 3.52 72.6 ? ?
50 glycine 3.54 42.8 ? ?
51 glutathione+Gln+Glu 3.69 55.7 ?
52 ?-glucose C3 3.69 73.9 ? ?
53 ?, ?-glucose C6 3.72 61.9 ? ?
54 glutathione (Gly) both froms 3.75 44.7 ?
55 alanine 3.75 51.7 ? ?
56 ?-glucose C5 3.82 72.6 ? ?
57 ?, ?-glucose C6 3.87 61.9 ? ?
58 creatine 3.91 55.0 ? ?
59 hippurate 3.94 45.1 ?
60 creatinine 4.09 56.9 ?
61 lactate 4.09 69.7 ? ?
62 ?-glucose C1 4.64 97.1 ? ?
63 ?-glucose C1 5.21 93.3 ? ?
64 urea 5.80 -------- ?
65 phenylalanine 7.31 130.5 ?
66 phenylalanine 7.34 128.0 ?
67 phenylalanine 7.41 129.9 ?
68 hippurate 7.50 129.9 ?
69 hippurate 7.59 133.2 ?
70 hippurate 7.79 128.2 ?
71 fumarate 8.46 147.9 ?
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Page 12
7. High Energy Phosphates (
31
P NMR)
Method: phosphorous nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: Tissues
Reference: N/A
Analytes:
phosphomonoesthers (PME)
phosphodiesters (PDE) (both precursors for membrane phospholipid metabolism)
sugar phosphates (UDPG)
phosphocreatine (PCr)
NAD
+
,
NMP
NDP
NTP.
Anorganic phosphate (can be used for monitoring in vivo pH changes in perfused organs and
cells)
NMP, NDP and NTP: nucleotide mono, di and tri phosphates such as AMP, ADP, ATP etc.
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Page 13
8. Lipid Patterns (
1
H NMR)
Method: proton nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: human and rat blood, plasma and tissues
Reference: N/A
Analytes:
poly- and mono-unsaturated fatty acids (PUFA and MUFA)
total fatty acids
triacylglycerols
glycerophosphates
phosphatidylcholine
phosphatidylethanolamine
cholesterol.
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Page 14
9.
13
C-Labeled Tracers (
13
C NMR)
Method:
13
C nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: tissues, ex vivo perfused organs, perfused and extracted cell cultures
Reference: N/A
Analytes:
Depending on
13
C labeled tracer used. For example in the case of 1-
13
C-glucose:
Metabolic fate of
13
C-label from [1?
13
C]glucose. Label distribution in glycolytic and tricarboxylic acid
(TCA) cycle intermediates during metabolism of [1?
13
C]glucose
3 2
1
O
5
4
OH
H
OH
H
OH
H
CH
2
OH
6
H
OH
OOC
CH
2
O PO
3
COO
CH
3
O H H
COO
CH
3
O
COO
CH
3
H H
3
N
SCoA
CH
3
O
COO
CH
2
COO
H O H
COO
CH
2
COO
O
CH
2
CH
2
COO
COO
COO
O H
COO
CH
2
COO
H H
3
N
CH
2
CH
2
COO
COO
O
CH
2
CH
2
COO
COO
CH
CH
COO
COO
COO
CH
2
CH
2
COO
H
3
N H
(CONH
2
)
2-
oxalacetate
malate
citric acid
aspartate
acetyl-CoA
1-13C-glucose
pyruvate
lactate
alanine
phosphoenol-
pyruvate
succinate
2-oxoglutarate
fumarate
glycolysis
PK
LDH
PDH
PC
ME
PEPCK
Krebs-cycle
+
-
-
PDH:
glutamate
PC:
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Page 15
10. Isotope Ratio Mass Spectrometry and Measurement of Isotope Enrichment
Using GC-MS
Carbon Dioxide Enrichment
Method: Automated carousel and reference gas system in combination with a double-
focusing sector field mass spectrometer
Status: partially validated
Matrices: breath and blood
Reference: N/A
Singly Labeled Water for Determination of Total Body Water and Doubly Labeled Water
Enrichment for the Measurement of Total Energy Expenditure
Method: double-focusing sector field mass spectrometer with autosampler, an HD
collector, dual inlet system, and an H/device for reduction of H
2
O to H
2
Status: partially validated
Matrices: human and rat plasma
Reference: N/A
Labeled Glucose and Glycerol in Plasma
Method: GC-MS
Status: fully validated
Matrices: human and rat plasma
Reference: N/A
The assay was developed and validated using 6,6-d
2
-glucose and d
5
glycerol. This method can be
easily adapted to glucose and glycerol with other
13
C and deuterium labeled analogues.
Labeled Essential and Non-Essential Amino Acids
Method: GC-MS
Status: fully validated
Matrices: human and rat plasma
Reference: N/A
The assay is established and validated for the measurement of stable isotope enrichment such as
methionine-d
3
, phenylalanine-1-
13
C, lysine-1-
13
C, tryptophan-d
5
and leucine-1-
13
C.
1-
13
C-labeled Fatty Acids
Method: GC-MS
Status: fully validated
Matrices: human and rat plasma
Reference: N/A
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Page 16
11. Non-Targeted Proteomics
Extraction, Separation and Analytical Technologies:
- 1D and 2D-gel eledctrophoresis
- Spot cutting, trypsination
- Immunoprecipitation
- Fractionation by semi-preparative HPLC
- 1D- and 2D HPLC, nano-LC, chromatography chip
- MALDI
- Protein identification: iontrap-MS, electron transfer dissociation iontrap MS, time-of-flight
mass spectrometry, quadrupole-time-of-flight mass spectrometry, triple stage quadrupole
mass spectrometry, triple stage quadrupole- linear ion trap mass spectrometry in
combination with database searches
Labeling Technologies:
- SILAC (in combination with cell culture facility)
- iTRAQ
Qualification of Database Hits:
- Western blot
- PCR
- gene knock down (in combination with cell culture facility)
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Page 17
12. Targeted Quantification of Proteins
General strategic approach:
Plasma
Sample
Extraction
- protein precipitation
- gel chromatography
- immuno capture
- immuno depletion
Digestion
LC-MS/MS
of peptides
Derivatization
Labeled internal
standard
CNRU Mass Spectrometry Core
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Version 05/26/2009
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Appendix II
Available strategies to assess drug metabolism
CNRU Mass Spectrometry Core
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Questions:
-Metabolite pattern?
-Phase I/ II metabolism?
-Which enzymes are involved?
-Drug-drug interactions?
-Enzyme induction?
-Structures of metabolites?
-Permeability trough blood-brain
And intestinal barriers ?
Study drug
Analytical assay (LC-MS/ LC-MS/ iontrap)
MS fragmentation
Extraction
Basic validation (linearity, recovery, stability)
Initial metabolism screen
- Pooled human liver microsomes, human hepatocytes, cytosol, mitochondria
?Metabolite patterns, preliminary structural information, phase I/II
Choice of appropriate in vitro models and analytics
Phase I Phase II Phase I +II
Human microsomes
?Cytochrome P450
e.g. Human microsomes
?UGT glucuronidation
Hepatic cytosol
?Sulfate conjugation
Human hepatocytes
and/or liver slices
Establish time-, drug-, and protein concentration dependency
Evaluate dependency on species and gender
Determine K
m
, V
max
and CL
int
(corrected for protein binding, several
species)
Identification of specific enzymes involved using:
- Isolated enzymes
- Specific chemical inhibitors
- Specific antibodies
Drug-drug interactions (inhibition, inhibitors will be selected on the basis of results above):
-Effect of study drugs on metabolism of other drugs
-Effect of other drugs on metabolism of study drug
-Mechanism-based inhibition by study drug
Drug-drug interactions (induction):
?Western blotting, metabolism of specific CYP probes, gene expression ?gene arrays (if necessary)
- Human hepatocytes
- After treatment of rats and isolation of liver microsomes
Structural identification of metabolites:
-If necessary: upscale production of metabolites (microsomes, animals, bacterial culture and preparative HPLC)
-Establish quantity and purity of metabolites (mass spectrometry, HPLC/UV)
-Mass spectrometry (MS/MS, MS/ion trap, MS/time-of-flight, validate fragment structures?HR/MS, H/D exchange)
-Mono- and heteronuclear, one- and two-dimensional high-resolution NMR, LC/NMR
Develop and validate LC/MS/MS or GC/MS assays of parent and metabolites
-High-throughput assays for animal studies and samples from other experimental sources
(required for enzyme kinetics, drug-drug interaction and permeability studies)
CNRU Mass Spectrometry Core
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Appendix III
Pricing Structure
CNRU Mass Spectrometry Core
303 724 5670, [email protected]
Version 05/26/2009
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CNRU Mass Spectrometry Core Pricing Structure 2008/2009
Proteomics First Sample Additional samples *
1D gel per sample $63.00 $29.25
11 cm 2D gel per sample $119.25 $94.50
24cm 2D gel per sample $221.25 $191.00
Gel Imaging small gel $24.00 $7.00
large gel $38.00 $24.25
2D Spot Analysis per hour $51.00 N/A
Spot Cutting per hour $51.00 N/A
Sample Preparation
Desalting column up to 6 samples $42.50 $7.75
Bradford up to 6 samples $46.75 $2.20
BCA p to 40 samples in du $57.25 N/A
2D Quant kit up to 6 samples $39.50 $0.50
2D clean up kit up to 6 samples $40.50 $5.50
Concentrator Tubes up to 6 samples $42.25 $7.25
HPLC Immunodepletion sample(triplicate) $243.00
single sample $75.50
Stains (small gel)
Coomassie per gel NC
Silver stain per gel $22.50
Sypro stain per gel $30.39
Phospho stain per gel $43.00
Stains (large gel)
Coomassie per gel NC
Silver stain per gel $92.50
Sypro stain per gel $146.50
Phospho stain per gel $400.00
Protein Identification (Mass Spectrometry) First sample Additional samples *
In Solution Protein Digest per sample $47.15 $7.00
In Gel Protein Digest per sample $76.70 $11.70
Nano-LC Trap per sample $90.80 $79.10
Chip-LC trap per sample $75.50 $67.50
ESI-TOF per hour $100.00 $100.00
Database Searching per sample $12.75
Data Analysis per hour $51.00
GC/MS and Metabolomics First sample Additional sample10-100 Samples
Single Amino Acid per sample $131.30 $39.00 $27.50
Amino Acid Panel per sample $150.00 $100.00
fatty acid per sample $111.80 $31.50 $12.60
Glucose/Glycerol per sample $112.00 $31.75 $21.80
Lactate (same as glucose) per sample $112.00 $31.75 $21.80
Breath CO2 $21.35
Body CO2 $26.00
DLW $404.50
Exact Mass Determination per hour $100.00
Instrument Rental
Triple Quadrupole per hour $60.00
GCMS per hour $50.00
Quadrupole Ion Trap per hour $50.00
Consulting per hour $51.00
Assistance per hour $35.00
*Additional samples are those in the same order up to a maximum of 12 gels for proteomics and 100 samples for GC/MS
Revision Date: 10/21/08
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Version 05/26/2009
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Mass Spectrometry Facility Structure
(National Jewish Hospital)
Contact:
Nichole Reisdorph, PhD
Assistant Professor, Immunology
Director, Mass Spectrometry Facility
National Jewish Health
303-398-1964
www.proteomicstraining.org
www.reisdorphlab.org
Services
A. Sample preparation, fractionation, and simplification/purification
a. Column chromatography (HPLC with fraction collector)
b. Sample cleanup, protein precipitation, dialysis, purification
c. Protein digestion
d. 1D gel electrophoresis
e. Small format 2D gels
f. Isoelectric focusing (Off-gel electrophoresis)
B. Protein identification and characterization
a. Identification of proteins from simple and complex mixtures
b. Post-translational modification analysis
c. Protein sequence determination
C. Quantitative
a. Proteomics
i. Labeling and non-labeling MS-based methods for differential protein
expression analyses
ii. Note: there are no large-scale 2D gel experiments at NJ, gels can be run
at UC Denver and analyzed at NJMRC
b. Small molecule analysis
i. Targeted
1. Leukotriene B4, C4, D4, and E4
2. PGE2
3. Steroid hormones (eg testosterone)
4. Vitamin D2 and D3
5. Amino acid panel
ii. Discovery-based Metabolic Profiling
c. Accurate mass and percent purity determination (for synthesized molecules)
D. Assay development
a. Basic science
b. Clinical diagnostics
E. Genomics
a. RNA quality assessment (Bioanalyzer)
b. Microarray applications
i. expression analysis
ii. comparative genomic hybridization
iii. methylation analysis
iv. splice variant analysis
v. microRNA analysis
F. Informatics
a. Protein database searching
b. Quantitative omics programs (Genespring, Mass Profiler)
c. Biostatistics
G. Training and education
a. International hands-on and web-based proteomics, metabolomics, genomics,
and informatics training program
b. Training of investigators, students, and technicians through collaborations, co-
investigator projects, and training program.
Mass Spectrometry Facility Structure
(National Jewish Health)
From: Reisdorph, Nichole [mailto:[email protected]]
Sent: Tuesday, November 17, 2009 4:44 PM
www.proteomicstraining.org
www.reisdorphlab.org
a) How is the quality of your measurements evaluated – quality control?
For protein identification and characterization experiments utilizing liquid
chromatography mass spectrometry (LC/MS), standards are analyzed at the beginning
and end of each set of samples. An aliquot of digested bovine serum albumin is analyzed
by LC/MS. Total ion chromatograms are reviewed to ascertain good resolution of peaks,
signal between 10
7
and 10
9
, background under 10
4
, and quality of MS and MS/MS data is
assessed. Data is searched against a protein sequence database, Spectrum Mill and a
minimum of 45% coverage is expected. A moderately complex mix of proteins is used
for QC when more complex samples (> 50 proteins) are analyzed.
For absolute quantization of small molecules (eg. Leukotrienes, Vitamin D, steroid
hormones, amino acids) an external calibration curve is generated daily, high/low
samples are analyzed throughout the runs, and labeled internal standards are spiked in to
each sample. Each of these assays has been extensively validated.
b) What is the turn-a-round time for the service you provide?
Analysis of samples using validated methods is generally conducted within 1 week.
Large batches (>500 samples) may take up to one month. Studies involving method
development can take anywhere from 2 weeks to 1 year.
c) Who documents the data provided and signs off on the data?
Individual technicians document the data which is stored on dedicated servers and backed
up on a weekly/monthly basis. The Core Director or Associate Director approves data
reports.
d) Have you had experience providing data for industry?
Yes although we do not have a formal reporting procedure/materials.
e) Do you have a standard operating procedure manual?
We have SOPs for individual assays and have begun the process of developing a
comprehensive manual.
f) How will you track billing and financial aspects of your core?
Financials are organized with the assistance of the Office for Academic Affairs. Core
personnel record analysis information in a master log. This includes the date of service,
customer and technician names, type and number of analyses provided, discount or
special pricing information, and miscellaneous information. At the end of each month
this information is used to create invoices which are emailed/mailed to individual
investigators. The Core accepts POs, checks, credit cards, and direct transfers within
NJH.
Medicinal Chemistry Core Facility
Michael F. Wempe, PhD
Associate Research Professor and Director, Medicinal Chemistry Core Facility
Department of Pharmaceutical Sciences, School of Pharmacy
University of Colorado Denver
C238-P15 Research 2, Room P15-4003,
12700 East 19th Avenue, Aurora, CO 80045.
“Medicinal or Pharmaceutical Chemistry is a discipline at the intersection of chemistry
and pharmacology involved with designing, synthesizing and developing pharmaceutical
drugs. Medicinal chemistry involves the identification, synthesis and development of new
chemical entities suitable for therapeutic use. It also includes the study of existing drugs,
their biological properties, and their quantitative structure-activity relationships (QSAR).
Pharmaceutical chemistry is focused on quality aspects of medicines and aims t o assure
fitness for the purpose of medicinal products.” (Wikipedia).
A medicinal chemistry c ore f acility at UC Denver – housed within t he Department of
Pharmaceutical Sciences (DOPS) – has been initiated. The facility has been established to
offer researchers with small molecule synthesis and drug metabolism expertise (i.e. pre-
clinical evaluation capabilities). The main goal of the core will be to help facilitate and
stimulate fundamental and collaborative research at the university; a chemical synthesis
core geared t o provide c ompounds t o help r esearches validate pr oof-of-principle t arget
discovery studies and/or assist in pre-clinical evaluation.
Services:
- Synthesis of known, but not commercially available compounds
- Design and custom synthesis of bio-active molecules
- Assistance in the identification and optimization of lead compounds
- Structure-Activity Relationship (SAR) elucidation
- In vitro Metabolic stability screening (mouse, rat, dog, monkey, human)
- Metabolite identification
- In vitro Permeability assessment, protein binding, plasma stability
- In vitro drug-drug interaction studies
- In vitro drug transporter studies
- Bio-Analytical Pharmacokinetic (BAPK) method development
- Determination o f d rug c andidate a nd me tabolite(s) in b iological ma trix
(i.e. plasma, liver, brain, kidney, heart, fat and muscle)
- Formulation development
* For consultation, research proposals, current facility and labor charges, contact:
[email protected] (Tel) 303-724-8982
Medicinal Chemistry Core Facility
Michael F. Wempe, PhD
a) How is the quality of your measurements evaluated – quality control?
Good Labororatory Practices (GLP) are used in the Medicinal Chemistry Core regarding non-
clinical studies conducted for the assessment of the safety of chemicals to man, animals and
the e nvironment. Therefore, our G LP m ethods (i.e. internal s tandards, qua lity c ontrols
samples, et c) provide a f ramework w ere l aboratory st udies a re p lanned, p erformed,
monitored, recorded, reported and archived.
b) What is the turn-a-round time for the service you provide?
Because the scope of the poject can significantly vary (i.e. synthesis, vs. in vitro, vs. in vivo
pre-clinical evaluations), the turn-a-round time is project specific.
c) Who documents the data provided and signs off on the data?
The Director of the Medicinal Chemistry Core signs off on data.
d) Have you had experience providing data for industry?
Yes, we have hands-on experience providing data to industry.
e) Do you have a standard operating procedure manual?
We are actively preparing SOP’s for various preclinical evaluations.
f) How will you track billing and financial aspects of your core?
Billing and financial aspects related to the core will be tracked using a ‘Service Center Cost
Study Summary’ template.
University of Colorado Cancer Center
Metabolomics Core
Contact:
Natalie Serkova, PhD, Director
Associate Professor, Dept. of Anesthesiology and Radiology
303-266-2910 pager
[email protected]
303-724-1086 phone
303-359-6574 cell
Manager: Andrea Merz (pager 303 266 7514)
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/metabolomics/index.aspx
Dr. Natalie Serkova
Metabolomics, one of the “omic” sciences in systems biology, is the global assessment and
validation of endogenous small-molecule biochemicals (metabolites) within a biologic system.
Metabolite detection and quantification is usually carried out by nuclear magnetic resonance
(NMR) spectroscopy while mass spectrometry (MS) provides another highly sensitive
metabolomics technology. The UCCC Metabolomics Core provides all NMR-related
metabolomics services on human and animal cells, bipsies, and body fluids. Various metabolic
biomarkers, related to glycolysis, mitochondrial citric cycle acid, choline, phospholipids and
fatty acid metabolism, were recently reported to play important roles in cancer development and
responsiveness to anti-cancer treatment using NMR-based metabolic profiling.
The Metabolomics Core consists of the high-resolution NMR facility, which is located at the
Anschutz Medical Campus, Research Complex-2 (Suite P15-1109).
The facility is fully equipped for all aspects of nuclear magnetic resonance spectroscopy (1H-,
13C-, and 31P-NMR and two-dimensional NMR). We performed expanded quantitative
metabolic analysis:
• on cells
• cell extracts
• human and animal tissues and biopsy extracts
• body fluids (including blood, plasma, urine, cerebral and prostatic fluids etc).
Our Services
• Project design and consultation: recommendations and advice on end points to be
monitored, budget, suggestions for data analysis.
• Sample Handling and Extraction for Metabolic NMR: Facilities for tissue, body fluids,
and cell extraction, sample lyophilization, and sample preparation for NMR. Sample
storage is also available.
• NMR based metabolic protocols: Structure determination based on two-dimensional
NMR is used for metabolite identification, specially designed 1D-NMR program is used
for precise metabolite quantification, various statistical packages are available to perform
principle component analysis (PCA), linear regression etc. analysis on metabolic data
sets.
• Data set collection is available.
• Access to computational facilities.
• Data analysis and publication and grants preparation/ assistance.
• Training in MR safety (for all users).
• Training in MR operation (for advanced users only)
• Data handling and storage
Metabolics Core Pricing for FY2008/2009
Full Service Self Service
Service Description
Member
Rate
Non Member
Rate
Member
Rate
Non Member
Rate
Biopsy $116 $144 $69 $70
Blood $59 $80 $23 $23
Cell Culture $324 $405 $188 $193
Quality Control (HSQC) $185 $190 $185 $190
Other - Minimum
Processing
$43 $54 $24 $24
• Prices effective 7/1/08 thru 6/30/09
Metabolics Core Pricing for FY2009/2010
2009/ 2010 Full Service Self Service
Service Description
Member
Rate
Non
Member
Rate Commercial
Member
Rate
Non
Member
Rate Commercial
Biopsy $121 $149 $69 $70
Blood $63 $84 $23 $23
Cell Culture $341 $422 $188 $192
Quality Control (HSQC) $185 $190 $185 $190
Other - Minimum Processing $45 $56 $24 $24
* only experienced NMR/ Radiologist scientists after on-site training by Dr. Serkova
NMR Metabolomics
From: Serkova, Natalie
Sent: Thursday, October 01, 2009 2:26 PM
a) How is the quality of your measurements evaluated – quality control?
For NMR Metabolomics: External s tandards f or NMR c hemical s hifts a nd me tabolite
quantification are re-evaluated every 3 months.
b) What is the turn-a-round time for the service you provide?
For NMR Metabolomics: 20 m in – 24 h rs pe r s ample. For a s ingle s tudy, t he pr oject
period can be up to 3 months.
c) Who documents the data provided and signs off on the data?
Metabolomics and Animal Imaging: The Core staff: NMR f acility manager and animal
facility manager. The Core Director provides monthly reports to the Cancer Center based
on the data from the staff.
d) Have you had experience providing data for industry?
Yes, we run 5-10 industry sponsored studies per year.
e) Do you have a standard operating procedure manual?
NMR Metabolomics (published, books) and for animal imaging (per requested, approved
by the IACUC).
f) How will you track billing and financial aspects of your core?
We do it already for the past 3 years: Cancer Center provides us with our cost study every
fiscal year. It is posted on our website
METABOLIC CORE LABORATORY
Services 2007
Contact:
Jacob E. (Jed) Friedman, Ph.D.
Director
(303) 724-3983
[email protected]
For body composition/calorimetry and assays of LPL and HSL, contact:
Robert Eckel, MD
Professor
(303) 724-3969
[email protected]
Pricing contact:
Rachel Janssen
303-724-3979
[email protected]
Website:http://www.uchsc.edu/nutrition/Friedman/MetabolicCoreLab.htm
I. Description:
The main services of the Metabolic Core are gene expression analysis using real-time
quantitative PCR and tissue procurement/preparation and processing for analysis of
phosphorylation and expression of key post-receptor insulin signaling proteins that regulate
insulin sensitivity and lipid metabolism at the cellular level. The Core also provides selected
assays for specific hormones and metabolites. This Core provides an array of assays over a
broad range of species (rat, mouse, human, sheep) and tissue types (fat, muscle, liver), for
multiple investigators studying the clinical consequences of nutrition-related disorders. The
Metabolic Core lab also provides members of the Center with reagents, access to
equipment, and exposure to new techniques (insulin clamping, insulin signaling, real-time
PCR) that have helped to expand the quantity and quality of nutrition research in the CNRU.
The services of the Metabolic Core Laboratory have been used by many investigators to
extend their research beyond the specific hypotheses proposed in their RO1 grants. For
example, many investigators who did not previously assess insulin action in their own
studies have taken advantage of this core laboratory to obtain these measures using the
insulin signaling assays. Thus, the Metabolic Core of the Nutrition Center achieves an
overall cost-savings and provides more important investigator time in their own laboratories
for their own experiments.
II. Organization and Description of Services:
The Core services the needs of the CNRU on a reduced fee-for service basis including:
• RNA isolation, analysis, quantitation, real-time quantitative RT-PCR. TaqMan probes
available from the Core range from genes involved in gluconeogenesis and
lipogenesis to neuropeptides and transcription factors, as well as reference genes
for normalization of gene expression.
• Western blot analysis of insulin receptor signaling cascade including (but not limited
to) IRS-1, PI 3-kinase, Akt, GSK3, JNK, TNFalpha, and GLUT4 protein levels in
muscle, fat, and liver from human, rodent, and sheep. The Core measures activity
and phosphorylation state (tyrosine and/or serine) where appropriate. Analysis of
insulin/IGF-1 cell signaling via mTOR, p70S6 kinase and E1F2alpha and 4E-BP1 as
cellular markers for protein synthesis, including site-specific activation in tissues and
cells.
• Radioimmunoassay of hormones including insulin, leptin, adiponectin and resistin.
• Substrate determination of glucose, triglycerides and free fatty acids.
• Consult for tissue and plasma assays for plasma lipoprotein lipase (LPL) and
hormone sensitive lipase (HSL).
• Consult for hyperinsulinemic-euglycemic clamp procedures in mice and rats.
New investigators, particularly CNRU pilot awardees, are encouraged to consult with Dr.
Friedman in advance to help plan experiments involving the services listed above.
The Metabolic Core lab is also a resource for providing expertise and technology for
analysis of genetically defined mouse and rat models relevant to nutrition research. We
provide experimental support and technical advice regarding measurement of insulin
sensitivity in vivo (insulin clamps) and end organ-based metabolism (e.g. glucose and fatty
acid uptake, oxidation, and synthesis) and metabolic biochemistry (cytokines, receptor
proteins) and gene expression (RNA analysis) These services promote interaction between
investigators and foster multidisciplinary research training in clinical nutrition and obesity
across the UCD campus.
Facilities: The Metabolic Core Laboratory is located in the Center for Human Nutrition within
basic science Division of Adult Endocrinology in Dr. Friedman’s laboratory (Research
Complex 1, 7 th floor at Anschutz Medical Campus). The laboratory is 1150 sq. ft. and
includes all of the major equipment needed for research in molecular nutrition (listed below).
The lab is adjacent to a satellite animal facility set up for performing chronic animal
surgeries, energy balance, and hormone infusion studies in mice. This section of the lab
includes a general work area, surgery set-up, lamps, Harvard infusion pumps and metabolic
chamber. Within the PI’s laboratory is a designated area with water bath for performing
glucose transport studies. Across the hallway is a 150 sq. ft. tissue culture facility used for
growing human and non-human mammalian cells, including tissue culture supplies, light
microscope, CO 2 incubators, liquid nitrogen storage tank, sink, and two laminar flow
hoods. The following major items of equipment are within the PI’s lab: real-time PCR
detection system, automated RNA and protein analysis system, two PCR thermal cyclers,
high-speed refrigerated centrifuge, microfuges, horizontal and vertical gel electrophoresis
systems and power supplies, gel documentation camera equipment and computer software
for image quantification, UV spectrophotometer, walk-in cold room, three -20C freezers, and
two ultra-cold -80C freezers for storing biological samples. The following major pieces of
shared equipment are located on the floor of the PI’s laboratory: Several refrigerated
ultracentrifuges and high-speed rotors, Beckman liquid scintillation counter, autoclaves, film
developer, fluorometer, luminometer, and distilled water purification system. The PI shares
the maintenance contract on these items with other members of the department and has full
access to this equipment.
III. Management of Core Operation – Cost Effectiveness/Quality Control:
The extent of resource support requested by the investigator is discussed with the PI during
the planning stages of the project and reviewed at a meeting with the PI prior to initiation of
the project. The extent of support provided by core staff will depend largely on the type of
extramural support available for the project, with priority given to those projects for which
funds for personnel expenses are limited (pilot/exploratory studies, career development
awards, etc). Detailed plans for prioritizing samples are based on the source of funding and
the type of award, as follows:
1. Pilot project recipients and members of the research base with NIH career
development awards (K Awards)
2. Members of the research base with federal funding. The source of funding plays a
role in the prioritization as follows: 1 = federal (NIH, NSF, USDA, VAMC, AHA, ADA
etc), 2 = foundation (Aging, Liver foundation, etc), 3 = industry, investigator-initiated,
4 = industry, not investigator-initiated.
3. Investigators proposing projects to collect preliminary data for nutrition-related NIH
grant applications.
4. Members of the research base with non-federal funding for nutrition/obesity projects.
5. Members of the research base with non-federal funding for non nutrition/obesity
projects.
6. Unfunded members of the research base.
The mechanisms for monitoring budgetary overlap of current funded projects and the
Metabolic Core lab are handled by Dr. Friedman in consultation with other core directors.
This Core continues to provide services at no cost to new investigators without grant funds
and at subsidized rates for pilot awardees in order to help them compete at the national
level for independent funding. The Core lab thus provides members of the Center with
reagents, access to equipment, and exposure to new techniques that have expanded the
quantity and quality of nutrition research in the CNRU. Because CNRU investigators
continue to submit new grant applications that propose the use of the core facility, we
suggest that core activity be planned in advance whenever possible.
Consultation /Research training: Quality control is part and parcel of the services provided
by this core. Core personnel are actively involved with investigators in providing assistance
with the selection of assessment methods and the design of experimental protocols to
insure the samples we receive are of high quality. Investigators receive assistance in
determining the most appropriate assay for a specific research study. In helping each
investigator to decide on which assay is best to use, the following issues are addressed: 1)
appropriateness of assay to the study, 2) appropriateness of a given assay to the scientific
question, and 3) cost. To insure the samples we receive are treated appropriately, when
assaying insulin sensitivity in human muscle biopsies for example, we routinely send an
assistant with the investigator to ensure the first biopsies are properly dissected, frozen
immediately, or placed in RNAlater for future use. For animal studies, we make sure the
time of fasting is controlled for, and that to the extent possible, hormone treatments are
carried out in conjunction with assay of proteins to examine phosphorylation patterns. In
terms of assay quality control, for hormones we assay known standards to ensure our inter-
assay and intra-assay variability is within 5%. For Western blotting, we use internal controls
(either manufacturer’s standard or excess sample from the study) on every blot to account
for inter-blot variability, and use GAPDH as a loading control to control pipeting error and/or
transfer of protein. For gene expression analyses, we run all quantitative real-time PCR
reactions in duplicate and normalize the data to reference genes.
IV. Personnelhttp://www.uchsc.edu/nutrition/Friedman/MetabolicCoreLabPersonnel.htm
List of Reagents:
Please see Website
Metabolic Cost Service Center costs prices revised 2/6/2009
Cost Per Set
Test Name
# of Tests
per Set CNRU Members Non-Pilot Non-CNRU Member
20% discount
RNA Isolation-muscle tissue 10 $182.98 $240.06
RNA isolation-adipose tissue 10 $197.27 $254.35
RNA Analysis and Quantitation 1 $53.32 $62.84
qPCR plate charge 1 $14.09 $14.09
RNA Duplicate (probe) 1 $19.88 $22.73
RNA Duplicate (SYBR) 1 $19.32 $22.18
cDNA Synthesis 10 $43.82 $53.34
DNA Duplicate (probe) 1 $11.83 $14.68
DNA Duplicate (SYBR) 1 $10.52 $13.37
Western Blot (in-stock primary antibody) 10 $347.06 $442.20
Lipid Extraction/TG Assay 10 $121.61 $159.66
FFA Assay 10 $95.78 $110.05
Glycerol Assay 10 $35.86 $45.38
BCA assay 10 $23.51 $33.02
PI3K Assay 10 $491.86 $653.59
ELISAs:
ELISA kit (insulin, adiponectin, resistin, etc) 1 variable variable
consumables for ELISAs 1 $16.06 $16.06
Metabolic Core
From: Friedman, Jed
Sent: Thursday, October 01, 2009 3:59 PM
a) How is the quality of your measurements evaluated – quality control?
Internal standards and regular calibration with known controls provide a means of
evaluating q.c.
b) What is the turn-a-round time for the service you provide?
This depends on the waiting list and how detailed/amounts of service is required.
Generally speaking 1-2 weeks.
c) Who documents the data provided and signs off on the data?
Dr. Friedman, the core director.
d) Have you had experience providing data for industry?
Yes, but not on this campus.
e) Do you have a standard operating procedure manual?
All protocols have been painstakingly tracked for purposes of creating a cost-center.
f) How will you track billing and financial aspects of your core?
Through the Administrative core for the NIH center grant “Nutrition and Obesity
Research Center”
Molecular Discovery (IDDRC)
Directors:
Frank Frerman, PhD
303-724-3807
[email protected]
Elaine Spector, PhD
303-724-3801
[email protected]
Mission:
The objective of the Molecular Discovery Core Unit is to provide advice, training and service to
Colorado IDDRC investigators in molecular IDD research, from hypothesis generation to
characterization of macromolecules. This includes: molecular bioinformatics focused on IDD;
genome transcriptome and proteome analysis; characterization of protein structure, activity and
interactions; and access to shared instrumentation, such as centrifuges and fluorescence imaging.
Staff:
Molecular Structure
• Frank Frerman, PhD
• Robert Hodges, PhD
DNA Sequencing, Comparative Genomic Hybridization
• Elaine Spector, PhD
Vector Construction
• Wallace Chick, PhD
• Kristina Williams, BS
Bioinformatics
• Katheleen Gardiner, PhD
• Xiaolu Sturgeon, PhD
Proteomics
• Kirk Hansen, PhD
• Mark Duncan, PhD
DNA Array
• Bifeng Gao, PhD
• Mark Geraci, MD
Quantitative PCR
• Umarani Pugazhenthi
• Bryan Haugen, MD
Services:
Several of the IDDRC services are provided through cooperative agreements with other units,
such as the University of Colorado Cancer Center.
IDD-focused bioinformatics.
Contact: Katheleen Gardiner, PhD
Website:http://gfuncpathdb.ucdenver.edu/iddrc/iddrc/GeneQuest.php
Goals: To provide Center investigators and the wider scientific community with a database of
comprehensive information on genes, gene products, and signaling pathways relevant to IDD.
The database searches and tools are designed to aid both basic and clinical researchers in
discovery and integration of IDD gene knowledge and in hypothesis generation. The IDD
Bioinformatics facility is being built on “The chromosome 21 gene function and pathway
database” initially developed for studies on Down Syndrome.
Mass spectrometry (MS)/proteomics.
Contact: Kirk Hansen, PhD
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/proteomics/index.aspx
Goals: To provide high-throughput, qualitative and quantitative analysis of proteins from
tissues, cells, and fluids that can change with respect to time, physiology, and pathology. In
addition to proteomic studies, the MS section of the facility also contributes to investigations
involving small molecule analysis.
The Mass Spectrometry/Proteomics core is operated by the Program in Biomolecular Structure
and the Colorado Cancer Center.
Expression Microarray, QPCR.
Contact, DNA Array: Bifeng Gao, PhD
Contact, Quantitative PCR: Umarani Pugazhenthi
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/gene-
expression/index.aspx
Goals: To characterize IDD-related physiological, developmental, and pathological alterations in
gene expression. Access to appropriate technologies is being provided through collaborative
agreements with the Gene Expression Core of the Cancer Center.
Real-time QPCR services to IDDRC investigators are provided through a collaborative
arrangement with the Gene Expression Core of the Cancer Center directed by Bryan Haugen.
IDDRC members are invited to watch a short video on Microarrays.
For additional information, IDDRC members are invited to watch a video on Demystifying
Microarrays.
Comparative genomic hybridization (CGH).
Contact: Elaine Spector, PhD
Websites:http://www.uchsc.edu/pathology/cgl/tests.htm
http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/cytogenics/index.aspx
Goals: To analyze subtle genomic variations, such as CNVs.
Array CGH detects subtle genomic abnormalities, such as unbalanced translocations and, most
importantly, copy number variations (CNV) genome-wide. In contrast to expression arrays,
CGH uses BAC (bacterial artificial chromosome) or, in some cases, oligonucleotide arrays.
IDDRC investigators can access the facilities of the Colorado Genetics Laboratory (CGL) for
BAC-based array assays of clinical samples. This is a well-established facility providing high
quality of service (CLIA- and CAP-certified). All array analyses are performed twice, with the
dyes switched between control and test samples to confirm gains or losses of genomic material.
Array CGH and other molecular cytogenetic techniques are also available through the Cancer
Center Cytogenetics core for research samples (M. Garcia, PhD, Director). E. Spector serves as
the coordinator of these activities for members of the IDDRC.
DNA sequencing.
Contact: Elaine Spector, PhD
Goals: To provide accurate, rapid-turn-around DNA sequencing to fit the needs of the individual
investigators (from small to large scales) with economy of service. E. Spector, who also is
involved in genotyping for the Animal Models Core, in the biobanking section of the
Translational Nexus (see those core descriptions), and in array CGH, is supervising DNA
sequencing for IDDRC members. This arrangement guarantees high quality (CAP and CLIA
certifications), local service with rapid turn-around (typically 24-48 hours), and very favorable
pricing. For high-volume needs (over 96 or multiples of 96 reactions at a time) sequencing is
outsourced to a commercial sequencing laboratory. This will be coordinated by E. Spector’s
laboratory. The laboratory also carries out DNA profiling for authenticating human cell line
identity, which includes access to a large database of in-house determined profiles of common
human cell lines (see Cell Systems and Analysis).
Lipidomics and glycomics.
Contacts: Frank Frerman, PhD; Karl Pfenninger, MD
Goals: To identify and quantify lipids, fatty acids and their derivatives; and to identify
oligosaccharide sequences. This Medical School has unique strengths in these areas. Dr. Robert
C. Murphy (Department of Pharmacology) directs one of the large NIH-funded “Lipid
Metabolites and Pathways Strategy (LIPID MAPS) Centers focusing on the characterization of
lipid compounds. Dr. Brad Bendiak (Department of Cell and Developmental Biology) is a
widely recognized expert in the field of oligosaccharide analysis and sequencing. Should
significant need arise the Center plans to develop cooperative agreements with these laboratories
to make their expertise accessible to IDDRC investigators.
Vector construction.
Contact: Wallace Chick, PhD
Website:http://www.uchsc.edu/neuroscience/Program/cores.htm
Goals: To provide the IDDRC members with state-of-the-art services for the design and
generation of genetically engineered mouse models of IDD. The vector facility constructs
vectors to generate transgenic, knockout and knockin animals and vectors with tissue-specific
promotors. The IDDRC has teamed with the NINDS-funded Vector Core of the RMND Center
to provide these services. In consultation with A. Messing and Q. Chang at the Waisman Center
of the University of Wisconsin, whose core performs the cell and animal work (see Animal
Models Core), W. Chick designs the constructs that are subsequently engineered by K.
Williams. Should the need arise the IDDRC Executive Committee will determine priority for
usage of this core. Criteria for judging priority include, but are not limited to, relevance to the
goals of the IDDRC and scientific merit.
Molecular Structure Analysis.
Contact: Frank Frerman, PhD
Website:http://biomol.uchsc.edu/index.html
Goals: To provide facilities and training in biophysical methods applied for the determination of
molecular structure and interactions. This is accomplished in cooperation with the Biophysics
Laboratories, a user facility operated by the Program in Biomolecular Structure at the University
of Colorado Denver (directed by R. Hodges). Instrumentation is available for the structural
characterization of proteins and nucleic acids by chemical and thermodynamic methods. The
Biophysics Laboratories offer training (group and one-on-one) for a fee. After training,
instrument user fees are assessed. Assistance also is available for peptide synthesis, purification
by HPLC, and composition analysis. More extensive structure analyses may be arranged through
collaborations with x-ray crystallographers and NMR spectroscopists in the Biomolecular
Structure Program.
IDDRC Shared Instrumentation
The major, shared instrumentation that is currently available to Colorado IDDRC members is
listed below. The Center maintains these instruments. The equipment is located on the 4th
floor, RC1 North. For access to equipment and further information, contact Frank Frerman.
Shared Instrumentation of the IDDRC
Shimadzu UV-2401PC UV-VIS recording
spectrophotometer
Shimadzu 5301PC spectrofluorophotometer
Beckman Syetem Gold high performance liquid
chromatograph
Hewlett-Packard 89090A diode array spectrophotometer
General Electric Acta FPLC
Savant lyophilizer
Beckman LS 3801 liquid scintillation counter
Beckman TL-100 ultracentrifuge
Beckman J-21 centrifuge
2 Beckman J-25 (Avanti) centrifuges
Beckman L8-M ultracentrifuge
For fluorescence imaging Colorado IDDRC members have access to a General Electric Typhoon
9410 multi-mode fluorescence laser scanner/phosphorimager. This instrument, equipped with
three lasers and capable of scanning gels, blots, storage phosphor screens, tissue sections, and
multi-well plates is located in the area occupied by the Biomolecular Structure Program and
easily accessible to Center members.
User Fees:
Services Fee for IDDRC
Member
Fee for Non-Member Contact
DNA Sequencing
Small Scale
$5.25/reaction $7.00/reaction Elaine Spector,
PhD
DNA Sequencing
Large Scale
$2.20/reaction for
multiples of ³ 96 PCR
reactions
Please inquire Elaine Spector,
PhD
IDD Bioinformatics No charge No charge Katheleen
Gardiner, PhD
Mass Spectrometry/
Proteomics
Instrument time charge
only
$1300 prep fees + $65-$100
instrument time per sample
Kirk Hansen,
PhD
Expression
Microarray
20% discount of
standard rate
$1000/sample (covers RNA
prep, RNA quality control,
analysis)
Bifeng Gao,
PhD
Quantitative PCR 30% discount of
standard rate
Please inquire Umarani
Pugazhenthi
Comparative
Genomic
Hybridization
Please inquire Elaine Spector,
PhD
Vector Construction $1500/vector Please inquire Wallace Chick,
Morphology and Phenotyping Core
Contacts:
Maranke Koster, PhD
Director
303-724-1640
[email protected]
Laura Hoaglin
Histology Technician
303-724-0528
[email protected]
Website:http://www.uchsc.edu/stemcell/resources/histo.htm
Although the Morphology and Phenotyping Core specializes in
processing and analyzing skin samples, it has expertise in the
processing of all types of tissues
Although all tissue samples can be processed by the Core, the Core particularly specializes in
skin samples. For instructions on preparing skin samples for histological processing, please see
below:
Harvesting skin samples for histological analysis
1. Samples for paraffin embedding
General:
Make sure that the volume of formalin used for fixing the tissue equals >10x the volume of the
sample. Fix your s amples i n 10% neutral buf fered f ormalin (NBF) O/N at 4°C. The next day,
replace the formalin with 70% EtOH and keep the sample at 4°C.
Fill o ut th e requisition f orm a nd email it to Laura Hoaglin ( [email protected]).
Leave your s amples i n Maranke Koster’s f ridge i n t he hallway ( RC-1N 8th floor, across from
P18-8403E). Make sure your samples are clearly labeled with your initials, the date, and sample
ID.
Back skin (E17.5-adult mice):
Within the same experiment, skin samples should be harvested from the same area of the body.
Often, t he ba ck of t he mouse i s c hosen f or t his pur pose. If you a re us ing ba ck s kin, t ake t he
biopsy f rom t he middle of t he b ack ( on t op of t he s pine) midway b etween t he h ead a nd t ail.
Using a r azor bl ade or s calpel, t rim t he bi opsy i nto a r ectangle, s uch t hat t he long axis of t he
rectangle corresponds to the A-P axis of the mouse. Unless otherwise indicated, the biopsy will
be sectioned along the long axis of the rectangle. If sectioned this way, your sections will provide
a good view of the interfollicular epidermis as well as the hair follicles. If you prefer sectioning
along a different axis, please indicate this clearly on the requisition form.
Place your rectangular piece of skin flat on a piece of Whatman filter paper or unlined index card
(dermis side down). This will ensure that the skin sample will remain flat while it is fixing. Then
place the paper with the skin in 10% neutral buffered formalin and proceed as above.
Embryonic skin (up to E16.5):
For e mbryos up t o E 16.5, f ix the e ntire e mbryo r ather than a ttempting t o r emove t he s kin.
Carefully dissect the embryo free from extraembryonic tissues, place it in 10% NBF or Bouin’s
fixative, and proceed as above.
Unless otherwise indicated, embryos will be sectioned from the midline along the sagittal axis.
Ear skin:
Remove the entire ear of an adult mouse and trim the biopsy into a rectangle, such that the long
axis of the rectangle is perpendicular to the head of the mouse.
Tumors:
After dissecting out the tumor, trim the tumor to prepare a biopsy with at least one straight edge.
The straight edge will be the cutting edge of the sample. If possible, the cutting edge should be
perpendicular to the skin of the mouse, such that your section will contain the most superficial as
well as the most basal part of the tumor.
1. Samples for OCT embedding
If you ha ve n ever e mbedded s kin i n O CT, pl ease c ontact M aranke K oster
([email protected]) for help with your first sample.
As a general guideline, prepare t he skin sample as above ( i.e. r ectangular pieces of back skin,
etc). Since the sample will be sectioned from the bottom of the cryomold, your sample should be
placed in the cryomold accordingly. For example, rectangular pieces of back skin must be placed
on the bottom of the cryomold on the edge of the long side (see figure [drawn by Irene Choi]).
Slowly fill the cryomold with OCT and place the sample in the middle of the cryomold. Once
you have pos itioned t he bi opsy i n OCT, make s ure t o r emove any bubbles t hat may s urround
your t issue, as t hey can cause pr oblems with cutting. You can r emove t he bubbl es with a t hin
needle. Place the cryomold + OCT + biopsy on dry ice to allow the OCT to freeze (it will turn
white). Once the OCT is frozen, store your samples at -80°C.
Embryos must be pr ocessed t hrough a s ucrose gradient pr ior t o e mbedding i n OCT. P lease
contact Maranke Koster for the protocol.
After embedding your s amples, f ill o ut th e r equisition f orm and e mail it to Laura
([email protected]). Leave the samples in a box labeled with your initials, date and
sample ID on t he t op s helf i n Maranke Koster’s -80°C freezer (RC-1N 8th floor, across from
P18-8212).
1. Further information
For more information on the use of different fixatives and on processing skin tissue:
Seymour R, Ichiki T, Mikaelian I, Boggess D, Silva KA, and Sundberg JP. 2004. Necropsy
Methods. In: Handbook of Experimental Animals: The Laboratory Mouse, Hedrich HJ (ed),
Academic Press, London, pp 495-516.
Core services include assistance with skin harvesting, preparation of paraffin blocks, sectioning
of paraffin and frozen blocks, and standard H&E histology.
For a histology request form, please go to website.
The following services are available:
Paraffin histology Regular price
*SDRC
Member
Processing and embedding (per sample) $12.00 $5.50
One unstained slide (per slide) $3.50 $1.75
H&E staining (per slide) $6.50 $3.25
Frozen section histology Regular price
*SDRC
Member
First unstained slide (per block) $10.00 $5.00
Additional unstained slides (per slide) $2.75 $1.50
H&E or toludine blue staining (per slide) $6.50 $3.25
* Skin Diseases Research Core Center Member Price
Please see the Pathology Shared Core (University of Colorado Cancer Center) for more
general dermal and tissue pathology services.
Morphology and Phenotyping Core
From: Koster, Maranke
Sent: Monday, November 02, 2009 8:43 AM
a) How is the quality of your measurements evaluated – quality control?
To ensure that investigators receive high quality skin sections, each Core user will receive
detailed instructions on harvesting and fixing skin/epithelial samples for histology. In
addition, reagents and equipment used for histological processing will be subject to quality
control. Reagents will be maintained and stored as specified by the manufacturer and
disposed of on expiration. In addition, equipment will be maintained and serviced on a
regular basis by a certified technician. Specifically, the tissue processor will be cleaned
daily, alcohols will be rotated every 100 blocks, all reagents will be changed every 400
blocks, and preventive maintenance will be performed annually. The embedding center will
be cleaned daily, the paraffin will be changed and refilled as needed, and preventive
maintenance will be performed annually. The microtome will be cleaned daily and
preventive maintenance will be performed annually. The paraffin pot will be emptied and
cleaned monthly.
Annual surveys will distributed to Core users to evaluate the quality of the current
services and to inquire about interests in new services.
b) What is the turn-a-round time for the service you provide?
The regular turn-around time is approximately 1-3 weeks (depending on the
workload). We also offer expedite processing, with a guaranteed 72-hour
turnaround time.
c) Who documents the data provided and signs off on the data?
The histology technician. If any questions arise regarding quality or billing, the Core
director will respond to these.
d) Have you had experience providing data for industry?
No
e) Do you have a standard operating procedure manual?
We do not have this at this time. We could certainly make one though.
f) How will you track billing and financial aspects of your core?
We maintain a database in which all service requests (and their costs) are entered.
Each month, we generate a billing statement for each Core user, which includes all
rendered services and their cost. Services are paid for by Interdepartmental
Invoices, and the funds are deposited in our service center account.
Mucosal and Vaccine Research Colorado (MAVRC)
Flow Cytometry Core Facility
Edward N. Janoff, MD
Director
Phone: 303-724-8499
Fax: 303-724-0802
[email protected]
Contact: Melissa Keays
303-399-8020 x3497
[email protected]
http://www.ucdenver.edu/academics/colleges/medicine/research/MAVRC/ResearchResources/S
haredFacilities/Pages/MAVRCCoreFacilities.aspx
The MAVRC/Denver VA Flow Cytometry Core is a user-supported facility purchased by
the VA (VA Eastern Colorado Health Care System) in January 2009. Located in Building
23 at the Denver Veteran's Administration, 1055 Clermont Street, the 3-laser instrument
evaluates from 1-14 colors, size and granularity of cells.
After initial training, the instrument can be operated successfully by laboratory personnel
without a core operator, although assistance is available from the Core Supervisor.
LSR II Flow Cytometer 3-Laser Configuration:
Each lettered circle represents a photomultiplier tube (PMT). The rectangle closest to the PMT is the
"high pass" filter that shows the range of wavelengths passing through the filter (e.g., 780/60 = 750-
810?). The lower rectangle is the "long pass" filter that shows the highest wavelength emitted to the next
alphabetical PMT (e.g, 755 LP). Additional filters: 635 LP; 600LP; 670/14; 610/20; and 585/42.
BILLING:
LSRII VA user $60/hr x ____ hours = $______
Alone: Non-VA user $80/hr x ____ hours = $______
LSRII VA user $75/hr x ____ hours = $______
Assisted: Non-VA user $90/hr x ____ hours = $______
** Charges are applied in 15 minute increments **
** Cancellations less than 24 hours prior will be charged 40% of reservation **
VA/MAVRC user____ Non-VA/MAVRC user____
SAMPLES:
Cell type/source: Human: Other:
Number of tubes:
Concentration:
Volume/tube:
Infected (e.g. HBV, HCV, EBV, HIV, etc.)? Yes ____ No ____
Fixed in at least 1% Paraformaldehyde? (Required) Yes ____
BILLING:
LSRII VA user $60/hour x ____ hours = $______
Alone: Non-VA user $80/hour x ____ hours = $______
LSRII VA user $75/hr x ____ hours = $______
Assisted: Non-VA user $90/hr x ____ hours = $______
Date: Time in: Time out:
User Name:
Billing Address:
User Email:
User Phone:
PI Name:
VA Grant Name or Speedtype:
VA Grant Name ____________ UCD Speedtype ____________
Department/Administrator contact:
Name: Email: Phone:
Eastern Colorado Health Care System, Denver VAMC
Mucosal and Vaccine Research Colorado (MAVRC)
FLOW CYTOMETRY CORE FACILITY
Billing Form
** Charges are applied in 15 minute increments **
** Cancellations less than 24 hours prior will be charged 40% of reservation **
Mucosal & Vaccine Research Ctr.
From: Janoff, Edward
Sent: Tuesday, November 03, 2009 10:43 PM
a) How is the quality of your measurements evaluated – quality control?
We test and record internal validation of the B-D LSR II flow cytometry daily and use
standardized fluorescent beads daily as well to standardize the equipment.
b) What is the turn-a-round time for the service you provide?
Samples can typically be run the same day
c) Who documents the data provided and signs off on the data?
The core supervisor reviews and validates all data run by the core technicians. Most
investigators test their own samples after instruction on the instrument's use.
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Not as yet.
f) How will you track billing and financial aspects of your core?
Investigators can be billed on University Speed types.
Pathology Shared Core Service
University of Colorado Cancer Center
Contacts:
Wilbur Franklin, MD, PhD
Director
[email protected]
303-724-3080
Jennifer Richer, PhD
Co-Director
[email protected]
303-724-3735
M. Scott Lucia, MD
Co-Director
[email protected]
303-724-3470
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/pathology/pathology.aspx
The University of Colorado Cancer Center Pathology Core ensures that well-characterized
human tumors and materials derived from human tumors to are provided to Cancer Center and
other funded investigators for research in human cancer. The Pathology Core:
1. Establishes priorities for tissue collection. With the support of the Core, members of the
UCCC have obtained separate funding to support large organ-based repositories
2. Serves as a central planning resource for these separate repositories
3. Interacts with the Biostatistics/informatics and Clinical Investigation Cores to provide an
optimal infrastructure for the conduct of translation research
4. Provides supplemental and backup support for the repositories
5. Offers diagnostic assistance and tissue processing services, including histological and
immunohistochemical services, to Cancer Center investigators who are not supported by
a separate tissue bank
The Core provides central infrastructure for separately funded banks that are increasing in
number and sophistication. In 2007, the Southwest Oncology Group solid tumor banks moved
entirely to Colorado.
Tissue Procurement Shared Core Service
The Tissue Procurement Core provides University of Colorado Cancer Center members and
other funded researchers with well-characterized human tumors and materials derived from
human tumors for research in human cancer. Our organ-based pathology subspecialists
contribute anatomic expertise to organizing collection protocols and verify histopathological
classification of specimens we collect.
We provide investigators with IRB-approved protocols and pathology subspecialist collaborators
with:
• frozen tissue fragments
• tissue sections
• DNA
• RNA
• cells purified by microdissection from tumors, preneoplastic lesions and matched normal
control tissue
Services We Provide
• Tissue grossing
• Tissue processing
• Tissue embedding
• Cutting paraffin and frozen sections
• HE staining
• Cell line fixation, including cell pallet creation
• Tissue array block creation from donor blocks
• Tissue array cutting
• Special cutting and staining sections for microdissection
• Immunohistochemistry staining, including antibody standardizations
• Tunnel assay staining
• Histology special stains #88312 & 88313
• Ventana Benchmark XT for automated immunohistochemistry
Turnaround time depends on the specimen or project. Please contact Betsy Baker for a time
estimate for your project.
Equipment
• Ventana Benchmark XT for automated IHC
• Tissue-Tek Vacuum Infiltration Processor
• Microm Tissue Embedding Unit
• Microm Paraffin Microtome
• Biocare Medical Decloaking Chamber for Antigen Retrieval
• Fisher Tissue Prep Flotation Bath for Paraffin Sections
• Thermo Shandon Slide Heater-Oven
• Fisher Isotemp 205 Water Bath for heating up reagents
• Fisher Isotemp Table Top Oven for Reagent Incuvation
• Forma Liquid Nitrogen Freezer with Inventory Storage System
Tissue Procurement Prices
The Tissue Procurement Core offers discounts to University of Colorado Cancer Center
Members. Other investigators are also welcome to use our services.
Description of Procedures
Cancer Center Member
Price
Non-Cancer Center Member
Price
Grossing $ 1.00 $ 2.00
Processing $ 4.00 $ 6.00
Embedding $ 2.00 $ 4.00
Cutting blanks $ 1.00 $ 4.00
HE stain from slide $ 4.00 $ 5.00
Special Fixation of Cell lines $ 2.00 $ 14.00
Cell Pallet Creation $ 1.00 $ 14.00
Tissue Array Block Creation $ 49.00 $ 554.00
Cut Tissue Array $ 4.00 $ 8.00
Cut 10µm blanks for
Micordissection
$ 1.00 $ 5.00
Stain blanks for Micro-dissection $ 3.00 $ 10.00
Cut 50µm rolls for DNA
extraction
$ 1.00 $ 2.00
Cytospins $ 1.00 $ 3.00
Remove Coverslips $ - $ 2.00
Cut 1st blank - Frozen $ 11.00 $ 24.00
Cut addn blanks - Frozen $ 2.00 $ 7.00
Cut-Stain (HE) - Frozen $ 16.00 $ 34.00
Manual IHC Stain $ 25.00 $ 68.00
Automated IHC Stain $ 24.00 $ 59.00
Tunnel Assay $ 8.00 $ 33.00
Scraping Microdissection $ 38.00 $ 38.00
Laser Microdissection - Manual $ 66.00 $ 66.00
Laser Microdissection -
Automated
$ 59.00 $ 59.00
Tissue Request $ 2.00 $ 28.00
Core Punch from FFPE Block $ 3.00 $ 16.00
DNA Extraction $ 20.00 $ 148.00
Lightcycler HRM Screening $ 18.00 $ 171.00
Direct Sequencing of Mutations $ 23.00 $ 279.00
Prices effective 7/1/08 to 6/30/09
Please see the Morphology and Phenotyping Core for specialty dermal and tissue pathology
services.
Peptide and Protein Chemistry Core
Contacts:
Robert Hodges, PhD
Director
303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
RC-1 South Tower, Room 9121
[email protected]
Dziuleta Cepeniene,
Operations Specialist
Voice: 303-724-3336
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
Website:http://biomol.uchsc.edu/cores/peptidechem/main.html
The Peptide and Protein Chemistry core at the University of Colorado Fitzsimons campus
provides peptide synthesis, purification and peptide/protein composition analysis as well as mass
spectrometry services for academic and industrial clients.
The Peptide and Protein Chemistry core personnel help users choose and design experiments
using appropriate chemistry/instrumentation, to obtain the necessary data, and interpret the
results. The Core also provides instruction for graduate students and postdoctoral fellows for the
use of HPLC and LC/MS approaches.
The core is equipped with state of the art instrumentation and technical support suitable for
diverse applications and samples.
Rates
PEPTIDE SYNTHESIS
• Minimum charge is for 10 residues ($250)
• 0.1 mM scale (50-100 mg crude peptide): $25 per residue
• 0.25 mM scale (100-300 mg crude peptide): $40 per residue
• All peptides are cleaved from the resin, resolubilized in appropriate solvent, and analyzed
by reversed phase HPLC and mass spectrometry
• Preparative HPLC purification of synthetic peptides: $100 per peptide
• Additional modification of peptides:
o phosphorylation: $100 - $150
o acetylation: $15
o C-terminal biotin: $175
o fluorescent label: $200
o N-terminal biotin: $100
o methylation: $175 - $400
AMINO ACID ANALYSIS
• $40 per sample
MASS SPECTROMETRY
• Mass determination of peptides by LC/MS: $15 per sample, $100/hour
• LC/MS/MS analysis: $30 per sample, $100/hour
Pharmacology Core
Contacts:
Daniel L. Gustafson, PhD,
Director
[email protected]
970-297-1278
Ryan J. Hansen, Ph.D.
[email protected]
Brad Samber
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/pharmacology/index.aspx
The University of Colorado Cancer Center Pharmacology Core, located at Colorado State
University in Fort Collins, was established to work with researchers and clinicians in a
collaborative manner to design and implement studies to measure xenobiotics (drugs, toxicants,
natural products, inc.) in biological systems and matrices.
• We are an analytical laboratory focused on drug measurement.
• We help investigators with study design, sample collection, sample analysis and data
interpretation.
The mission of the Pharmacology Core is to assist in the prospective design of studies to assess
drug exposure in biological systems, to measure drug levels using validated analytical assays,
and to analyze, model and interpret the results.
Pharmacology Core Services
We offer services based on our experience with use requests through our years of operation. We
regularly modify the services we offer depending on Cancer Center members' needs and how
they use the Core. We offer members discounted fees for service, which are calculated either per
sample or on an hourly basis.
We offer the following services.
1. Analyte determination and quantitation in matrix (per sample)
2. Assay setup and validation (hourly)
3. Metabolite identification and analysis (hourly)
4. Sample analysis and identification (hourly)
5. Pharmacokinetic modeling (hourly)
6. Animal treatment and sampling (hourly)
How to Order Services
To order services, you will need to consult with either the Core Director or Core Personnel by
telephone or email. See the contact panel on the right for phone and email information.
Prices
The cost for various core services is based on either hourly charges or per sample charges
depending on the requested service. For the quantitation of an analyte in a submitted sample,
prices depend on whether we have a validated assay for that analyte and the number of samples
submitted. Listed below is our current pricing structure:
Service UCCC Member UCCC Non-Member
Analyte Quantitation (per sample)
Batch size 1 - 40 samples $78.35 $126.44
Batch size 41 – 500 samples $45.00 $72.62
500+ samples Contact for Quote
Assay Setup and Validation (per hour)
$144.75 $204.54
Metabolite ID and Analysis (per hour)
$225.36 $333.50
Sample Analysis and ID (per hour)
$225.36 $333.50
Pharmacokinetic Modeling (per hour)
$64.40 $159.89
Animal Treatment and sampling (per hour)
Contact for Quote
*Batch size is determined by the number of samples expected to be analyzed at a given time. For
example, if a study includes a total of 200 samples but are shipped to us and expected to be
analyzed in groups of 20 for data reporting, the batch size is 20.
The Pregnancy Core
Peggy Neville, PhD
303-724-3505
[email protected]
The Pregnancy Core in the Department of Ob/GYN is designed to assist researchers from all
departments at University of Colorado Denver with their research on pregnant women and
eventually their offspring. We offer assistance with recruiting of subjects in a number of venues,
a biological sample repository with facilities for bar coded samples is available at cost, services
on labor and delivery including cord blood and placental samples, a database with about 500
variables collected on all subjects who deliver at University Hospital, information on studies
conducted on the adult CTRC on pregnant women. Use of these facilities is subject to project
review by the OB/GYN Research Review Committee and relevant fees will be charged for most
services. For additional information please contact [email protected].
University of Colorado Cancer Center
Protein Production/MoAB/Tissue Culture
Shared Core Service
Contacts:
Steve Nordeen, PhD
Director
[email protected]
303-724-4301
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/tissue-
culture/index.aspx
The Protein Production/MoAB/Tissue Culture Core, located on the Anschutz Medical Campus,
offers services to UCCC members, other academic investigators and private companies. We have
more than 10 years of experience with protein production in the baculovirus system cell fusion,
as well as developing new monoclonal antibodies and small- to large-scale culture of a wide
range of cell lines.
Services We Offer
Custom Hybridoma Services
• Construction of new hybridomas
• In vitro production of monoclonal antibodies from existing hybridomas
Custom Baculovirus Services
• Construction of recombinant virus
• Amplification and titering of recombinant baculovirus stocks
• Protein production in insect cells
Cell Line Repository
• >150 cancer cell lines, including 51 different lung cancer cell lines and 11 breast cancer
cell lines
On-Site Culture Media/Serum Supply Center
Offered to all UCCC and UC Denver investigators at prices substantially below list
• Liquid cell culture medium from Invitrogen and HyClone
• Supplements
• Serum from HyClone
Tissue Culture & Monoclonal Antibody Core
Prices
Members
Non-
Members
Commercial
Baculovirus
Co-transfection $95 $470 $940
Bacmid Transfection $132 $208 $417
Titer a virus $18 $66 $133
Plaque Purify Existing Viral Stock $53 $248 $495
Produce 500 ml viral stock $126 $450 $899
150 ml protein production $36 $162 $324
300 ml protein production $49 $176 $351
500 ml protein production $67 $199 $398
2.0 liter bioreactor $258 $470 $939
5.0 Liter bioreactor $428 $664 $1,328
Fusions
Mouse Injections and Bleeds/Animal $216 $286 $572
Fusion including ELISA screenings $541 $1,210 $2,421
Cloning of 1 positive hybridoma $117 $380 $760
Isotyping/hybridoma $2 $12 $24
Freeze additional 1 polyclonal-2
ampules
$43 $139 $279
Storage for 1 year of 6 ampules of 1
hybridoma
$16 $63 $126
Monoclonal Antibody Production
Produce 1-4 liters of hybridoma supt./
liter
$146 $348 $697
Produce 5 - 20 liters of hybridoma supt./
liter
$112 $179 $358
Hybridoma CL1000 Startup $162 $254 $508
Hybridoma CL1000 10weeks culture $1,066 $1,529 $3,059
Purification of hybridoma supt. for 1-4L $290 $484 $967
Purification of hybridoma supt 5L $557 $842 $1,685
Cell Culture
Freeze six ampule of 1 cell line $81 $180 $361
Cell lines - live cultures $51 $124 $248
Cell lines - frozen ampule $17 $65 $130
Mycoplasma Test $24 $45 $90
Mammalian Transfection and Large Scale Cell
Culture
Mammalian Cell Stable Transfection $270 $627 $1,254
Freeze down of additional 1
Mammalian Stables
$60 $132 $264
Cloning of 1 positive Mammalian
Stables
$203 $473 $947
Produce 1-4 liters of cell culture/liter $187 $287 $574
Produce 5-20 liters of cell culture/liter $90 $152 $305
CL1000 Flask Start up $259 $305 $609
CL1000 culture/week $84 $166 $331
Prices effective 07/01/08-06/30/09
Protein Production/MoAB/Tissue Culture Shared Core Service (UCCC)
From: Nordeen, Steve
Sent: Friday, October 02, 2009 2:46 PM
a) How is the quality of your measurements evaluated – quality control?
We provide more product than measurements and most of the evaluation of
that is done by the end users since each it specific for the individual lab and
project.
b) What is the turn-a-round time for the service you provide?
From consultation with the core and submission of the request projects are
begun from one day to 4-6 weeks depending on the project. The longer times
are for production of protein via baculovirus and we have purchased new
equipment and hired a part time technician recently in order to decrease the
waiting time on these projects. The actual projects may take less than a day
to 3 or 4 months depending on the project.
c) Who documents the data provided and signs off on the data?
Data is collected by the technical staff doing the production.
d) Have you had experience providing data for industry?
We have several industrial clients.
e) Do you have a standard operating procedure manual?
Yes
f) How will you track billing and financial aspects of your core?
The Lab Manager fills out the invoices and the Cancer Center administration
does the billing. We work closely with the Cancer Center administrative
staff on our budgets.
price list:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/tissue-
culture/prices.aspx
Mass Spectrometry/Proteomics Core Facility and Cancer Center
Proteomics Shared Core Service
Contacts:
Mark Duncan, PhD
Co-Director
[email protected]
303-724-3343
Natalie Ahn, PhD
Co-Director
[email protected]
303-492-4799
Kirk Hansen, PhD
Anschutz Facility Core
Manager
[email protected]
303 724-3325
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/proteomics/index.aspx
The University of Colorado Cancer Center's Proteomics Shared Core Service aims to provide the
expertise, technical resources, training and collaborative interactions that enable Cancer Center
members to undertake detailed proteomic studies.
Cancer Center members have access to proteomics labs on two campuses:
• Anschutz Medical Campus
• Boulder Campus -http://www.colorado.edu/Chemistry/masspec/
Overview
The goal of the Proteomics Facility is to provide investigators with the capabilities to identify,
characterize and quantify the proteins present in tissues, cells and biological fluids. Through the
development of advanced methods, the Facility aims to assist members with solving difficult or
previously intractable problems in biomedical research. Methods for protein and peptide
isolation, separations, quantification, identification and bioinformatics analysis, together with
expert guidance in study design, are integrated into expertise offered by the Facility. The Facility
has access to several analytical technologies thereby allowing investigators to adopt multiple
strategies and to independently verify their findings. The Facility also provides training in
proteomics analysis and experimental design
Facility Fees
A charge is applied to all users of the resource to offset, the running costs associated with
maintaining this facility. Details of the fees are given in the following table.
Trained Individuals may use equipment in the facility at the following rates:
Equipment Usage (Trained Personel) Cancer
Center
Member
Non-
Member
2D Gel Electrophoresis Contact Facility
Protein Chromatography $55 $80
MALDI-TOF (per hr) $25 $35
LC/MS/MS ion trap (per hr) $58 $80
LC/MS/MS Qq-TOF (per hr) Contact Facility
Analysis Cancer
Center
Member
Non-
Member
Sample Preparation $18 $283
Protein Separation 1D-GE $25 $111
Protein Seperation 2D-GE $200 $588
Protein Separation 2D-LC $34 $211
Protein ID by Peptide Mass ID-MS $10 $78
Protein ID by Tandem Mass ID-MSMS $58 $200
Protein Molecular Weight Determination $44 $191
RADScIence Clinical Trial Physics Support
Ann Scherzinger, PhD
Chief, Division of Radiological Sciences
Department of Radiology, C-278
U of Colorado Denver, School of Medicine, Anschutz Medical Campus
Aurora, CO 80045
303-724-3766http://www.uchsc.edu/ucbirl/index.php
If your core business isn’t the assessment of radiological images or the use of radiation, how
do you effectively evaluate a centralized radiology reading center, provide IRBs and
regulatory agencies with safety information, or assess novel imaging techniques or analyses?
What HIPAA issues and technology hurdles will impact your operations and data submission
timelines? RadScience can provide valuable insight during the due diligence and startup
processes.
DCE-MRI, TOF PET, fMRI....
If you're awash in a sea of strange acronyms and technology, we can help. RadScience
provides quality educational services to transform even the most daunting technologies into a
concise, comprehensible framework. Whether you need support for your clinical development
group, CRAs, medical writers or investigators, trust RadScience to keep you informed and
educated in the fast-paced world of medical imaging and radiation technology.
Protocol Development and Quality Control
A new imaging technique looks promising for your clinical study. But what are the pitfalls of
implementing it in a multi-site environment? What factors may bias the results or drown out
that important signal with noise? If you’re going to invest in an imaging biomarker, consult
with RadScience regarding protocol feasibility, optimization and quality control issues and
services.
Dosimetry Services
Don’t try looking it up in a book. With the advent of multi-slice CT, dual modality systems
and increasingly complicated imaging protocols, estimating patient radiation dose can be a
daunting task. RadScience provides concise, accurate dose estimates for your imaging studies
that can be submitted for IRB and regulatory review.
Risk Analysis
So you know the radiation dose, but what does that mean? Age, organ type, exposure duration
and frequency are just some of the factors that can influence health risks. Know the risks
associated with your imaging study so you can better inform your subjects and comply with
GCP requirements.
Fees:
Under Construction
Research Design and Analysis Core
Contacts:
Samantha MaWhinney, ScD
Core Director
303-724-4368
[email protected]
Website:http://www.uchsc.edu/ccfar/cores/virology.htm
The Research Design and Analysis Core (RD&A) within the Colorado Center for AIDS
Research (CFAR) provides assistance with HIV/AIDS-related grant applications. Limited
statistical consulting is available to CFAR members for $75 per hour. Overflow is directed to
the Colorado Biostatistics Consortium for $125 per hour. Statistical training and mentoring
opportunities include short courses, lectures and online tutorials. The RD&A Core is in the
process of integrating these educational programs with the Colorado CTSI.
The overall goal of the CFAR Research Design and Analysis Core is to assist researchers across
a wide range of specialties in their goal of a scientifically rigorous approach to understanding
and preventing HIV-1 disease. Assistance will be provided through consulting, training,
communication and research collaboration. We will employ the most appropriate methods
combined with graphical summaries to aid interpretation. We strive to enhance the biostatistical
contribution to HIV/AIDS research within the Colorado CFAR through better understanding of
HIV/AIDS immunology, virology and laboratory assays. We will develop new methods and
pursue new research agendas in Epidemiology and Community Health to increase the quality and
breadth of HIV/AIDS research in Colorado.
The Research Design and Analysis Core will expand the range of Biostatistical, Epidemiological and
Community Health services for D-CFAR investigators. We will offer educational opportunities,
training and mentoring to junior faculty; and provide leadership in research design and analysis in
concert with a public health perspective to the overall D-CFAR. Motivated by interdisciplinary work
we will develop innovative analytic approaches to identify research gaps and further HIV/AIDS
research in Colorado.
The Research Design and Analysis Core (RD&A) within the Colorado Center for AIDS
Research (CFAR) provides assistance with HIV/AIDS-related grant applications. Limited
statistical consulting is available to CFAR members for $75 per hour. Overflow is directed to
the Colorado Biostatistics Consortium for $125 per hour. Statistical training and mentoring
opportunities include short courses, lectures and online tutorials. The RD&A Core is in the
process of integrating these educational programs with the Colorado CTSI.
Research Design & Analysis Core (CFAR)
From: MaWhinney, Sam
Sent: Monday, November 09, 2009 2:35 PM
For the CFAR Research Design and Analysis Core (Sam MaWhinney, Core Director)
a) How is the quality of your measurements evaluated – quality control?
Biostatistical Services: Not applicable
b) What is the turn-a-round time for the service you provide?
Services related to study design for grants get priority, but we try to meet with
investigators within a few days of receiving requests. Projects then range from a
few hours to months.
c) Who documents the data provided and signs off on the data?
The primary investigator for the project is responsible for data integrity. We
generally do logical checks and graphical analyses to identify data outliers, which
will be double checked for accuracy.
d) Have you had experience providing data for industry?
Not through the CFAR RD&A core
e) Do you have a standard operating procedure manual?
No
f) How will you track billing and financial aspects of your core?
We have a charge back system.
Rodent Neurophysiology
Contact:
Yogendra Raol, PhD
Director
University of Colorado Denver- Anschutz Medical Campus
303-724-4257
[email protected]http://www.uchsc.edu/peds/research/cores/RIVNC.pdf
The UCD Rodent I n Vivo Neurophysiology Core
The c ore f acility p rovides c ontinuous r odent be havioral a nd ne urophysiological/EEG
monitoring ( including c erebral e lectrical pa tterns dur ing w aking a nd s leep, he art r ate,
respiration, E MG). T his t ype o f mo nitoring will p ermit in vestigators a t U CD to mo re
thoroughly ph enotype t he r odents t hey are us ing i n t heir r esearch a nd s pecifically address
issues of whether they have abnormalities of neurophysiological functioning such as interictal
epileptiform di scharges, s leep di sturbances and s eizures. T his c an be i mportant f or t he
characterization of translational models of nervous system disorders including stroke, epilepsy,
head trauma, neurodegenerative, psychiatric, genetic and developmental disorders. Equipment
available i n t he R odent In V ivo N europhysiology M onitoring C ore f acility i ncludes a n
inhalational anesthesia system, Angle 2 stereotactic apparatus with rat and mouse at lases and
video microscope for electrode placement and cerebral injections, microinfusion pump, and 48
cages ( 32 r at a nd 16 m ouse) e quipped f or vi deo_EEG m onitoring ( Stellate a nd P innacle
systems).
Core Personnel
Yogendra H. Raol, PhD (Director) is an Assistant Professor in the Department of Pediatrics,
School of Medicine. Dr. Raol has over 14 years of experience with in vivo neurophysiological
recording in rodents. Dr. Raol is responsible for the management of the daily operations of the
core facility, and training and supervision of the technicians.
Doron Shmueli, is a technician for the core. He obtained his BS degree i n Engineering from
the University o f Colorado. Doron i s a n e xpert i n i ntracranial electrode i mplantation, EEG
recording an d an alyses and was t rained with n eurologist Dr. Andy White a t University of
Colorado Denver.
Services Rate
Neurophysiology/EEG monitoring $8.35/day
Electrode implantation surgery $140/procedure
(surgery performed by core personnel)
Use of surgical supplies/facilities for $46/procedure
electrode implantation
(surgery perform by investigator)
1
Shared Analytical Service Laboratory (SASL)
J eff Boon
Laboratory Manager
303-556-2964
J [email protected]
http://thunder1.cudenver.edu/clas/sasl/index.html
Oversight Committee:
Dr. Dave Albeck, Department of Psychology
Dr. Larry Anderson, Department of Chemistry
Dr. Timberly Roane, Department of Biology
- Mission Statement -
The Shared Analytical Services Laboratory provides basic and analytical chemistry related
resources, including advanced analytical instrumentation. With the increase in the
interdisciplinary nature of research, the SASL supports the analytical chemistry needs across all
scientific disciplines. Additionally, the continuing effort to more efficiently use University
resources has created a demand for sharing resources.
The SASL allows researchers from a variety of disciplines to utilize analytical tools without
having to invest time, money, or resources towards maintaining the effort in their own research
groups. At the same time, the Laboratory allows faculty the freedom from duplicating
instrumentation and other resources that are used only peripherally. Finally, the SASL works to
support the efforts of the other colleges of the UCD, and to support the wider community.
- Instrumentation -
The following instrumentation is available for use in the Shared Analytical Service Laboratory.
While this equipment is fully functional, in some cases, like the gas and ion chromatographs and
the Hitachi GFAA, instruments have been shut down to save on the cost of the consumables.
Restarting the instrument may take several days before it would be ready for analytical use.
Perkin Elmer Model 5000 Flame Atomic Absorption Spectrophotometer – The flame
AA is a quick, easy, and inexpensive method to determine the concentration of a metal in
a liquid sample. The detection limits for the AA are dependent on the desired analyte and
the sample matrix, but are typically in the low parts-per-million range. Solid samples,
and some samples with complex matrices (i.e. blood), must be digested prior to
performing the analysis.
Hitachi Z-8270 Polarized Zeeman Graphite Furnace Atomic Absorbance
Spectrophotometer - Like the PE 5000 AA, the Hitachi GFAA is used to determine the
2
concentration of a metal in a sample. Unlike the PE 5000, which uses a flame to atomize
the metal species, the Hitachi uses an electrically heated graphite tube to turn the solvated
metal species into gaseous metal atoms, for analysis. The Hitachi uses a very small
aliquot of the sample (20 microliters for most analysis) and has detection limits in the low
parts-per-billion range.
Leeman Labs, Inc. PS 200 II Automated Mercury Analyzer – It is very difficult to
analyze for mercury using either the PE 5000 AA or the Hitachi GFAA. Sample prep is
time consuming, the instruments must be reconfigured, and either result in poor detection
limits. To address these shortcomings, Leeman Labs created their dedicated mercury
analyzer. The mercury analyzer combines an aliquot of the sample with tin chloride to
convert all of the mercury containing species in the sample and liberates ground state
gaseous mercury. This gaseous mercury is then analyzed in a manner similar to the PE
5000 and the Hitachi. Depending on how the instrument is configured, the detection
limits for the mercury analyzer can be in the low parts-per-trillion range.
HP 5890 Gas Chromatograph fitted with both a Perkin Elmer ATD 4000 Thermal
Desorption Sampling System and a Dynatech DynaSoils Purge and Trap Sampling
System. – The combination of these three instruments allow for the determination of
volatile and semi-volatile organic compounds in either gaseous or liquid samples. Bothe
systems are fitted with autosamplers for more convenient sample analysis. The HP 5890
uses a flame ionization detector which offers very good detection limits but doesn’t allow
for the analyte confirmation that the GC-MS would.
Applied Biosystems 4000 Q Trap Triple Quad Mass Spectrometer coupled with an
Eksigent Temp nano MDLC (LC-MS) – The LC-MS is the newest instrument in the
lab. The LC-MS is used to separate and identify mixtures of organic compounds that
would be too big for analysis by the GC-MS. The liquid chromatograph separates a
mixture of compounds which are then introduced into the mass spectrometer as they elute
off of the end of the LC column. The LC-MS has a wide range of applications, ranging
from the analysis of proteins in a cell to the identification of drugs in forensic toxicology,
to the determination of organic pollutants in environmental monitoring. The LC is a
“nano” scale chromatograph, meaning that it uses extremely small amounts of sample
(about 1 microliter) and small eluant flow rates (typically 250 nanoliters per minute).
The mass spectrometer is a triple-quad, meaning that as the compound comes off of the
chromatographic column and into the MS, the compound is ionized. The instrument can
either display all of the produce ions, or one ion can be selected for further fragmentation.
These subsequent fragments can be displayed or further fragmented. The multiple
fragmentations can be used to isolate one compound out of a complex mixture.
Dionex 4500i Ion Chromatograph – The IC allows for the separation and quantitation
of ionic species in a liquid matrix. Most frequently this involves the determination of
anions such as fluoride, chloride, nitrate, nitrite, sulfate, and sulfite, or cations such as
ammonium, sodium calcium, and potassium. The IC is equipped with both conductivity
and pulsed electrochemical detectors.
3
Hewlett-Packard 5890 Gas Chromatograph coupled with a Hewlett Packard Model
5970B Mass Selective Detector. This system, most commonly referred to as a GC-MS
is used to separate and quantify the volatile chemical compounds in a liquid sample. The
GC-MS is a commonly used instrument with a wide range of columns available for the
analysis of different classes of compounds. In some instances sample preparation or
method development can be time consuming.
Tekmar Model 6000 Thermal Desorption System – The Tekmar is a sampling system
attached to the Hewlett Packard GC-MS discussed above, and allows for the
determination of volatile and semi-volatile species in a gaseous sample. Unlike the ATD
400 discussed above, the Tekmar is a single-tube system, requiring the analyst to
physically mount and remove each of the sample for analysis.
Technicon TRAACS 800 Continuous Flow Analytical System – The Techincon is
typically used by engineers and industry to monitor a range of inorganic species. The
system adds a series of reagents to a portion of the sample to create a color change in the
sample. The intensity of the color is an indication of the concentration of the species in
the sample. A series of analyte-specific modules are installed in the instrument for each
analysis. Some of the possible analytes include nitrogen species, some of the industrial
important metals, and a range of water-quality related ions.
Thermo Separations Products P4000 Liquid Chromatograph and UV1000 Detector
(LC) – The LC is a widely used instrument for the separation of organic compounds that
are too big to be determined by the GC or GC-MS. After separation, the compounds are
passed through the UV detector where any compounds with a UV absorbance are
detected. Currently the LC is set up for the separation and determination of the tricyclic
antidepressants, but through the installation of the appropriate column most organic
compounds can be determined with the LC. Without the presence of a mass spectrometer,
the identification of the eluting species is determined by the time it takes the species to
come off of the column. Because of this lack of verification, a careful method
development cycle is important for any analysis.
Cary 1E UV-Vis Spectrophotometer – The Cary is a general purpose UV-Vis
spectrophotometer, designed to show which wavelengths of ultra-violet and visible light
are absorbed by a compound. It is typically used for the characterization of a compound
prior to analysis by another technique, or to follow the process of a reaction, where one of
the reactants or products absorbs in the UV-Vis region.
Nicolet Analytical Instruments MX-S Infrared Spectrophotometer (FTIR) – Like the
Cary, the FTIR is a general purpose spectrophotometer, but instead of the UV-Vis region,
the Cary determines the absorption characteristics of a compound in the IR region of the
spectrum. The Nicolet FTIR is a general use instrument and not necessarily a “research-
grade” instrument.
4
The following pieces of instrumentation are currently in various states of repair. All are
expected to become operational as time and money for repairs are available.
Thermo Jarrell Ash ICAP 61 Inductively Coupled Argon Plasma
Spectrophotometer (ICP) – The ICP is used for the observation and quantitation of
metals in a liquid matrix. The ICP has detection limits that are significantly better than
the PE 5000 flame AA and slightly better than the Hitachi GFAA. Like the AAs,
detection limits vary from element to element. The ICP requires a large amount of argon
for operation, so the cost per sample is relatively high.
Perkin Elmer ELAN 6000 Inductively Coupled Argon Plasma Mass Spectrometer
(ICP-MS) – The ICP-MS is very comparable to the ICP, but instead of optically
determining the presence of a metal, the ICP-MS determines the presence of a metal by
observing the masses of the ions coming out of the plasma. There are several major
benefits to observing the masses of the ions. First, the ICP-MS has better detection limits
than the ICP for virtually all elements. Second, the ICP-MS is capable of analyzing for
all of the metallic elements simultaneously. Finally, the ICP-MS is capable of observing
and determining the concentrations of the different isotopes of a particular element. With
this capability, it is possible to perform experiments like carbon 14 dating. Like the ICP,
the ICP-MS uses a lot of argon, so the cost per sample is high.
JEOL 5300 Scanning Electron Microscope (SEM) – The SEM is a microscope that can
observe small samples at up to 200,000 X magnification. The stage of the SEM is only
about 2” x 2”, and must be evacuated, so the type of samples can be limited.
Mattson Polaris Fourier Transform Infrared Spectrophotometer (FTIR) – The
Mattson is a “research-grade” instrument that provides the same basic information as the
Nicolet described above. The Mattson is designed to be fitted with an external long path
gas cell for the determination of atmospheric species.
5
Administration - Pricing
Note - The charging mechanisms used by the Centers and Service Units of the University of
Colorado Denver (UCD) are currently being reviewed and revised. These revisions are required
to adhere to new policies instituted by several federal granting agencies. Our revised pricing
schedule will be published to this page once the new policies have been finalized. Until that time
the current schedule is in use and any pricing questions should be directed to the Laboratory
Manager.
The price schedule for analytical services or use of the Laboratory is based on the affiliation of
the customer to the University and to the College of Liberal Arts and Sciences. The charge to
faculty is based on the cost of performing the analysis. These costs are calculated from the
analyst cost, instrument depreciation, and the cost of the materials and supplies consumed to
perform the analysis. Typically, the analyst cost is the major expense in an analysis. It is possible
to decrease the cost of the analysis by using either a student working for the Laboratory, or an
acceptable qualified and trained student of the faculty member. Costs associated with particular
instrumentation can be found under the instrumentation section.
Since the budget for the Laboratory is provided by the College of Liberal Arts and Sciences,
CLAS Faculty pay 150 percent of the cost of the analysis. In some cases, the costs of a short
study to investigate the feasibility of a procedure, with an eye towards submitting a grant
proposal using the method, may be underwritten by the Laboratory.
Non-CLAS Faculty are charged 250 percent of the cost of the analysis. As with CLAS faculty,
the cost of the analysis can be minimized by using a student analyst.
The Laboratory actively seeks and invites industrial use of the Laboratory. Because of issues
regarding tax-payer funded competition with private laboratories, we are required to charge a
minimum of 95% of the cost for a comparable analysis performed by a private laboratory. If
trade secrecy aspects and time frame required for the analysis permit, we encourage industry to
perform the analysis as a research contract with the University. In this mode, the analysis would
be performed by a student, under the oversight of the Laboratory Manager and a responsible
faculty member. This type of interaction enhances the education of the student while, at the same
time, providing a cost effective analysis to the client.
Finally, we recognize the connection of the University to the community in which we live. The
Laboratory supports small, limited scale work to the general community. In practice this has
involved helping primary students with some chemical aspects of their science fair projects.
Contact the Laboratory Manager for pricing and a complete listing of services.
Statistical Consulting Service
Contact:
Loren Cobb, PhD
Director
303-880-8279
[email protected]
Statistical Consulting Service
Department of Mathematical & Statistical Sciences
CU Building, Sixth Floor
The Statistical Consulting Service (SCS) of the University of Colorado Denver in the
Department of Mathematical and Statistical Sciences provides quantitative consulting of many
kinds to the university community, to industry and government in the Denver metropolitan area,
and to state, federal, and international agencies. For university graduate students engaged in
thesis research this service is free, all others pay on a sliding scale. Our consultants range from
university professors with thirty years of consulting experience, to PhD- and MS-level graduate
students who work on selected projects under faculty supervision.
SCS offers the services of professionals who have experience with both statistical analysis and
mathematical modeling in many areas, as described below.
Statistical Analysis
Research design
Factorial designs, blocking, split-plot designs, randomization, power analysis, contrasts,
multiple comparison adjustments, response surface designs, repeated measures and
covariates, cross-over and time series designs, retrospective studies, prospective single-
and double-blind studies, case control studies, cohort studies, quasi-experimental designs.
Sampling
Probability sampling: random, systematic, stratified, size, cluster, and multistage
sampling; non-probability sampling: quota, purposive, and accidental sampling; political
polling; census methods; sampling for industrial quality control; bootstrap resampling
techniques.
Measurement
Validity and reliability of existing and proposed measures; bias and error patterns in
measurement; dimensionality reduction; performance improvement; measurement
instrument evaluation; latent trait analysis; vector and field measures; transformations;
frequency-domain measurement techniques (spike separation, signal processing,
wavelets, filtering).
ANOVA-related methods
Univariate and multivariate analysis of variance, analysis of covariance, ANOVA with
repeated measures, ANOVA for complex experimental designs.
Regression-related methods
Multiple, polynomial, logistic, weighted, and nonlinear regression; data mining; survival
analysis; principal components and factor analysis; errors-in-variables models; path
analysis; Bayesian regression; robust and non-parametric regression; splines; time series
analysis; spectral and cross-spectral analysis; forecasting.
Genomics and informatics
DNA and RNA microarray analysis; BLAST-like algorithms; structural genomics; Monte
Carlo methods; error modeling and analysis.
Filtering and image methods
Kalman filtering; signal processing; image analysis and pattern recognition; ensemble
and particle filters for spatial filtering, spatial kriging.
Computational statistics
Assistance with R, SAS, MatLab/Maple, Mathematica, Data Desk, and SPSS; numerical
methods; statistical modeling and simulation; genetic algorithms; neural networks;
hierarchical, partition, and spectral clustering; data fusion; dynamic and persistent
statistical databases.
Mathematical statistics
Creation of maximum likelihood and Bayesian estimators; tests of convergence;
nonparametric and robust statistics in Hilbert space; stochastic calculus; stochastic
differential and integral equations; stable distributions; multimodal distributions; implicit
equation models; statistical theory for differential topology; statistical theory for
nonlinear and chaotic systems; fuzzy statistics.
Modeling
Business and industrial operations
Mathematical models of industrial processes, product and process failure models,
information and decision flow, network modeling, catastrophic event models, stochastic
control theory, supply chain modeling, scheduling and queueing, pricing formulas,
predictive models.
Finance
Risk modeling, asset price models, cash flow models, stock price and volatility models,
investment screen development, pooled investment models, survival and actuarial
models, rare event models, econometrics.
Social Science
We offer decades of experience with mathematical modeling in all of the social sciences,
including anthropology, clinical psychology, communication, demography, economics,
education, geography, history, law, linguistics, military science, political science, public
administration, psychology, social work, and sociology.
Biology and Medicine
Genomics modeling, pharmacokinetics, enzyme kinetics, tumor growth models,
competing risks models, ecosystem modeling, fluid flow and transport models,
evolutionary games, epidemic models, population dynamics, spatial models, swarm
models, cellular automata, fishery dynamics, limit cycles and chaos.
Physical Science
Ordinary, partial, and stochastic differential and difference equations, numerical analysis,
statistical error propagation models, thermodynamic models.
Engineering and applied math
Linear and nonlinear systems, stochastic systems, graph and network models, operations
analysis, optimization, numerical analysis, queueing models.
Military
Models of peacekeeping, peace enforcement, and humanitarian operations, post-conflict
stabilization, asymmetric and irregular conflict, national security models, refugee and
displaced-person models, nation-building, satellite coverage optimization, cellular
automata models, models of information warfare.
Fee Schedule (draft-under review)
Client type Consultant type Hourly rate
UC Denver graduate thesis Any FREE
Any Graduate student
under supervision
$50
Unfunded faculty research Math faculty $100
Funded faculty research Math faculty $135 and up
State of Colorado Math faculty $135 and up
Industry Math faculty $150 and up
All rates are negotiable. Call Dr. Cobb for more information: 303-890-8279.
Version of August 2009.
Statistical Consulting Service
Loren Cobb, PhD, Director
a)
We have not yet established a quality control system. We may set up a feedback and
comment system in the future.
How is the quality of your measurements evaluated – quality control?
b)
When a client asks for a statistical analysis, our turn-around time is typically one to seven
days.
What is the turn-a-round time for the service you provide?
c)
We don't provide data; we offer advice on research design, measurement, models, and
analysis. When these services are provided by graduate students, then they do so under
my close supervision. In that restricted sense, I (Loren Cobb) am the person ultimately
responsible.
Who documents the data provided and signs off on the data?
d)
Again, we don't provide data. But yes, we have one or two industrial or business clients
every semester. They come seeking advice on research design, measurement, models, and
analytical methods.
Have you had experience providing data for industry?
e)
No. However, I am teaching a seminar on statistical consulting, and the notes from that
seminar will become the foundation for a consulting manual.
Do you have a standard operating procedure manual?
f)
For each paying client, I record billable hours in a simple spreadsheet. Once a month I
send out an invoice. The majority of our clients are graduate students working on thesis
research, for which our services are free.
How will you track billing and financial aspects of your core?
University of Colorado Cancer Center Small
Animal Imaging Core
Contact:
Natalie Serkova, PhD, Director
Associate Professor, Dept. of Anesthesiology and Radiology
303-266-2910 pager
[email protected]
303-724-1086 phone
303-359-6574 cell
Radiologist Technologist: Kendra Hasebroock (pager 303 266 2247)
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/small-animal-
imaging/index.aspx
The major goal of the small animal imaging program is establishment of novel imaging
approaches to cancer and cancer experimental therapeutics using animal models and
pharmacodynamic endpoints. State-of-the-art imaging facilities are extremely expensive and
require advanced technical personnel. Modern non-invasive imaging technologies include:
• Magnetic Resonance Imaging (MRI for anatomic, physiologic, and molecular imaging)
• Computed Tomography (CT for anatomic imaging)
• Positron Emission Tomography (PET for metabolic and molecular imaging)
• Optical Imaging (Bioluminescence, Fluorescence)
• Ultrasound
Our Small Animal Imaging Core is a developing resource that includes three areas:
• MRI/CT/PET, supervised by Natalie Serkova, PhD (Anesthesiology/ Radiology)
• VisualSonic Ultrasound, supervised by Peter Buttrick, MD (Cardiology)
• IVES (bioilluminescence), supervised by Chuan Li, PhD (Radiation Oncology)
• Irradiation, supervised by David Raben, MD (Radiation Oncology)
MRI/CT/PET Services
The University of Colorado Cancer Center Small Animal Imaging Core offers MRI, CT and PET services to
members and non-members.
Facility
Our facility is fully equipped for magnetic resonance imaging and proton spectroscopy (MRI/
MRS) studies on small animals. All 18FDG-PET and bone- and coft-tissue (enhanced) CT
protocols are available. All standard operating procedures (SOP) for animal imaging are in place.
The facility is currently comprised of approximately 660 sq ft of laboratory space, in which are
housed three imaging modalities (MRI, PET and CT), animal anesthesia equipment, one
physiological monitoring system, animal warming equipment, and computers and data
processing systems.
• The Small Animal Imaging has been in existence since 2005 and is in a nascent stage of
development.
• The MR scanner was purchased in 2005 with support from an NIH-sponsored Shared
Instrumentation grant (PI: N. Serkova).
• The combined microPET/CT system was purchased in July 2007 from collaborative internal grant
to the School of Medicine (PI: N. Serkova, supported by the Cancer Center, Depts. Radiology,
Anesthesiology, the National Jewish Center as well as the Dean Office).
• All equipment maintenance, protocol development, quality controls, as well as assistance
provided to users of the resource is performed by the Dr. Serkova and Radiologist Technologist
Kendra Hasebroock (B.S., MRT).
Equipment
The facility is fully equipped for all aspects of MRI, PET and CT evaluations on small animals,
ex vivo specimens and vivo cell models:
• 4.7 Tesla Bruker Pharmascan MRI/MRS scanner with 1H resonance frequency of 200 MHz, RT
bore without shims 160 mm. The system is equipped with an actively shielded gradient system I
(90 mm inner diameter: x,y,z with 3 mT/m/A); maximum gradient strength 300 mT/m.
• Three volume transmitter/ receiver coils of different diameters (from 22 to 68 mm diameters).
• Siemens Inveon microPET (field of view 12 cm allowing for one-bed position for the whole-body
mouse scan).
• Siemens Inveon microCT (to be installed in February 2008).
• Bruker computer platform is equipped with a high-performance MR-workstation X2000 for use
with Bruker MR softwares (NMR SUITE and PARAVISIONTM 3.0). The PC is configured with Intel
Pentium 1.5 Hz, 1 Gbyte RAM, SCSI Controller Adaptec 29160, 73 GByte Disk, Red Hat LINUX,
20” TFT LCD monitor with graphics 1024, HP printer, Ethernet card etc. ×resolution of 1280
• Anesthesia machines, physiological monitoring system, warming pads and fans, as well as other
additional accessories are available in the animal preparation room.
Prices
Metabolics Core Pricing FY2009/2010
Full Service Self Service
Service Description
Member
Rate
Non Member
Rate
Member
Rate
Non Member
Rate
Biopsy $116 $144 $69 $70
Blood $59 $80 $23 $23
Cell Culture $324 $405 $188 $193
Quality Control (HSQC) $185 $190 $185 $190
Other - Minimum
Processing
$43 $54 $24 $24
* only experienced NMR/ Radiologist scientists after on-site training by Dr. Serkova
$
additional costs for radioactive glucose: $50 per animal
How to Use the Core
To schedule an appointment for animal MRI-, PET- and CT-based studies, please
contact Dr. Natalie Serkova. You must have an approved animal protocol, including
animal imaging procedure, for all imaging-based animal studies. Please contact Dr.
Serkova to discuss your animal protocol approval application and/or incorporating
imaging SOP into an amendmentSmall Animal & Cell Radiation Sciences Shared Core
Service
The Radiation Sciences Core supports radiation biology studies of cell cultures and small
animals receiving moderate-dose radiation. We also enable investigators to study low dose-rate
irradiation in cell culture. And we provide irradiation services for investigators who need this
tool in support of other efforts, such as using total body irradiation for immunosuppression of
animals before stem cell transplantation.
Services We Offer
• Project design and consultation, including advice on radiation delivery to in vitro experiments
and animal models
• Design assistance for single or fractionated radiation protocols and study duration
• Radiation safety training (all users) and radiation operation training (advanced users)
• Animal tumor and partial-body irradiation at doses comparable to external beam radiotherapy
• Cell suspension irradiation
• High-dose irradiation to sterilize implant material
• Dosimetry calculation
• Calibration in support of stem cell research
• Blocking cellular division in in vitro cell cultures
• Immune function assays
• Radiation-induced DNA damage repair studies
• Data analysis an publication preparation assistance
Equipment
• Cesium Irradiator, which allows for deep tissue irradiations with notable accuracy
• Electronic Monitoring System for tracking and recording system use
Prices
The Radiation Sciences Core offers a discounted rate for UCCC members. Non-members are
welcome to use our services as well, but we give members scheduling priority. We issue all users
a key card that operates the equipment and tracks your time for easy billing.
Time is charged in one-minute increments, including warm-up time, regardless of the number of
samples irradiated.
• Member price per minute: $1
• Non-member price per minute: $2
How to Use the Core
• All users must undergo radiation safety training. To schedule your training, contact Chastiti
Vetter.
• Please contact Dr. Angela Hu or Francis Newman to schedule irradiator time or for help
designing and implementing your irradiation experiment.
In Vivo Optical Gene Service
The In Vivo Optical Gene Imaging Facility offers UCCC members and other investigators the
tools to image biological processes in live experimental animals based on powerful, non-invasive
bioluminescence and fluorescence imaging. We use a state-of-the-art Xenogen IVIS200 imaging
device that is specifically designed to visualize genetically labeled cells, such as tumor cells, and
proteins, such as those that stimulate cancer growth in live animals. It does so by recording light
emitted from the genetic labels, such as firefly luciferase, located within the animals.
Requirements for Animal Protocols
All animal studies using using the Xenogen IVIS200 must have an approved animal protocol.
Please visit the Institutional Animal Care and Use Committee website or Dr. Margaret Turner for
more information.
Dr. Fang Li can help you prepare your IACUC submission. She will give you PQ forms for
imaging personnel who will be conducting scans.
How to Use the Core
1. Have your animal protocol approved
2. Arrange for instrument training with Dr. Fang Li .
3. Dr. Li will then give you a key card to access the instrument, and assign each user group (PI) a
user ID for the computer system attached to the Xenogen system.
4. Request user time via email to Dr. Li. Please understand that you are not automatically
guaranteed you will get the dates and times you request. Please place your request several days
in advance to make sure your requested slot is available.
5. We will email you when your request is approved.
Prices (effective 7/1/08)
• Member: $63.35 per hour
• Non-Member: $86.13 per hour
D-luciferin
• $25/ml from the facility
• $800/gram directly from Caliper Life Sciences
Leadership & Staff
Chuan-Yuan Li, PhD
Director
[email protected]
303-724-1542
Fang Li, PhD
Manager
[email protected]
303-724-1625
Ultrasound Service: the fee schedule is under
construction
Small Animal Imaging Core (UCCC)
From: Serkova, Natalie
Sent: Thursday, October 01, 2009 2:26 PM
a) How is the quality of your measurements evaluated – quality control?
CT and PET calibration using manufacturer’ phantoms i s performed every 1-2 months;
MRI phantoms are run every 3 months.
b) What is the turn-a-round time for the service you provide?
10-30 m in pe r a nimal; for a s ingle s tudy, t he pr oject pe riod c an b e up t o 1 ye ar
(longitudinal studies on animals).
c) Who documents the data provided and signs off on the data?
The Core Director provides monthly reports to the Cancer Center based on the data from
the staff.
d) Have you had experience providing data for industry?
Yes, we run 5-10 industry sponsored studies per year.
e) Do you have a standard operating procedure manual?
Yes, per requested, approved by the IACUC.
f) How will you track billing and financial aspects of your core?
We do it already for the past 3 years: Cancer Center provides us with our cost study every
fiscal year. It is posted on our website.
Transgenic and Gene Targeting Core
Core Personnel:
Peter J. Koch, Ph.D.
Associate Professor of Dermatology
Director, Transgenic and Gene Targeting Core
Charles C. Gates Regenerative Medicine and Stem Cell Biology Program
University of Colorado Denver
(P) 303 724 0051
E-Mail: [email protected]
Joseph Anderson, M.S., Laboratory Manager
Senior PRA
Embryo Manipulation Services
E-Mail: [email protected]
Ling Wang, M.D.
PRA
Gene targeting in ES cells
E-Mail: [email protected]
Wallace Chick, Ph.D.
Instructor
Transgene and Gene Targeting Vector Design
E-Mail: [email protected]
Shawna Johnson, B.S.
PRA
Breeding and maintenance of genetically engineered mouse lines
E-Mail: [email protected]
Abby Knight, CVT, RLAT
PRA
Colony and Data Management
E-Mail: [email protected]
Website:http://www.uchsc.edu/stemcell/resources/transgenic.htm
Message from the Director:
A new "Transgenic and Gene Targeting Core" has been established in the Charles C. Gates
Regenerative Medicine and Stem Cell Biology Program at UCD. Our core facility replaces the
Transgenic/Knockout Core that was part of the UCD Cancer Center. We are committed to
provide the UCD research community with state-of-the-art services. Our goal is to assist PIs in
designing and generating genetically engineered mouse lines to further biomedical research.
Our services include pronuclear injections (conventional and BAC transgenic mice), ES cell
injections (e.g. knockout and knockin mice), cryo-preservation of embryos and embryo re-
derivation (see below for a detailed
Embryonic stem Cell Iinjections (courtesy of Eppendorff Inc.)
list of services and prices). We also conduct gene targeting experiments. The PIs will provide the
gene targeting construct and test ES cell clones for homologous recombination. We will conduct
the entire cell culture work and inject recombinant ES cell clones into mouse embryos to
generate chimeric mice. If requested, we will breed these chimeras to test for germline
transmission of mutant alleles.
Pronuclear DNA Injection (Courtesy of Eppendorff Inc.)
We also provide consultation services for the UCD community. Usually, we discuss
experimental design before we actually initiate the project. The goal is to ensure that the
experimental strategy employed is likely to result in the successful generation of the desired
mouse line. The initial consultation (usually a one hour meeting) is provided free of charge.
Further consultations and assistance in designing the experimental strategy to generate and
analyze mouse lines will be provided on a fee-for-service basis.
To streamline our communication with PIs, we have established an e-mail account that should be
used to schedule services and to request consultations ([email protected]). All core
members have access to this e-mail account. To facilitate correct routing of your requests, please
include the PI name and the requested service in the header of your e-mail (e.g. John Doe
“schedule transgene injection"; John Doe “schedule consultation"). We will then route the
request to the appropriate core member.
We are planning to introduce new services to accommodate the needs of our research
community. This might include the generation of transgenic rats, and the use of retroviral vectors
to generate transgenic mice. We will evaluate requests for services from the research community
for new services on a regular basis.
We are also planning to provide you with transgene and gene targeting vector design and
construction services in the near future. Please stay tuned. I will need your feedback with respect
to the introduction of new services. Feel free to drop me an e-mail at
[email protected]
Lastly, our core services are partially supported by a grant from the SOM dean. We are planning
to become self-sufficient within three years. This will not be possible without your support.
Please use our services and provide us with feedback so that we can continue to improve our
services and help you to achieve your research goals.
Peter J. Koch
To request or schedule services please send an e-mail to:
[email protected]
Please include the PI name and the type of service requested in the subject line.
Information and Protocols:
Producing Fertile Embryos for Cryopreservation and Rederivation
Information and requirements for producing embryo donors and breeder males for
optimal embryo production for efficient cryopreservation and rederivation of investigator
colonies.
DNA preparation for Microinjections
DNA preparation for Gene Targeting
BAC DNA Construct Preparation
Please contact [email protected]
Re-derivation and Cryopreservation Information
This information pertains to the TGTC standard rederivation and cryopreservation
procedures and is not part of the VC sponsored rederivation project. These two
procedures are separate. Crypreservation provides for long-term storage of mouse lines
and rederivation is the means to regenerate these lines. Cryopreserved embryos can also
be shipped directly to other institutions without the complicated regulations needed for
live animal shipments.
Application Forms:
Note: Please use the latest versions of application forms from this list. Outdated forms will be returned to the
investigator and resubmission on the current appropriate forms required.
Vice Chancellor's Cryopreservation and Rederivation into RC-2
Use for Vice Chancellor's rederivation project.
Standard TGTC Cryopreservation or Rederivation
The application allows separate selections of cryopreservation for storage and/or
rederivation for colony speed expansion and rederivation without the need for prior
cryopreservation.
DNA Constuct Microinjection
Your DNA construct will be validated for microinjection by our personnel and the
application forwarded to TGTC for scheduling. The TGTC will inform you by email
when your microinjections are scheduled.
Embryonic Stem Cell Services
Used to submit your DNA to the Cell Services Lab, where it will be processed for stem
cell injections. Please follow the instructions on the form. Following completion of
processing, you will be notified.
Stem Cell Injection
Please use this form to apply for ES cell injections. You will be notified when the
injections are scheduled.
Terms of Service Agreement
Please review this agreement prior to utilizing the services of the TGTC and the stem cell
facility.
Approval to Generate Genetically Engineered Mice
Note: you must have an approved Production and Experimental I ACUC protocol in order to produce transgenic
animals.
Please visit the Institutional Animal Care and Use Committee (IACUC) web page for
information regarding the approval of animal experimentation at UC Denver.
Transgenic & Gene Targeting Core Pricing, 2008-2009
Prices subject to change.
Gene Targeting Service Price
Electroporation/Drug Selection (First 288 clones) $2,863
Additional Clones (Per 96 well plate) $600
Clone Expansion (Per Clone) $371
Karyotyping (cost per clone) [mandatory before blastocyst injection] $390
Removal of loxP- or FRT-flanked genomic sequences by transient transfection
of ES cell clones with Cre expression plasmids or FLPE expression plasmids
(contact us at [email protected] for details)
$2,863
Gene Targeting Consultation with Peter Koch, PhD. (per hour) $100
Chimeric Mouse Model Development $1543
Listed price inlcludes Injections (~50 blasts minimum), minimum of three
recipient females and embryo transfer surgeries. Additional
recipients/surgeries extra.,
Embryo donor purchase and estimated per diems included in listed price.
These charges billed separately through CCM.
Transgenic Mouse Model Development $1693
Price includes construct microinjections, minimum of three recipient females
and embryo transfer surgeries. Additional recipients/surgeries extra.
Embryo donor purchase and estimated per diems included in listed price.
These charges billed separately through CCM.
Strain Rederivation (per line) $1,765
Price includes minimum of three recipient females and embryo transfer
surgeries. Additional recipients/surgeries extra.
45 day of animal per diems included (billed separately through OLAR).
Embryo Cryopreservation (per transgenic line) $540
Line regeneration charges will be dependent upon the recipient female costs,
embryo transfer surgery costs and facility per diems in effect on that date.
Miscellaneous Services
DNA Purification $163
Pseudopregnant Recipient Females - each $65
Embryo Transfer Surgeries - each $106
Mating, Weaning, Tagging, Biopsies $21
Weaning Only $13
Repeat Biopsies $26
Timed Pregnancies $33
Miscellaneous Services hourly rate, (billed in 15 minute increments) $35
PCR Genotyping of Mice (per 10 PCR reactions) $33
Consultation with TGTC personnel (per hour) $51
The Transgenic and Gene Targeting Core can test your chimeras or
transgenic founder mice for germline transmission of the desired mutations.
Please contact the Core ([email protected]) for details. These
experiments will be conducted in our own animal room, which is shielded from
the general mouse population at CCM to ensure that your mice are efficiently
protected from common mouse pathogens.
The prices listed above are charged to investigators affiliated with UCD who
conduct non-commercial basic or clinical research. For prices charged to
commercial entities, please contact us at [email protected]
Response form the Transgenic and Gene Targeting Core
From: Koch, Peter
Sent: Monday, October 05, 2009 1:37 PM
a) How is the quality of your measurements evaluated – quality control?
Internal quality control procedures:
- Pronuclear Injections (conventional and BAC transgenes): Periodic injections of
control constructs (e.g. CMV-GFP) into fertilized eggs. Determine the recovery of
life embryos with integrated and expressed transgene. Compare efficiency of two
senior embryologists.
- ES Cell Injections, surgical procedures: Compare success rate of two embryologists
to identify techniques that can be improved/optimized.
- Transgene generation: Collect data on the percentage of transgene-positive founders
generated by us (information provided by our customers).
- Gene targeting and ES cell injections: Collect data on the number and quality of
chimeras produced by us (% chimerism, germline transmission of mutations)
b) What is the turn-a-round time for the service you provide?
- Most services are initiated within 2-3 weeks (gene targeting in ES cells, pronuclear
injections of conventional or BAC transgenes; ES cell injections; cryo-
preservations).
- The turnaround time depends on the service requested:
ES cell targeting: 4-6 weeks after initiation of ES cell work
Pronuclear and ES cell injection: One day after initiation; turn around time from
service request to generation of pups: 6-7 weeks
Rederivation 6-8 weeks
c) Who documents the data provided and signs off on the data?
Database manager (Abby Knight, Shawna Johnson) in conjunction with the Core
Manager (Joseph Anderson). Evaluation of efficiency and trouble-shooting is done
collaboratively with the Core Director (Peter J. Koch)
d) Have you had experience providing data for industry?
So far we had one request from a small biotech company. Our main customer basis is
the University of Colorado (Denver and Boulder campuses) as well as a few out of state
Universities (e.g. University of Alabama).
e) Do you have a standard operating procedure manual?
We have standard operating procedures for repetitive procedures, such as the
rederivation program sponsored by the Vice Chancellor of Research. All SOPs are
updated regularly to ensure the best practices.
f) How will you track billing and financial aspects of your core?
Core prices are based on a cost analysis which is revised twice a year. Detailed reports
of monthly revenue are kept both electronically and as a paper copy. All services are
charged though Granite and additional reports are available upon request from
Carolyn Russell.
Translational Neuroscience Nexus Core (IDDRC)
Website:http://www.ucdenver.edu/academics/colleges/medicine/Centers/IDDRC/research/translational/Pa
ges/default.aspx#directors
Mission
The Translational Nexus (Nexus) is a database, patient registry and biological sample bank
focused on pediatric neurological, cognitive and behavioral disorders (IDD). Its major goal is to
advance research on neurodevelopmental disabilities (i) by linking human neurological,
cognitive, behavioral phenotypes to biological samples, especially DNA, and (ii) by facilitating
access to appropriate patient cohorts for clinical trials.
IDDRC members are invited to learn more about the services available from the Translational
Neuroscience Nexus core by watching a short video.
Staffing
Core Experts: Elaine Spector, PhD; Scott Lucia, MD
System Managers: Tom Yaeger, BS (consultant)
Technical Personnel: Katrina Merrion, MS, CGC; Kathy Acha, MS
Because of the special nature of the functions of the Nexus, a special 7-member Steering
Committee oversees the development and operation of the Nexus. The Steering Committee
represents the various user groups (programs, departments) and is composed of:
a. IDDRC director
b. The Nexus director and Nexus co-director
c. The Study Coordinator and/or a genetic counselor
d. 1-2 IDDRC member investigators (appointed for a 2-year term)
e. A representative of the CCTSI-IT core
f. A laboratory coordinator
Director:
Cordelia Robinson, PhD, RN
303-724-7680
[email protected]
Associate-Director:
Gunther Scharer, MD, FACMG
303-724-1571
[email protected]
Services
1. IDD Clinical Data Registry (Nexus CDR). The Nexus CDR is an extension of the
Intellectual and Developmental Disabilities Registry, which is already IRB-approved. The
Registry is a standard-of-care protocol to be used with all individuals who present for
multidisciplinary evaluation services at one of the IDDRC participating clinics listed below.
Partnering clinics invite all appropriate individuals who present for care to enroll in the Nexus
Registry. Clinical data is collected from consenting individuals and entered into a
secure electronic enrollment list. Data is collected during every follow-up outpatient visit to
these clinics as well as to Adult General Psychiatry, Rehabilitation Medicine, and Assistive
Technology Partners for as long as the subject remains in the study.
Registry Entry Points
Clinical Service Clinicians in Charge (All IDDRC Members)
Child & Adolescent Psychiatry
Developmental and Behavioral Pediatrics
JFK Partners
Pediatric Neurology
Pediatric Clinical Genetics
Inherited Metabolic Disease Clinic
Pediatric Special Care Clinic
Adult Medical Genetics
R. Ross
A. Reynolds, N. Tartaglia
C. Robinson, S. Hepburn
T. Benke, A, Brooks-Kayal, G. Wilkening, A. Yee
G. Scharer
R. Gallagher
E. Elias
M. Taylor
IDDRC investigators interested in data from the Nexus-CDR for their research proposals submit
a data query request to the Nexus. If sufficient subjects are available and the Nexus Study
Selection Committee has confirmed the merit of the study, then the investigator is asked to
submit an IRB protocol (exempt, for de-identified data-sets; full review for data linked to PHI or
for human subject research). Upon approval, the IDDRC investigator then is given full access to
the requested information. Contact Cordelia Robinson at [email protected] or
303-724-7680.
2. Nexus Biobank (Nexus-BB) stores biological samples from individuals enrolled into the
Nexus-CDR, and who are consenting to collection of a venous blood sample (for lymphoblast
transformation and for serum), as well as a buccal smear, blood sample, or saliva sample for
DNA extraction. Other biological samples, such as urine may be collected. Biological samples
are stored secure in the UCD-Biorepository Core Facility. Sample access is monitored
electronically using tracking software (Freezerworks®).
IDDRC investigators interested in accessing the biobank for their research proposals will submit
a sample request to the Nexus. If sufficient biological samples are available and the Nexus Study
Selection Committee has confirmed the merit of the study, then the investigator is asked to
submit a COMIRB protocol (exempt, for de-identified samples; full review for samples linked to
Nexus-CDR data). Upon approval, the IDDRC investigator then is given aliquots of the
requested samples. Contact Gunter Scharer at [email protected] or 303-724-1571.
3. Clinical Study Design Assistance is available from the CCTSI. However, in addition to basic
design expertise there is the need for specific expertise regarding recruitment and retention of
individuals with IDD and their families as subjects. In that regard. the Nexus Director (C.
Robinson) and several of the JFK faculty, including Susan Hepburn and adjoint faculty member
William MacLean, are available to provide advice on study design. Senior investigators of the
IDDRC with specific content expertise will be consulted on an ad hoc basis. Contact Cordelia
Robinson at [email protected] or 303-724-7680.
4. Biostatistics Support for IDDRC investigators is available through the CCTSI design
biostatistics and clinical research ethics program (a consortium of nine programs across the
Schools of Medicine, Pharmacy, Nursing, The Children's Hospital, and National Jewish Health).
The following specific focus areas are available: statistical genetics, methods for analysis of
high-throughput data, design and analysis of classification and discrimination studies, modeling
of pharmacokinetic/pharmacologic dynamic statistics, clinical trials epidemiological methods,
design and analysis of community studies, and evidence-based practice and meta-analysis.
Access to the CCTSI consortium is through a single portal. Contact Gunter Scharer
at [email protected] or 303-724-1571.
5. IRB Protocol Consulting and support is provided by the Nexus research coordinator (K.
Merrion) and, when necessary, the Nexus-associate director (G. Scharer). This is intended to
facilitate access to the Nexus resources. For example a general research protocol covering the
policies and procedures of the Nexus is currently under review by the COMIRB. It was
developed by the directors of the Nexus with the support of the Nexus research coordinator.
Contact Katrina Merrion at [email protected] or 303-724-2349.
Fees for Services
Service Cost, annual
(IDDRC member)*
Cost, annual
(Non-member)*
Contact
1. Clinical Data
Registry
10 data-sets (free)
$ 800 (unlimited)
Subject to review
$1,200
C. Robinson
2. Biobank 10 samples (free)
$1,600 (per 80 samples)
$2,000 (combined with 1.)
Subject to review
$2,400
$3,000
G. Scharer
3. Clinical Study
Design Support
Included in IDDRC
membership
TBD
C. Robinson
4. Biostatistics
Support
Included in IDDRC
membership
TBD
G. Scharer
5. COMIRB Protocol
Consulting
Included in IDDRC
membership
TBD
K. Merrion
UCH CTRC Core Lab
Contacts:
Bryan Haugen, MD
Core Director
303-724-3921
Pamila Allen, MS, MT(ASCP)
Core Laboratory Supervisor
720.848.6665
Leprino Office Building
Room 327
Kayla Carstens, BS,
MT(ASCP)
Core Laboratory Supervisor
720.848.6877
Leprino Office Building
Room 327
Website:http://ctsa1.uchsc.edu/Research-Resources/Clinical-Research-
Resources/Pages/UCHCTRCCoreLab.aspx
UCH CTRC Core Lab Accreditations
CAP Accreditation
CLIA Accreditation: 06D0644347
Important Assay Information
PLEASE READ CAREFULLY
Currently available CTRC Core Laboratory assays have priority over newly developed assays.
Occasionally, the laboratory director will negotiate with the investigator to reduce the number of
requests for expensive or time-consuming assays. Assays which are not available in the routine
hospital lab or the CTRC Core Laboratory are generally expected to be paid for by the
investigator's individual research funds; although the CTRC Core Laboratory can often help with
sample processing. Any shipment of specimens to an off-site laboratory is the sole responsibility
of the investigator.
Results from routine assays completed in the hospital laboratory are available through Clinical
Workstation. Results from assays performed at the CTRC Core Laboratory are available through
a server. Tom Yaeger, Director of Research Informatics, will work with the investigator to set up
a system that works best for the research project.
Approval of additional assays (and requests for current assays) is based on scientific merit. The
investigator must initiate the request to add additional assays by writing a letter to the Laboratory
Administrator and Chairman of the Scientific Advisory and Research Committee (SARC).
Complex requests may need approval of the full SARC.
CCTSI Core Lab Assays
Discounted pricing may be available, please contact Pamila Allen at 720.848.6665
or Kayla Carstens at 720.848.6877 for pricing specific to your study.
CCTSI Core Lab Assays
Assay
Pricing
Manufacturer
8-Isoprostane, urine $45.75 Cayman
Adiponectin $7.25 Linco Research
Adrenocorticotropic Hormone (ACTH) $29.25 Siemens
Aldosterone $9.50 Diagnostic Products Corp.
Angiopoietin-2 $27.25 R&D Systems
Angiotensin II $29.00 Evaluating Data
Beta-Carotene $59.00
Bile Acid, Total $19.25 Diazyme
Bone Specific Alkaline Phosphatase $31.75 Quidell
Brain Naturetic Peptide (BNP)
Bronchoalveolar Lavage Fluid $59.75
Caffeine $14.25 Siemens
Cell Culture
Cell Isolation
Cell Staining
Cholesterol $3.25 Olympus America
Coenzyme Q10 $35.50
Cortisol, serum/plasma $5.00 Beckman Coulter
Cortisol, urine Beckman Coulter
Cotinine $27.25 Siemens
Cotinine, salivary $16.00 Salimetrics
C-Peptide $6.50 Diagnostic Products Corp (DPC)
Creatinine, serum/plasma $3.25 Roche Diagnostics Systems
Creatinine, urine $3.75 Roche Diagnostics Systems
CRP-hs $5.75 Olympus America
DHEA $16.50 Diagnostics Systems Lab (DSL)
DHEA-S $14.25 Diagnostic Products Corp (DPC)
Differentials $64.75
DNA Extraction, >10 $40.00
DNA Extraction, blood $75.00
DNA Extraction, other $75.00
DNA Extraction, saliva $50.00
DNA Sequencing (PCR fragment) $50.00
EGF $27.00 Milliplex
Elastase, Free (neutrophil) $17.00
Elastase, PMN $19.25 ALPCO
Endoglin $28.00
Endothelin-1 $14.50 Peninsula Labs (Antibody)
Eosinophil Cationic Protein $23.00 Siemens
Epinephrine $14.50 BioRad
E-Selectin Milliplex
Estradiol $12.00 Diagnostic Systems Laboratories (DSL)
Estrone $13.25 Diagnostics Systems Lab (DSL)
Exotaxin $27.00 Milliplex
F-Actin, sputum $200.00 Cytoskeleton/BioRad
Ferritin $17.75 Siemens
FGF-2 $27.00 Milliplex
Flow Cytometry
FLT-1 (sVEGF R1) $27.25 R&D Systems
Flt-3Li $27.00 Milliplex
Fractalkine $27.00 Milliplex
Free Fatty Acid $3.50 WaKo Chemicals USA
FRO $27.00 Milliplex
FSH $5.25 Beckman Coulter
Galactose $8.50 R-Biopharm
G-CSF $27.00 Milliplex
Genotyping (PCR, digest) $50.00
Genotyping (PCR, sequencing) $90.00
Ghrelin $7.50 Linco Research
Glucagon $5.25 Linco Research
Glucagon-Like Peptide-1
Glucose $3.25 Olympus America
Glutathione Peroxidase $5.25 Randox Laboratories
Glycerol $4.00 R-Biopharm
GM-CSF $27.00 Milliplex
HDL-C, direct $6.00 Olympus America
HDL-Sub 3 $6.00 Warnick and Co.
HDL-T (Prec) $6.00 Warnick and Co.
ICAM-1 Milliplex
IFN-alpha2 $27.00 Milliplex
IGF-1 $21.50 Diagnostic Systems Lab (DSL)
IGFBP-3 $21.50 Diagnostic Systems Lab (DSL)
IL-1 alpha $27.00 R&D Systems or Milliplex
IL-1 beta $27.00 R&D Systems or Milliplex
IL-10 R&D Systems or Milliplex
IL-11 $24.25 R&D Systems
IL-12p40 Milliplex
IL-12p70 Milliplex
IL-13 Milliplex
IL-15 $27.00 Milliplex
IL-17 $27.00 Milliplex
IL-18 $25.50 R&D Systems
IL-1ra $27.00 R&D Systems or Milliplex
IL-2 $27.00 R&D Systems or Milliplex
IL-23 $27.25 R&D Systems
IL-3 R&D Systems or Milliplex
IL-4 R&D Systems or Milliplex
IL-5 R&D Systems or Milliplex
IL-6 $25.50 R&D Systems
IL-7 R&D Systems or Milliplex
IL-8 R&D Systems or Milliplex
IL-9 R&D Systems or Milliplex
Immunoreactive Trypsinogen $24.50 DiaSorin
INSULIN $5.25 Diagnostic Systems Lab (DSL)
IP-10 $27.00 Milliplex
LACTATE $4.00 Olympus America
Lactulose/Mannitol Ratio $87.50
LEPTIN $7.25 Linco Research, Inc.
LH $5.25 Beckman Coulter
Lymphocyte Proliferation $214.00
Macrophage Inhibitory Factor $27.25 R&D Systems
Matrix Metalloproteinase-7 $40.50 R&D Systems
Matrix Metalloproteinase-9 $40.50 R&D Systems
MCP-1 Milliplex
MCP-3 Milliplex
MDC $27.00 Milliplex
Micro Total Protein $9.00 Sigma
Microalbumin, urine $13.25 Siemens
Microcarotenoids $77.50
MIP-1 alpha $27.00 Milliplex
MIP-1 beta Milliplex
MLPA
Myeloperoxidase $44.50 Prognostix
Nitrates/Nitrites $84.25 Waters
Nitrogen, urine $43.50 Antek
Norepinephrine, plasma $14.50 BioRad
Norepinephrine, urine $40.50 BioRad
N-Telopeptide, urine $75.00 Wampole Osteomark
NT-pro BNP $27.50 Milliplex
OXI-LDL $33.00 ALPCO Diagnostics
Parathyroid Hormone (PTH) $31.25 Siemens
PBMC Isolation $43.25
PCR (no set-up, fragment) $40.00
PCR (set-up/exon, fragment) $100.00
PCR multiplex (set-up) $500.00
PDGF-AA $27.00 Milliplex
PDGF-AB/BB $27.00 Milliplex
PROGESTERONE $8.75 Diagnostic Products Corp (DPC)
PROLACTIN $5.25 Beckman Coulter
PYY $8.25 Linco Research, Inc.
RANTES $27.00 Milliplex
RENIN (PRA) $16.50 Diasorin
Retinal Binding Protein $17.25 Siemens
RNA Extraction, blood $80.00
sCD40L $27.00 Milliplex
Secretory Leukocyte Protease Inhibitor $24.25 R&D Systems
SHBG $21.50 Diagnostics Systems Lab
sIL-2Ra $27.00 R&D Systems or Milliplex
Sputum Processing $80.00 TDN Protocol
sTransferrin Receptor $19.00 Siemens
T3-UPTAKE Beckman Coulter
T4, FREE $6.50 Beckman Coulter
TAS $12.50 Randox Laboratories
TESTOSTERONE $6.00 Beckman Coulter
TGF-alpha $27.00 Milliplex
TGF-Beta 1 $29.00 Milliplex
Tissue Inhibitor of Metalloproteinase $23.25 R&D Systems
TNF-a $26.00 R&D Systems
TNF-beta IFN-y $27.00 Milliplex
TOTAL T3 $4.25 Beckman Coulter
TOTAL T4 Beckman Coulter
TRIGLYCERIDE $3.25 Olympus America, Inc.
TSH $5.50 Beckman Coulter
URINE NITROGEN See link below
VCAM-1 Milliplex
VEGF Milliplex
Vitamin A $50.25
Vitamin D 1,25 diOH $48.50 DiaSorin
Vitamin D 25OH $37.50 DiaSorin
Vitamin E $49.25
X-inactivation
Fees are not guaranteed
UCH CTRC Core
From: Carstens, Kayla for Bryan Haugen, MD (Director)
Sent: Monday, November 02, 2009 2:53 PM
Our core is the Laboratory. Our director is Dr. Bryan Haugen. Managers are Pamila Allen and
Kayla Carstens
a) How is the quality of your measurements evaluated – quality control?
For every assay that is performed here, quality control samples are assayed along with the
unknown samples. The controls are either purchased separate from the instrumentation
or kits, from an outside source, or for some of our kits, the quality control is provided.
For our more routine chemistries, quality control is assayed once a day, otherwise it is
run when the assay is performed. Other quality control measures include, but are not
limited to, refrigerator/ freezer monitoring, centrifuge calibration, electrical safety checks
on all equipment, instrument maintenance and function checks, pipette calibrations,
reagent performance checks, deionized water quality, safety inspections, etc.
b) What is the turn-a-round time for the service you provide?
For our more routine chemistries, such as lipids, glucose, and TSH, we assay these 2-3
times per week. Most of our researchers need these for screening purposes. Other assays
are performed on a batch basis whereby we wait until we have enough samples to justify
setting up the assay or when our researchers need the data. Most of our turn-around-time
is driven by our researchers and the cost to run the assay.
c) Who documents the data provided and signs off on the data?
Data generated from our lab is entered into our Access database by the technologist
performing the assay. The data is verified before release by one of the core lab
managers. This is documented on every assay worksheet.
d) Have you had experience providing data for industry?
For industry studies, we offer specimen processing and temporary storage, but have not
provided any data.
e) Do you have a standard operating procedure manual?
Our core lab has a standard operating procedure manual (we call it “Global Procedures”),
procedures for all of our assays, safety procedures, processing procedures, etc. We are
certified by the College of American Pathologists (CAP) and CLIA both of whom require
procedure manuals for nearly all aspects of laboratory work.
f) How will you track billing and financial aspects of your core?
We are currently in the process of setting this up with our administrative group. Our
administrative contact is Pat Kittelson.
Vivarium Animal Facility
Office of Laboratory Animal Resources Recharges and
Per Diem Rates For Fiscal Year 2008-2009
Contact:
Jori Leszczynski, DVM DACLAM
303-724-3987
[email protected]
Website:http://www.uchsc.edu/animal/
OLAR i s obl igated to recover t he cos ts a ssociated with the procurement and car e of and use o f
animals. These costs are billed to investigators monthly. Per di em rates f or animal care or di rect
charges for personnel costs and supplies are based on a cost analysis and recovery program outlined
by NIH Cost Analysis and Rate Setting Manual for Animal Resource Facilities.
The following t able gives t he per diem r ates for the care and housing of laboratory animals. Per
diems cover these basic services: feed, special diets, health checks, cage changes and cleaning.
Cost Center Per Diems Current Rate
Cat Per Diem Per animal 3.68
Chinchilla Per Diem Per animal 3.44
Dog Per Diem Per animal 18.93
Ferret Per Diem Per animal 3.24
Fish Aquarium Per Diem Per aquarium .45
Frog Tank Per Diem Per tank 3.24
Frog Tank-Maller Per Diem Per tank 3.43
Gerbil Per Diem Per Cage .58
Ground Squirrel Per Diem Per Cage 1.07
Hibernating Ground Squirrel Per Diem Per Cage .52
Guinea Pig Per Diem Per Cage 1.64
Hamsters Per Diem Per Cage 1.62
Mouse Autoclave Per Diem Per Cage 1.00
Mouse Microisolator Per Diem Per Cage .57
Mouse Quarantine Per Diem Per Cage .66
Mouse Quarantine Static Per Diem Per Cage .76
Mouse Static Per Diem Per Cage .67
Opossum Per Diem Per Cage 1.27
Pig Per Diem Per animal 23.74
Rabbit Per Diem Per Cage 3.71
Rat Autoclave Per Diem Per Cage 1.66
Rat Microisolator Per Diem Per Cage 1.15
Rat Quarantine Per Diem Per Cage 1.37
Rat Quarantine Static Per Diem Per Cage 1.47
Rat, Metal Suspended Per Diem Per Cage .39
Rat Static Per Diem Per Cage 1.25
Zebrafish Per Diem Per Rack 2.94
Zebrafish(Shared) Per Diem Per Rack 1.46
Animal Administrative Purchasing Fee I Per Animal Order 20.00
Denver Health
Denver Health Mouse Per Diem Per Cage .69
Denver Health Rat Per Diem Per Cage 1.46
Technician Fees
Animal Care Tech Time Tech Time Per Hour 16.17
Vet Tech Time Tech Time Per Hour 18.15
Surgery Fees
Table Charge Internal Customer Per Event 120
Table Charge External Customer Per Event 289
Anesthesia Per Hour 22.27
Admin Charge External Customer Per Event 140.00
Special Order Goods Per Item Cost
Veterinarian Time Per Hour 69.23
Vivarium – Animal Housing & Care
From: Leszczynski, J ori
Sent: Thursday, October 01, 2009 9:29 PM
a) How is the quality of your measurements evaluated – quality control?
We monitor all housing rooms for temperature, humidity, and light cycle.
The system will alarm if there are any issues. All equipment is calibrated on
a set schedule. Cage changing is handled on a specific basis. All treatments
and husbandry procedures are accurately recorded. This is checked on a
regular basis by supervisors.
b) What is the turn-a-round time for the service you provide?
This depends on what type of service the PI is looking for. The specific
service due dates are negotiated with each PI.
c) Who documents the data provided and signs off on the data?
This could be the PI, the veterinary staff or the animal care staff depending
on the information required. At this point we are not performing GLP
studies which would require a study director and other more formal data
reporting requirements.
d) Have you had experience providing data for industry?
There are people in the organization that have experience with providing
data for industry. We currently are not set up as a GLP lab though. We
would require prep time to be able to do this. However if someone needs to
do pre-GLP discovery work, we can definitely provide this service.
e) Do you have a standard operating procedure manual?
Yes, we can make this available
f) How will you track billing and financial aspects of your core?
We use the Granite system by Topaz Technologies. We can accept checks
or charge by credit card.
X-Ray Core Facility
Contacts:
Mair Churchill, PhD
Professor, Director of the X-ray core facility
Department of Pharmacology
University of Colorado Denver
12801 E. 17
th
Avenue, Mail Stop 8303
Aurora, CO 80045
Phone: 303-724-3670
Fax: 303-724-3663
Email: [email protected]
Sarah Roemer, PhD
Instructor, Facility Manager of the X-ray Core
Facility
Department of Pharmacology
12801 E. 17
th
Avenue, Mail Stop 8101
Aurora, CO 80045
Phone: 303-724-3672
[email protected]
Website:http://biomol.uchsc.edu/cores/xray/
The X-ray core facility was set up in 1999. The facility is fully equipped for biomolecular
crystallization, crystal screening, data collection, data processing, structure-determination and
model building. It currently has a Rigaku/MSC Ru-H3R X-ray generator, two Raxis IV++ area
detectors, and two X-stream cryo-cooling apparatus. The facility is located in RC1 South
Building Rm 1301. It is directed by Dr. Mair Churchill (Department of Pharmacology), and is
managed by Sarah Roemer (Department of Biochemistry and Molecular Genetics).
User Fees and Policies
For 2008-2009 the fees are:
Service
Cancer Center
Member-major
user
Cancer
Center
Member
Non Cancer
Member
Private
Sector User
Service contract $2500/yr 0 0 0
Data Collection $10 /hr $25 /hr $35 /hr $50/hr
Crystallization
access per quarter 0 $100 $250 $500
Alchemist (block w/own
reagents and supplies)
$2 $2 $4 $50
Alchemist (block
w/facility reagents and
supplies)
?$30 ?$30 ?$50 ?$75
Phoenix (tray w/own
reagents and supplies)
$2 $2 $4 $50
Phoenix (tray w/facility
reagents and supplies)
~$16 ~$16 ~$32 ~$64
Minstrel per image $2 $2 $4 $10
Materials at cost
Labor for service cost cost cost $50/hr
Crystal Screening $250 / half day
$250 /
half day
$500 / half
day
$1500 /
half day
Beamline usage
Crystal screening $25 $25 $25 N/A
Data set $100 $100 $100 N/A
*Price are subject to change
• Access to facility by other faculty, staff, postdoc and students: Facility open to all
UCHSC faculty, staff, postdocs and students, but need approval of the X-ray facility
steering committee to arrange details.
Services Currently Provided
• Project design and consultation: Assistance with starting projects includes advice on
protein expression and purification, and crystallization. Until now these services have
been provided in direct collaboration with the primary users. Since the manager has just
become available, these services will be more broadly available to all members of the
cancer center.
• Crystallization screening: Facilities for setting up crystal growth trays is available.
• Screening crystals: Crystal (diffraction) screening is available.
• Data collection: Data collection service is available.
X-Ray Crystallography
From: Mair Churchill [mailto:[email protected]]
Sent: Monday, November 02, 2009 11:04 AM
Structural Biology core UCCC core facility (X-ray)
a) How is the quality of your measurements evaluated – quality control?
Standard practices in Structural Biology
b) What is the turn-a-round time for the service you provide?
N/A
c) Who documents the data provided and signs off on the data?
The users
d) Have you had experience providing data for industry?
No but the facility can be used by industry users for a fee that is already set for each type
of service or access.
e) Do you have a standard operating procedure manual?
For safety protocols only.
f) How will you track billing and financial aspects of your core?
The core manager does this.
Zebrafish Transgenic Core
Contact:
Angie Ribera, PhD
Director
303-724-4517
[email protected]
http://www.uchsc.edu/neuroscience/Program/cores.htm
The NINDS P30 Center Zebrafish Core has three Specific Aims:
1. Create transgenic lines of zebrafish that express different fluorescent proteins in specific
populations of pre- and postsynaptic neurons
2. Create transgenic zebrafish strains that express genetically-encoded calcium indicator
dyes in specific neuronal populations
3. Maintain transgenic and wild type zebrafish strains for the UCD neuroscience community
During the first year of the grant, the fish facility at the Fitzsimons campus is being optimized
and we are focusing on Aim 3. In subsequent years, Aims 1 and 2 will be a priority. The Core
can cover the expenses associated with breeding wild type fish for pilot experiments. If you
would like to use zebrafish embryos for pilot experiments, please contact Angie Ribera
([email protected]) for further information.
Zebrafish transgenic lines express GFP in specific
neuronal subpopulations.
In the Figure, GFP expression is driven by the flh
promoter. (This transgenic line was developed by Drs.
Marnie Halpern and Josh Gamse - Carnegie Institute of
Washington). At 48 hours post fertilization, GFP
expression (green) is present in specific populations of
motor neurons that extend axons either ventrally (down,
asterisks) or dorsally (up, arrowhead). A subset of the
axons also expresses the zn-8 epitope (red). Zn-8 is a
marker for axons of later-born (secondary) motor
neurons.
Scale Bar: 25 µm.
Zebra Fish Transgenic
From: Ribera, Angie
Sent: Friday, October 02, 2009 10:10 AM
a) How is the quality of your measurements evaluated – quality control?
Quality is assured by two means: 1 – The RMNDC Steering Committee meets on a
regular basis to review Core performances. 2 – Users: most users come back and use
services again, meaning that they were at a minimum satisfied with previous use.
b) What is the turn-a-round time for the service you provide?
Depends on the Core and the request. For use of a microscope, turn around can be
immediate. For construction of gene targeting vector, turn around can be several months.
c) Who documents the data provided and signs off on the data?
Each Core’s Manager/Director.
d) Have you had experience providing data for industry?
NO
e) Do you have a standard operating procedure manual?
NO
f) How will you track billing and financial aspects of your core?
Each Core’s Manager/Director.
doc_396173378.pdf
University of Colorado Denver Anschutz Medical Campus Core Facilities
University of Colorado
Denver| Anschutz Medical Campus
Core Facilities
Prepared by
Richard J. Traystman, PhD
Vice Chancellor for Research
and
Paula McGuigan
Executive Assistant
Office of the Vice Chancellor for Research
Fees & Services are not guaranteed
Tab
Core Name Director/Contact Name
A
Administration (IDDRC) Karl H. Pfenninger, MD
Administration (UCCC) Dan Theodorescu, MD, PhD
Adult CTO (CCTSI) Barbara DiMercurio, RN, MBA
Advanced Microscopy Core Facility
Andrew Millard, PhD
Moshe Levi, MD
Altitude Research Center
Ben Honigman, MD
Robert Roach, PhD
Animal Models (IDDRC) Ken Maclean, PhD
B
A
Bard Center for Entrepreneurship Catherine Kunst, MBA, PhD
Bio-Imaging Research Laboratory (BIRL) David Miller, PhD
Bimolecular NMR Core Facility David Jones, PhD
Biophysics Core Facility Robert Hodges, PhD
Biorepository Core Facility Scott Lucia, MD
Biostatistics & Bioinformatics (UCCC) Anna Baron, PhD
B
C
Cellular Systems and Analysis (IDDRC) Karl Pfenninger , PhD
Center for Computational Mathematics (CCM) Jan Mandel, PhD
CCTSI CTRC Behavioral Medicine (NJH) Fred Wamboldt, MD
CCTSI CTRC Inflammation & Immunology (NJH) Lisa Maier, MD
CCTSI CTRC Nursing Diane Branham, RN, BSN
CCTSI CTRC Nutrition Janine Higgins, PhD
CCTSI CTRC Research Nursing & Facilities (NJH) Donald Leung, MD., PhD
CCTSI CTRC Research Nursing & Facilities (UCB) Elizabeth Connick, MD
Clinical Investigations Core (CFAR) Cara Wilson, MD
Clinical Investigations Core (UCCC) Anthony Elias, MD
Clinical Sciences PhD & MS Program Lisa Cicutto, PhD., RN
Clinical Trials Organization Jill McHale
Colorado Advanced Photonics Technology (CAPT) Larry Scherrer
Colorado Biostatistics Consortium John Neal
Colorado Genetics Lab
Karen Swisshelm, Ph.D., FACMG
Loris McGavran, Ph.D., FACMG
Colorado Health Outcomes Program (COHO) David West, PhD
Colorado Multiple Institutional Review Board (COMIRB) Marie Wade
Computational Biology Core Robert Hodges, PhD
Cytogenetic Core Laboratory (UCCC) Marileila Varella-Garcia, PhD
D
C
Developmental Core (CFAR) Myron Levin, MD
Diabetes & Endocrinology Research Center (DERC) John C. Hutton, PhD
DNA Diagnostic Laboratory Elaine Spector, PhD
DNA Sequencing and Analysis Core (UCCC) Christopher Korch, PhD
E Evaluation Center Bonnie Walters
D
Tab
Core Name Director/Contact Name
Flow Cytometry and Cell Sorting (CFAR) Brent Palmer, PhD
Flow Cytometry Services (UCCC) Christopher J. Hogan, PhD
Gene Expression, Microarray & PCR(UCCC) Mark Geraci, MD
Gene-Targeting/Viral Vector Core Mark Dell'Acqua, PhD
Grants & Contracts Pam Jones, PhD
High-Throughput Genome Sequencer David Pollock, PhD
HLA (Histocompatibility) Testing and Umbilical Cord Blood Bank Brian M. Freed, PhD
Histology Core Roberto Gianani, MD
Informatics Core (UCCC) Jessica Bondy, MHA
Institutional Animal Care and Use Committee (IACUC) Mark Douse, PhD
Interdisciplinary Transcranial Magnetic Stimulation Benzi Kluger, MD
Laboratory Science Core Elizabeth Connick, MD
Laser Capture Core Wilbur Franklin, MD
Light Microscopy Bill Betz, PhD
Machine Shop Ulli Bayer, PhD
Mass Spectrometry (CNRU) Uwe Christians, PhD., MD
Mass Spectrometry Facility (NJH) Nichole Reidorph, PhD
Medicinal Chemistry Core Facility Michael F. Wempe, PhD
Metabolomics Core (NMR) Natalie Serkova, PhD
Metabolic Core (CNRU) Jed Friedman, PhD
Molecular discovery (IDDRC)
Frank Frerman, PhD
Elaine Spector, PhD
Morphology and Phenotyping Core Maranke I. Koster, PhD
Musosal and Vaccine Research Colorado (MAVRC) Ed Janoff, MD
Pathology Core (UCCC) Wilbur Franklin, MD
Peptide and Protein Chemistry Core Robert Hodges, PhD
Pharmacology (UCCC) Daniel L. Gustafson, PhD
Pregnancy Core Peggy Neville, PhD
Protein Production-Moab-Tissue Culture (UCCC) Steven Nordeen, PhD
Proteomics (Mass Spectrometry) (UCCC) Mark Duncan, PhD
RADScience Clinical Trials Physics Support Ann Scherzinger, PhD
Research Design & Analysis Core (CFAR) Samantha MaWhinney, ScD
Rodent In Vivo Neurophysiology Core Yogendra Raol, PhD
Shared Analytical Service Laboratory Jeff Boon
Statistical Consulting Service Loren Cobb, PhD
Small Animal Imaging Core (UCCC) Natalie Serkova, PhD
S
M
P
R
F
L
H
G
I
Tab
Core Name Director/Contact Name
Transgenic and Gene Targeting Core Peter Koch, PhD
Translational Nexus (IDDRC) Cordelia Robinson, PhD
U UCH-CTRC Core Laboratory (CCTSI) Bryan Haugen, MD
V Vivarium - Animal Housing & Care Jori Leszczynski, DVM DACLAM
X X-Ray Crystallography Mair Churchill, PhD
Z Zebrafish Transgenic Angie Ribera, PhD
UCCC - University of Colorado Cancer Center
CFAR - Center for Aids Research
CCTSI - Colorado Clinical and Translational Sciences Institute
IDDRC - Intellectual and Developmental Disabilities Research Center
CAPT - Colorado Advanced Photonics Technology
COHO - Colorado Health Outcomes
ARC - Altitude Research Center
NJH - National Jewish Hospital
NMR - Nuclear Magnetic Resonance
T
Administration (IDDRC-UCD)
The Colorado Intellectual & Developmental
Disabilities Research Center (IDDRC)
The Administrative Core unit provides the Center’s personnel and fiscal management
infrastructure, as well as the interface with the NICHD, other IDDRCs, the AUCD, the
University, and the public. Furthermore, this core acts as the information hub of the IDDRC and
organizes educational activities, junior faculty mentoring, and collaborator referral.
Contacts:
Karl H. Pfenninger, MD
Director
303-724-3466
[email protected]
Frank Frerman, PhD
Associate Director
303-724-3809
[email protected]
Carrie John
IDDRC Administrator
303-724-3839
[email protected]
Carmel Harberg
Program Assistant
303-724-4349
[email protected]
http://www.ucdenver.edu/academics/colleges/medicine/Centers/IDDRC/research/admincore/Pages/IDDR
CAdministration.aspx#directors
The IDDRC Administration is located in the RC-1 North Building of the University of Colorado
Denver Anschutz Medical Campus in Aurora, CO. Click here for IDDRC contact information.
Services
1) Educational Activities
Contact: Alberto Costa, MD, PhD ([email protected])
Goals: to advance knowledge, to enhance interaction among IDDRC members, and to explore
and stimulate collaborations in IDD research.
The Administrative Core organizes annually three or four workshops or mini-symposia focused
on a particular topic of IDD. The format of these conferences is interdisciplinary, with only brief
presentations from individuals working in epidemiology, basic science, clinical research, and
rehabilitation as they relate to the selected topic. Most of the meeting time is spent on
discussion.
2) Collaborator Referral and Faculty Mentoring
Contact: Karl Pfenninger, MD ([email protected])
Goals: To assist with the identification of potential collaborators for interdisciplinary projects.
The CCTSI hosts InfoEd software to facilitate the search for appropriate collaborators. The
Center Director also assists with advice regarding potential collaborators and identifying
appropriate faculty mentors for young investigators. The IDDRC is committed to not only
recruiting new investigators to IDD research but also helping them develop strong and
competitive research programs.
3) Liaisons with other IDDRCs and local entities that deal with IDD
Contact: Karl Pfenninger, MD ([email protected])
4) Community Outreach
Contact: Karl Pfenninger, MD ([email protected])
Goals: To educate the public in the area of IDD and to share information on important research
advances and new treatments. The Colorado IDDRC present public lectures about twice a year.
The IDDRC’s website (see below) has a special section for public use that is designed to
disseminate information on access to appropriate clinics, the performance of clinical trials in
specific areas of IDD, and progress in research on IDD. Furthermore, there are links to NIH
websites and to those of specific support groups in the area and nationally.
The IDDRC also maintains contact with a number of State and local agencies that serve people
with IDD and with local support groups, such as the Mile High Down Syndrome Association,
Autism Society of Colorado, Colorado Family Voices, the Colorado Arc, and the Colorado
Developmental Disabilities Council.
Administrative Core
University of Colorado Cancer Center
The Administrative Core provides administrative and fiscal oversight for the University of
Colorado Cancer Center (UCCC) entities as described in the NCI Cancer Center Support
Grant that funds UCCC, for the Lung Special Program of Research Excellence (SPORE)
and any other grants in the Cancer Center.
Contacts:
Dan Theodorescu, MD, PhD
Director
303-724-3150
[email protected]
Mark Kochevar
Associate Director for Administration & Finance
303-724-5724
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/administration/Index.aspx
Administration
Sets business objectives, mission, vision
• Manages daily operations
• Negotiates contracts
• Manages relationships with affiliates
Manages & allocates physical space
•
Grants & Contracts Management
• Administers daily business procedures for all multidisciplinary funded grants routed
through UCCC
• Pre- and post-award
• Manages the CCSG and Lung SPORE
• Manages subcontracts
Supports all multidisciplinary funded grants and contracts held by UCCC members
• Manages the American Cancer Society Institutional Research Grant/UCCC Seed
Grants program
• Maintains membership publication database
Human Resources and Finances
• Recruitment, hiring, personnel issues and payroll
• Manages institutional funds, gift accounts and facility funds
• Manages compliance with Federal, State and CU policies
• Grant account reconciliation
• Accounts payable/accounts receivable
• Budgeting
• Audits
Membership, Education & Career Development
Coordinates the UCCC membership program, including applications and database
• Coordinates the weekly UCCC Symposium
• Coordinates the Lung SPORE and Thoracic Oncology Program seminars
• Manages the UCCC Student Cancer Research Fellowship Program
Public Relations & Communications
• Publications, including the weekly Director’s Newsletter and TOPICS, a three-times
yearly external newsletter
• Web site development and management
• Media relations
• Internal communications, including monthly newsletter Six Things from the Sixth Floor
• UCCC marketing/marketing communications
• Event management
• Legislative communications
• Fundraising communications
Fundraising
UCCC employs one full-time fundraiser. The University of Colorado Foundation and
AMC Cancer Research Center both also employ development staff who raise money
for UCCC.
• Donor cultivation, solicitation and stewardship
• Fundraising events
• Grateful patient program
• Manages the Community Advisory Board
• Maintains relationships with Cancer League of Colorado, Cancer Cure,
the American Cancer Society and other groups that support UCCC
No fees
Adult CTO
Barbara DiMercurio, RN, MBA
Clinical Nursing Director
Colorado Clinical and Translational Sciences Institute
Clinical Translational Research Centers
UCH/TCH/UCB/NJH
12605 East 16th Street, Room 12.062
Aurora, CO 80045
[email protected]
Office: 720-848-6420 Fax: 720-848-7347
Cell: 303-524-5967
SIMS
CODE
Facility Fee Charge
1672 CTO Review Fee $525.00
1600 Inpatient Med Surg Room Rate $857.74
1601 Inpatient Med Surg with Tele Room Rate $1,000.00
1602 Inpatient Step Down Room Rate $1,500.00
1603 Inpatient ICU Room Rate $1,566.92
1604 Inpatient Short stays (0-4 hours) $142.96
1605 Inpatient Short stays (5-13 hours) $464.62
1606 Inpatient Short Stays (14-23 hours) $822.00
1607 Telemetry monitoring $50 per hour
1609 Outpatient exam room 20 mins $60.00
1610 Outpatient exam room 20 mins without RN $40.00
1611 Outpatient exam room 21-39 mins $70.00
1612 Outpatient exam room 21-39 mins without RN $50.00
1613 Outpatient exam room 40-59 mins $85.00
1614 Outpatient exam room 40-59 mins without RN $60.00
1615 Outpatient exam room 60-120mins $130.00
1616 Outpatient exam room 60-120mins without RN $80.00
1617 Outpatient exam room > 120 mins $200.00
1618 Outpatient exam room > 120 mins without RN $110.00
1619 Infusion Chair 1st Hour $125 1st hour
1621 Infusion Chair each additional hour $30 each additional hour
1620 Infusion Chair 1st Hour without RN $60 1st hour
1622 Infusion Chair each additional hour without RN $20 each additional hour
Physician Assistant (PA) Services
1683 Investigator Initiated (A) study PA consult $15 per 15 min.
1684 CTO PA consult $ 25 per 15 min.
1685 CTO PA ON CALL $ 200 per night
1686 Investigator Initiated (A) study PA ON CALL $100 per night
1687 CTO PA H&P $100.00
1688 Investigator Initiated (A) Study H&P $50.00
1689 Investigator Initiated (A) PA Stress Treadmill Testing $50.00
1690 Investigator Initiated (A) PA + RN Treadmill Testing $100.00
1633 CTO Stress Treadmill Testing ( basic) $375.00
1634 CTO VO2 Max Testing $375.00
Inpatient and Outpatient Testing Charge
1692 TB Skin Testing $50.00
1623 Venipuncture ( 1 time only) $25.00
1640 After Hours Blood draw $40.00
1624 Port or central line blood draw $100.00
1625 Pharmacokinetics ( + 1 Venipuncture charge) $12 per draw
1691 Pharmacokinetics Sample processing $ 5 per draw
1626 Pulse Ox ( 1 time only) $20.00
1627 Pulse Ox ( serial or continuous) $100.00
1681 ECG ( low) $50.00
1628 ECG ( 1 time only) $100.00
1629 ECG ( serial) $200.00
1608 One to One RN charge ( hourly) $100 per hour
1630 Intravenous Glucose Tolerance Test (IVGTT) $300.00
1631 Oral Glucose Tolerance Test (OGGT) $200.00
1632 Mix Meal Tolerance Test (MMT) $200.00
1633 Stress Treadmill Testing ( basic) $375.00
1634 VO2 Max Testing $375.00
1635 Calorimetry Room stay (per hour) $100 hour
1636 Calorimetry Room stay $800.00
1637 RMR ( includes interpretation) $300.00
1638 Bike Exercise Testing $375.00
1679 D-Xylose Absorption Test $300.00
1682 Liver Biopsy ( ultrasound) $50.00
1677 Kidney Biopsy $300.00
1680 Complex Infusion $620.00
1678 6 Min Walk Test $24.99
1641 Supplies (low) $30.00
1642 Supplies (mod) $60.00
1643 Supplies (high) $90.00
1644 DXA Lumbar spine $250.00
1645 DXA Proximal femur $250.00
1646 DXA Total body $250.00
1647 DXA SPINE, FEMUR, WHOLE BODY $500.00
Core Echo Laboratory
1648 Ejection Fraction (EF) ONLY $150.00
1649 2-D ECHO BASIC $250.00
1650 2-D ECHO DOPPLER & FLOW MAP $400.00
1651 Tissue Doppler /Tissue Track/Stain $450.00
1652 Exercise Stress Echocardiogram $500.00
1653 Stress ECHO-PHARM $600.00
1654 3-D Echocardiogram $450.00
1655 Arterial INTIMA-MEDIAL Thickness (IMT ONLY) $100.00
1656 Femerol Artery imaging $100.00
1657 BRACHIAL ARTERY FLOW MED VASODIL(FMD) $250.00
1658 CAROTID DUPLEX-BILATERAL $350.00
1659 US MACHINE W ASSISTANCE 60 MIN UNITS $75.00
Nutrition Services Cost
Inpatient meals $0.00
1668 Breakfast ( Basic select menu) $8.00
1669 Lunch ( Basic select menu) $13.00
1670 Dinner ( Basic select menu) $19.00
1671 Snack ( Basic select menu) $5.00
1673 Breakfast-metabolic $16.00
1674 Lunch -metabolic $22.00
1675 Dinner -metabolic $32.00
1676 3 day weighed, metabolic diets $195.00
1660 Gourmet meals $38.00
1661 Personalized eating plan $200.00
1662 Recipe modification (simple) $40.00
1663 Recipe modification (complex) $85.00
1664 Weight loss counseling $65/hour (plus personalized eating plan
1665 Food preparation classes $65/hour plus ingredients at cost
1666 Supermarket tours $65/hour
1667 Travel $30/hour
Advanced Microscopy Core Facility
Contacts:
Andrew C. Millard, PhD
Tel: 303-724-4856
[email protected]
For reservation and equipment questions
Moshe Levi, MD
Tel: 303-724-4825
[email protected]
Rachael Fuhrman
Tel: 303-724-4849
[email protected]
For invoice and billing questions
Facility Overview
We have several microscopes in the R2 DOM-SOM Facility including: 1) a Laser-Scanning
Confocal/Multiphoton-Excitation (MPE) and Second Harmonic Generation (SHG) fluorescence
microscope with a Meta spectral detection system (Zeiss NLO 510 with META) and an
environmental chamber; 2) a Total Internal Reflection Fluorescence (Zeiss TIRF) microscope
with an environmental chamber; 3) a Fluorescence Correlation Spectroscopy (FCS) and
Fluorescence Lifetime Imaging Microscope (FLIM) (ISS) equipped with an environmental
chamber; and 4) a forthcoming Coherent Anti Stokes Raman Scattering (CARS) Microscope
equipped with an environmental chamber. These microscopes allows for the high-resolution
analysis of fixed samples as well as the time-resolved imaging of live cells. These microscopes
are also set up to conduct biophysical studies in live cells such as fluorescence recovery after
photobleaching (FRAP), fluorescence resonance energy transfer (FRET), fluorescence
correlation spectroscopy (FCS) and fluorescence lifetime imaging (FLIM). These techniques are
of considerable use in studying the dynamics of lipids and protein in live cells and the
interactions of transcription factors and signaling molecules.
Recent Publications
PTH-Induced Internalization of Apical Membrane NaPi2a: Role of Actin and Myosin VI by
Judith Blaine et al., American Journal of Physiology - Cell Physiology (Sept. 2009)
Liver Cyst Cytokines Promote Endothelial Cell Proliferation and Development by Kelley
Brodsky et al., Experimental Biology and Medicine (July 2009)
Noggin Enhances Dopamine Neuron Production from Human Embryonic Stem Cells and
Improves Behavioral Outcome after Transplantation into Parkinsonian Rats by Shunmai
Chiba et al., Stem Cells (Sept. 2008)
Advisory Committee
William Betz, PhD, University of Colorado Denver
Eric Betzig, PhD, Howard Hughes Medical Institute
Emily Gibson, PhD, University of Colorado Denver
Enrico Gratton, PhD, University of California, Irvine, Lab for Fluorescence Dynamics
Tim Lei, PhD, University of Colorado Denver
Jennifer Lippincott-Schwartz, PhD, National Institute of Child Health and Human
Development
William Mantulin, PhD, University of California, Irvine, Lab for Fluorescence Dynamics
George Patterson, PhD, NIBIB (National Institute of Biomedical Imaging and
Bioengineering)
Eric Olaf Potma, PhD, University of California Irvine
Diego Restrepo, PhD, University of Colorado at Denver and Health Sciences Center
Bruce Tromberg, PhD, University of California, Irvine, Beckman Laser Institute
Paul Wiseman, PhD, McGill University
X. Sunney Xie, PhD, Harvard University
UC Denver Participants
Kurt Beam, PhD, Department of Physiology and Biophysics
Peter Buttrick, MD, Division of Cardiology
Sean Colgan, MD, Division of Gastroenterology and Hepatology
Elizabeth Connick, MD, Division of Infectious Diseases
Brian Doctor, PhD, Division of Gastroenterology and Hepatology
Curt Freed, MD, Division of Clinical Pharmacology and Toxicology
Glenn Furuta, MD, Gastrointestinal Eosinophil Disease Center
Mark Geraci, MD, Division of Pulmonary Sciences and Critical Care Medicine
Emily Gibson, PhD, Department of Physics
Michael Holers, MD, Division of Rheumatology
John Hutton, PhD, Barbara Davis Center for Childhood Diabetes
Richard Johnson, MD, Division of Renal Diseases and Hypertension
Chifong (Tim) Lei, PhD, Department of Electrical Engineering
Simon Rock Levinson, PhD, Department of Physiology and Biophysics
Susan Majka, PhD, Division of Cardiology
James McManaman, PhD, Department of Physiology and Biophysics
Raphael Nemenoff, PhD, Division of Renal Diseases and Hypertension
Jane Reusch, MD, Division of Endocrinology, Metabolism and Diabetes
Hugo Rosen, MD, Division of Gastroenterology and Hepatology
Pepper Schedin, PhD, Division of Medical Oncology
Robert Schrier, MD, Division of Renal Diseases and Hypertension
Natalie Serkova, PhD, Department of Anesthesiology
Kurt Stenmark, MD, Department of Pediatrics
Lisa Wise-Faberowski, PhD, Department of Anesthesiology and Pediatric Cardiology
The Zeiss LSM 510 META microscope system (in conjunction with the Coherent
Chameleon for both two-photon and confocal fluorescence imaging) is available for routine
use, including demonstrations, hands-on training and research support.
The other microscope systems are also available for specialized projects.
Advanced Microscopy Core Facility
From: Levi, Moshe
Sent: Wednesday, December 02, 2009 1:46 PM
.
a) How is the quality of your measurements evaluated – quality control?
We have quality controls depending on the individual microscopes and individual
techniques that we use to align our lasers, optics, and images.
b) What is the turn-a-round time for the service you provide?
In our case the investigators/technicians sign up depending on the available spots and
they perform their imaging usually within the same week.
c) Who documents the data provided and signs off on the data?
Dr. Andrew Millard
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Yes: for each microscope and imaging technique.
f) How will you track billing and financial aspects of your core?
We have administrative personnel who takes care of the billing and Dr. Andrew
Millard and Dr. Moshe Levi go over the finances on a periodic basis.
Altitude Research Center (ARC)
Benjamin Honigman, MD
Director ARC
Professor of Emergency Medicine
F524 - PO Box 6508
12469 East 17th Place
Aurora, CO 80045-0508
[email protected]
Robert Roach, PhD
Research Director
Associate Professor of Emergency Medicine
303-724-1641
[email protected]
For clinical consultations at the
Altitude Clinic: 720-848-2631
ARC-Foundation: 720-284-7074
http://www.altituderesearch.org/
The Importance of Oxygen
A continuous supply of oxygen i s essential f or proper physical and mental f unctioning. If t his
supply is compromised for any reason, a condition called hypoxia, or a lack of oxygen, results.
Everyone who t ravels t o hi gh a ltitude e xperiences s ome de gree of h ypoxia b efore t heir bod y
adapts to the lower oxygen levels, and they know the feeling well. Simple physical tasks become
much more difficult and mental deficits begin to appear. But altitude isn't the only factor causing
hypoxia: millions of people experience chronic hypoxia and these same symptoms every day at
sea level due to common cardiovascular and respiratory diseases.
Despite this s ignificant i mpact on quality of lif e, large gaps s till exist in our understanding of
how the body is impacted by hypoxia. There is little to no research exploring how altitude affects
vulnerable popul ations, s uch a s aging popul ations with unde rlying c ardiovascular, respiratory,
and metabolic di seases. The pr essing ne ed t o u nderstand s uch ba sic p roblems be comes e ven
clearer when the economic impact of hypoxia is considered. The Altitude Research Center exists
to address these problems using the full array of modern medical research tools.
Our Mission
Improving life through research on how hypoxia affects health and performance
Our Goal
Developing distinguished research programs in four key areas:
1. epidemiology of altitude problems in travelers and the impact of hypoxia on common
diseases in residents of altitude
2. clinical outcomes research
3. integrative physiology
4. cell, molecular and genomic mechanisms of hypoxia
The Impact of Hypoxia
A continuous supply of oxygen i s essential f or proper physical and mental f unctioning. If t his
supply is compromised for any reason, a condition called hypoxia, or a lack of oxygen, results.
Everyone who t ravels t o hi gh a ltitude e xperiences s ome de gree of h ypoxia be fore t heir bod y
adapts t o t he l ower oxygen l evels. At hi gh altitude, s imple physical t asks become much more
difficult and mental deficits begin to appear. But altitude isn't the only factor causing hypoxia:
millions of pe ople a t sea l evel experience c hronic h ypoxia e very day due t o common
cardiovascular and respiratory diseases.
Despite this s ignificant i mpact on quality of lif e, large gaps s till exist in our understanding of
how the body is impacted by hypoxia. There is little to no research exploring how altitude affects
vulnerable popul ations, such as elderly people with underlying cardiovascular, r espiratory, and
metabolic diseases. The pressing need to understand such basic problems becomes even clearer
when t he economic i mpact o f h ypoxia i s co nsidered. The Altitude Research Center ex ists t o
address these problems using the full array of modern medical research tools.
The center has research programs in four distinct areas:
1. epidemiology
2. clinical outcomes research
3. integrative physiology
4. cellular, molecular, and genetic biology
Each a pproach bui lds o n t he ot hers i n or der t o a chieve t he m ost c omplete unde rstanding
possible. Epidemiological s tudies qua ntify t he s cope of a ltitude r elated problems a nd i dentify
specific at risk populations. Integrative studies look at physiological changes on t he level of the
organism w hile c ellular, m olecular, and genomic i nvestigations e xamine t he f undamental
mechanisms underlying these changes. This understanding ultimately improves clinical treatment
of problems related to altitude.
Research
The Altitude Research Center studies hypoxia to improve health and
performance. The Center conducts international, cutting edge work in
hypoxia research from the basic physiological to the molecular level.
The Altitude Research Center Laboratory staffs 6 renowned
scientists:
• Robert Roach, PhD
• Andrew Subudhi, PhD
• Benjamin Honigman, MD
• Colleen Julian, PhD
• Megan Wilson, PhD
• Deborah Thomas, PhD
The ARC laboratory is equipped with a state-of-the-art altitude chamber, comprehensive
laboratory facilities, extensive computing resources, and novel instrumentation.
Original research at the Altitude Research Center:
• Brain Response to Low Oxygen and Relation to Acute Mountain Sickness
• Genetics of Acute Mountain Sickness
• Genetics of Human Athletic Performance
• Genetics of Low Birth-weight Babies at High Altitude
A natural pr ogression i n s cience i s pr oof of concept by s mall, i nnovative exploratory r esearch
programs that can lead into larger, fully funded programs. This is key because at the University
of Colorado Denver Anschutz Medical Campus our ARC researchers and their staffs are 100%
supported by research funding. We support a number of exploratory i nternally funded research
programs that we hope lead to funding opportunities:
• Multiple Sclerosis Progression at Altitude versus Sea Level
• Longevity and Cardiovascular Disease at Altitude
• Malaria and Altitude
Hypobaric Chamber CORE
The hypobaric chamber is an i ntegral CORE of the Altitude Research Center ( ARC). It has 2
sealed rooms in series and each room has a port connected to a vacuum source. When vacuum is
applied to either the main chamber or the lock using chamber controls, air is removed from the
room(s) causing t he pressure i nside t o drop. This pressure drop creates a simulated i ncrease i n
altitude and the resultant hypoxia associated with the specific elevation attained. Hypoxia can be
controlled easily by adjusting the altitude and the pressure and the rooms can then be used for a
variety of research experiments testing the effects of hypoxia on humans.
The CORE can h ouse b etween 2 -4 r esearch s ubjects an d an eq ual n umber o f r esearchers i n
addition t o e quipment which c an measure c erebral f low, ve ntilation a nd ox ygenation, NIRS,
ECHO and a number of other cardiac and pulmonary functions. Any device that is portable can
be used in the chamber in order to measure other physiologic functions such as EEG, EKG etc.
Areas of research interest of the ARC for which the CORE can be used include:
Migraine Headaches
Genetic testing and exercise performance
Cerebral blood flow and auto regulation
CSF vascular dynamics
Pulmonary functions
Cardiac function
Drug metabolism and Kinetics
Hypoxia based Drug development
Prices for CORE use:
Chamber testing: 1 subject-- $1000/day; 2 subjects $1500/day; 3 -4 subjects--$2000/day—may
vary depending on the protocol needs
Protocol Development and Consultation: $200/hr
Animal Models Core (IDDRC)
Director:
Ken Maclean, PhD
303-724-3818
[email protected]
Co-Directors:
Tim BenkeMD, PhD (Design of behavioral studies)
303-724-3568
[email protected]
Michael Mesches, PhD (Behavioral testing operations)
[email protected]
Natalie Serkova, PhD (Imaging and Metabolomics)
303-724-1086
[email protected]
Mission
The objectives of the Animal Models core are three-fold: (1) to provide animal husbandry and
genotyping services to IDDRC investigators; (2) to provide expertise, assistance and facilities for
assessing the behavioral phenotype of genetically modified or other experimental rodents; (3) to
provide access to equipment and expertise for small-animal radiologic imaging and for in-situ
and in-vitro metabolomic analysis using NMR spectroscopy.
Staffing
Consultants
Albee Messing, PhD, DVM Mouse genetic engineering
Elaine Spector, PhD PCR genotyping [email protected]
Gary Zerbe, PhD Biostatistics (behavioral assessment) [email protected]
Technical Staff
Hua Jiang, PhD [email protected]
Marian Maslak [email protected]
Megan Ferguson [email protected]
Services
1. Use of Animal Models; Protocols
Contact Person: Ken Maclean ([email protected])
Dr. Maclean advises IDDRC investigators in the development phase of grant proposals involving
animal models and provides assistance with preparation of animal protocols (he is a member of
the IACUC). A variety of approved standard protocols are maintained in a database and available
for incorporation by investigators into their animal protocols.
2. Animal Husbandry and Genotyping.
Contact Person: Ken Maclean ([email protected])
The Animal Models core maintains a number of colonies of mouse models of IDD and normal
control animals, together with a comprehensive database on the animals, including normative
data on control subjects on each genetic background.
List of Wild-Type and Mutant Mice Currently Available
C57BL/6J wild-type controls
FVB/N wild-type controls
Ts65Dn (female offspring that carry the
Ts65Dn mutation are bred with hybrid
C57BU6J Ei x C3H/HeSnJ F1 males)*
Down syndrome model
Maeda CBS knockout** CBS-deficient
1181*** Transgenic for human CBS gene; Down
syndrome
ho.CBSDH (selective crossing of 1181
with heterozygous Maeda knockout mice)
CBS-deficient homocystinuria
GCDH knockout**** glutaric acidemia
* Reeves, R.H., et al., 1995. Nat. Genet. 11, 177-84.
** Watanabe, M., et al., 1995. Proc. Natl. Acad. Sci., USA 92, 1585-9.
*** Butler, C., et al., 2006. Behav. Genet. 36, 429-38.
**** Koeller, D.M., et al., 2002. Hum. Mol. Genet. 11, 347-357.
The core, in consultation with IDDRC investigators, breeds the mice, provides timed generation
of pregnancies and newborn mice, administers special diets and collects blood and/or tail
samples for genotyping. PCR and FISH-based genotyping are available. The core also provides
training in the correct technique for making blood smears suitable for FISH analysis.
Fees: Occasional use of mice from the Center’s breeding stocks is free. However, the
investigators’ grants must pay for extra mouse cages needed to breed and supply mice on a
regular basis. Please contact Ken MacLean for information regarding these fees.
3. Transgenic/knockout/knockin mouse generation.
Contact: Ken Maclean ([email protected])
In addition, the IDDRC has a collaborative agreement with the Rodent Models Core of the
Waisman Center under the leadership of Dr. Messing whereby vectors can be sent to the
Waisman Center, where all cell and animal work required to generate transgenic/knockout/
knockin mice is performed. Founder mice are then shipped back to Colorado (the investigator
pays for this service, at the Waisman Center’s IDDRC rate). The Colorado IDDRC Animal
Models core breeds and maintains these mice.
The Waisman Center guarantees injection of a minimum of 100 eggs or at least two transgenic
founders. For investigators who require transgenics to be made in non-standard genetic
backgrounds, such as C57BL/6J, special arrangements can be made at an additional cost.
Vectors: The IDDRC’s Molecular Discovery Core provides a vector design and production
service.
4. Behavioral Assessment.
Contact persons: Tim Benke ([email protected]) and Mike Mesches
([email protected])
The Animal Models Core provides animal housing in close proximity to testing with identical
light/dark cycles to avoid artifacts involved in transportation from housing to testing rooms; the
testing suite is sound-proofed and offers the ability to provide a wide range of behavioral tests.
The Animal Models Core provides IDDRC investigators with a battery of standard behavioral
assays to assess cognition, emotionality, motor and sensory function in mice and rats:
Cognition: Morris water maze, radial arm water maze, novel place and novel object recognition,
contextual fear conditioning, stimulus discrimination, learning by instrumental conditioning,
inhibitory avoidance, and conditioned taste aversion.
Altered emotionality: Elevated plus maze, light/dark discrimination, tail suspension, acoustic
startle, and prepulse inhibition.
Motor function: Rotorod, open field, grip strength, and cat walk gait analysis.
Sensory tasks: Visual cliff test, tail flick, and foot shock assessment.
IDDRC investigators with little experience in rodent behavioral analysis can consult with Drs.
Benke or Mesches to develop an experimental strategy (including choice of tests, design of
protocols and power analysis for proper selection of animal numbers).
Limited technical assistance for behavioral testing is available. Typically, Dr. Michael Mesches
trains technical personnel of the investigator’s laboratory in the performance of behavioral tests.
Dr. Mesches also can establish contact with qualified part-time personnel to conduct the
behavioral studies (at the investigator’s cost). Some projects may be beyond the scope of the
standard behavioral phenotyping services offered by the core. In these cases, the Core assists the
investigator with establishing additional behavioral assays designed to enable critical secondary
or follow-up studies. From the design stage to data interpretation of behavioral studies, Dr. Zerbe
is available for biostatistics consultation.
5. Small-Animal Radiologic Imaging
Contact Person: Natalie Serkova ([email protected])
Website
Non-invasive imaging technologies allow for the assessment of anatomical as well as functional
parameters in rodents and enable longitudinal studies of time-dependent effects in the same
animal. The core provides access to the following imaging technologies, at reduced fees to
IDDRC investigators, through the University of Colorado Cancer Center:
• Anatomic MRI: provides high-resolution brain images with superb soft tissue contrast.
The spatial resolution is approximately 90 ?m, which allows both visualization and
volumetric measurements of various parts of the brain (as small as the pituitary gland - 4
mm3) without the use of ionizing radiation or contrast agents.
• Anatomic CT: provides high-resolution images (50 ?m) of bone and soft-tissue structures
(soft tissue resolution is poorer than that of MRI).
• Functional FDG-PET: Injection of radioactive 18fluorine-D-deoxyglucose (FDG) allows
for assessment of brain activity during a 1-hour uptake period (no anesthesia required for
the uptake period). Higher brain activity will correspond to higher intensity on FDG-PET
scans. This is a novel and, to our knowledge, unique imaging application that is currently
under development in the facility.
• Gadolinium-enhanced MRI: Clinically used gadolinium-based contrast agents (for MRI)
are incapable of crossing the blood-brain barrier. Therefore, a disruption of the blood-
brain barrier can be visualized using gadolinium-enhanced MRI.
• Diffusion-weighted MRI: allows for assessment of brain edema and brain necrosis based
on diffusion coefficients (ADC mapping) for tissue water.
• In-Vivo 1H-MRS: allows (after localized MRI) to determine non-invasively major brain
endogenous metabolites, such as the MR neuronal marker N-acetyl-aspartate, glial
marker myo-inositol, neurotransmitters GABA and glutamate, as well as total choline
(membrane biosynthesis) and total creatine (energy metabolism). Additional, expanded
(ex vivo) metabolic profiling can then be achieved by high-resolution NMR after tissue
sampling (see below).
• Molecular Imaging: Using novel radiolabeled or MR relaxing reporters (for PET and
MRI, respectively) attached to a specific compound (e.g., metabolic substrate/precursor),
it is possible to visualize molecular targets (such as certain proteins or metabolic activity)
in vivo.
6. Metabolomics.
Contact Person: Natalie Serkova ([email protected]).
Website
Metabolomics refers to technologies that detect and quantify the low- molecular weight
molecules or metabolites (constituents of the metabolome) produced by active, living cells under
different conditions and times in their life cycles. The metabolomics facility offers IDDRC
investigators the opportunity to analyze genotype-phenotype as well as genotype-envirotype
relationships. N. Serkova is an expert in the field and offers access to the following metabolomic
technologies:
High-resolution one-dimensional metabolic analysis (including 1H-, 13C-, and 31P-NMR
analysis). Over 50 metabolites are quantified simultaneously from a single tissue biopsy/cell
extract:
• From 1H-NMR: neuronal markers, such as neurotransmitters, amino acids, ketone body,
and lipid metabolism;
• From 13C-NMR: glucose and fatty acid fluxes;
• From 31P-NMR: high-energy phosphates and phospholipid precursors.
High-resolution two-dimensional NMR analysis (2D-COSY, NOESY, HSQC) for structural
elucidation of metabolites (see above for the list of metabolites, or identification of unknown
metabolites.
Data Interpretation
Chemical Shift libraries for spectral interpretation (including in-house generated data sets, the
Human Metabolome Database and the NMR Database are available). These databases include
NMR chemical shifts for over 200 endogenous metabolites.
Fees
This section is under construction. For information on pricing, please contact the core director
Ken MacLean.
Bard Center for Entrepreneurship Business Incubator
Contact Information:
Bard Center for Entrepreneurship
535 16th Street, Suite 300
Denver, CO 80202
Office: 303-620-4050
Office Fax: 303-217-8064
[email protected]
www.business.ucdenver.edu/bard
Catherine Kunst, MBA, PhD
Executive Director
Bard Center for Entrepreneurship
Business School at the University of Colorado Denver
Start or Grow Your Company with the Bard Center
The Richard H. and Pamela S. Bard Center for Entrepreneurship was established in 1996 to foster economic
development in Denver and the Rocky Mountain Region. Richard and Pamela Bard's generous endowment turned their
dream into a reality, creating a program that prepares future leaders for success in any business venture.
As part of the Business School at the University of Colorado Denver, the Bard Center provides people with
opportunities to create partnerships with the business community through academics, mentoring, and programs
designed to foster innovation and entrepreneurial development. The Bard Center provides all of the necessary
resources to build a successful business. Our unique combination of experiential courses, scholarships, internships,
access to mentors and alumni networks, on-site incubation and funding allow entrepreneurs to make their dreams
become real. The Bard Center Incubator is open to early stage Colorado companies who meet our admission criteria.
Admission Criteria*
• Executive Summary on Innovative Business Idea
• Growth strategy to exit incubator within 12 to 18 months
• Goals & objectives to execute strategy
• Successful interview(s) with Advisory Council member(s)
*Preference given to University of Colorado (Faculty, Staff, Students, & Alumni) or Bard Center (e.g. Business Plan Winner) affiliates
Incubation Process
• Matched to specific business mentor for optimal growth & success of the company
• Potential for meetings with mentors-in-residence for legal, accounting, public relations & others as needed
• Quarterly updates on financial progress and goals toward meeting milestones to Incubation & Mentorship
Committee or Bard Center Advisory Council
• Access to Rutt Bridges VC Fund or Angel Investors in our community ?
Office Amenities
• Furnished Offices
• Private Kitchen & Meeting
Room
• Wireless and Wired Internet
Service
• Nightly Cleaning Service
• Moderate Fax/Copy Usage
• Scheduled use of shared
conference and class rooms
Leasing Options (per month):
• 6 month lease to start
• Virtual - $150 (mailing address,
usage of shared spaces up to 10
hrs per month)
• Small Office - $500
• Medium Office - $750
• Large Office - $1000
320B
Large
$1000
320C
Medium
$750
320D
Small
$500
320E
Medium
$750
320F
Small
$500
320G
Small
$500
300E
Large
$1000
Computer
Lab
300F
Small
$500
Conf
Kitchen
Shared
Meeting
Space
Large
Classroom
Shared
Meeting
Space
Copy
320H
Large
$1000
300G
Medium
$750
closet
Library
Kitchen
Small
Classroom
BC/GA
Office
BC
Office
BC
Office
Computer
Lab
11 M
MBA
Office
Incubator
Shared Spaces
University of Colorado
11 M
MBA
Office
Shared
UCD
office
320B
Large
$1000
320C
Medium
$750
320D
Small
$500
320E
Medium
$750
320F
Small
$500
320G
Small
$500
300E
Large
$1000
Computer
Lab
300F
Small
$500
Conf
Kitchen
Shared
Meeting
Space
Large
Classroom
Shared
Meeting
Space
Copy
320H
Large
$1000
300G
Medium
$750
closet
Library
Kitchen
Small
Classroom
BC/GA
Office
BC
Office
BC
Office
Computer
Lab
11 M
MBA
Office
Incubator
Shared Spaces
University of Colorado
11 M
MBA
Office
Shared
UCD
office
Bio-Imaging Research Laboratory (BIRL)
David Miller, PhD
Associate Professor
303-724-3464
[email protected]
http://www.uchsc.edu/ucbirl/index.php
UCD Home | Campus Directory | Anschutz Medical Campus
A sampling of UC BIRL clients and tested pharmaceuticals.
The University of Colorado Bio-Imaging Research Laboratory (UC BIRL) provides image
analysis and radiology review services for all clinical phases of drug development, ranging
from small Phase I studies to large, international trials. Our services have been instrumental in
the testing of new compounds, particularly in multiple sclerosis and the approval of Avonex™.
The lab is composed of GCP and HIPAA trained professionals who have extensive
training and experience in radiology, medical physics, computer science and clinical
trials management. UC BIRL provides experienced project managers, interfacing with
both sponsors and sites to ensure the timely receipt, review and reporting of quality
data.
The UC BIRL facility supports both film and digital data, with the ability to convert between
the two. Fully digital (filmless) studies can be accommodated. 21 CFR 11 compliant systems
allow UC BIRL to electronically receive, QA, process, and archive medical image data in a
secure manner.
Typical analyses include lesion counting and volumetrics, focal or whole-brain atrophy measures, serial
registration, RECIST evaluation and lung histogram analysis. The laboratory also has the ability to
process more complicated acquisitions, including diffusion tensor imaging (DTI), magnetization-transfer
(MTR), and functional imaging (fMRI) using BOLD contrast. Custom data analysis for new or emerging
biomarkers is available.
UC BIRL prides itself on providing high quality site management, image analysis, and radiology review.
Our on-staff radiology, medical physics, and technologist support ensure that trials are performed in a
competent, technically sound, professional manner. Please contact us for more information regarding
our services or to schedule a facility visit.
Complete Analysis Support
UC BIRL offers a comprehensive list of services to aid sponsors in their clinical
investigations.
Our services include:
Protocol Design
o Selection of Relevant Imaging Biomarkers
o Determination of Sample Size
o Imaging Intervals
o Image Acquisition Parameters
Site Selection and Training
International Site Management
Image Quality Assurance
Centralized Image Review and Analysis
o Lesion Tracking
o Semi-automated Segmentation and Volumetrics
o RECIST Evaluation
o Brain Atrophy
o Serial Registration
o fMRI
o Dynamic Imaging
o CT Fat Quantification
o Magnetization Transfer
o Diffusion Tensor Imaging
o Perfusion
o MRS
HIPAA Compliant Image Archiving
Experienced Project Management
The Project Managers of UC BIRL are some of the best trained in the industry, with over 25
years combined experience in regulatory compliance, imaging site management and quality
control, data analysis and reporting. Project managers work with both imaging sites and
sponsors, while supervising research associates who assist with data receipt and analysis.
Fees: Under Construction
UC BIRL Image Processing offers state-of-the-art analysis and review capabilities. New technologies
are constantly being explored, developed and integrated into the processing toolbox. Below is a
sampling of current capabilities
• Digital Image Receipt (Internet, MOD, CD, DVD, DAT)
• mini-PACS
• Film Digitization
• Light Box Viewing
• Inter- and Intra-modality Image Registration
• Automated and semi-automated segmentation (Whole Brain, Gray / White Matter, CSF, lesion
volumetrics, etc.)
• fMRI Analysis
• Magnetization Transfer Imaging
• MRS with multinuclear capability
• Tractography
• Dynamic Studies (e.g., DCE-MRI, perfusion)
• Bone density CT measures
• Automated CT fat measures
• ROI Analysis
• Multi-planar reconstruction with sinc or trilinear interpolation
• Inhomogeneity Correction
• Adaptive Filtering
• Motion Correction
• Annotation
• File Format Conversion (ANALYZE, DICOM, ACR-NEMA, vendor specific formats)
Bio-Imaging Research Laboratory (BIRL)
From: Miller, David E
Sent: Thursday, October 01, 2009 2:32 PM
a) How is the quality of your measurements evaluated – quality control?
As part of our standard operating procedures we require training and testing of
core staff prior to their participation on new projects. Additionally we perform
periodic evaluation of our measurement techniques, within and across analysts.
b) What is the turn-a-round time for the service you provide?
Turnaround time is variable, based on the needs of the client and their funding
capabilities. We have turnaround times of less than 24 hours and some on the
order of weeks.
c) Who documents the data provided and signs off on the data?
Signoffs vary based on regulatory requirements and the nature of the research.
A trained PRA or project manager may approve some analysis results while a
medical physicist or radiologist signoff may be required for FDA reviewed
research.
d) Have you had experience providing data for industry?
We have provided image analysis, protocol development and program
management services for phase I-IV clinical trials. Some of our past clients
include Biogen-Idec, BMS and Genentech.
e) Do you have a standard operating procedure manual?
We have standard operating procedures for all laboratory activities. Our SOPs
have been reviewed by quality experts and auditors from a number of different
pharmaceutical companies and clinical research organizations.
f) How will you track billing and financial aspects of your core?
BIRL project managers track study billing and coordinate with the lab director
and Dept. of Radiology Research/Business Manager for all billing activities.
Biomolecular NMR Core Facility
Contacts:
David Jones, PhD
NMR Director
[email protected]
303-724-3600
Website:http://biomol.uchsc.edu/cores/nmr/
Geoffrey Armstrong, PhD
Operational Specialist
800/900 MHz NMR
Phone: 303-724-3331
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Here you will find information about the facilities available, a brief introduction to NMR, the
sort of information can get from it and how can it help your research.
Introduction and History
Nuclear Magnetic Resonance (NMR) spectroscopy is a technique that provides high resolution
information about the structure and dynamics of molecules in solution at the atomic level. It used
to study a wide variety of molecules from small drug like molecules to macromolecules such as
proteins and nuceic acids.
The NMR Core facilities provideaccess to state of the art
instrumentation to researchers at UCHSC and its affiliated
institutions for the study of the structure and function of biological
macromolecules. NMR core staff and faculty provide assistance to
other users through training or through the development of
collaborations.
The NMR core was established in 1996 through a grant from the
Howard Hughes Medical Institue and the National Cancer Institute.
Ongoing support for the NMR facility is provided primarily by the
University of Colorado Cancer Center and the School of Medicine.
The NMR facility is located in Room L18-1300 on the first floor of
the RC-1 South Building on UCHSC campus at Fitzsimons.
The facility has Varian INOVA spectrometers operating at 500
MHz and 600 MHz, and an 800 MHz NMR spectrometer, which is
located at the UC Boulder campus. Recently a 900 MHz
spectrometer was installed in the facility as part of the Rocky
Mountain Regional NMR Resource. A variety of probes are
available that are suitable for the solution NMR studies of
biological macromolecules including proteins, nucleic acids and
carbohydrates. There is a small wet lab that can be used for sample
manipulations, and an office/computer room for visitors while
using the facility.
Information on access to the core, user fees, documentation etc, can
be found through the links at the top of this page.
Policies and Rates
• Management Committee
• Access to the Facility
• Financial Resposibility
• Acknowledgements
NMR Management Committee
All policies for the the NMR Core are formulated in consultation with the NMR
Management Committee, which consists of faculty members with research programs in
NMR spectroscopy. The commitee meets on an as needed basis.
Access to the NMR Facility and its Services
The NMR facility is open to all researchers from UCHSC and its affiliated institutions,
including other groups within the CU system. The NMR facility is a Cancer Center Core
facility, and members of the Cancer Center are given priority in using the instruments.
Private-sector customers are also welcome to discuss use of the facility with the facility
director.
The NMR Core facility is funded in part by the National Istitutes of Health. Therefore all
users of the facility are required to submit a short annual report on their research efforts
in the core. This report should summarize the results obtained, all grants that are
dependent on the core facility and any publications arising from use of the facility. This
information is used to ensure continued funding of the core.
Successful completion of a BiSMaRC User Training Course by individuals responsible
for executing the NMR experiments will be required, unless prior NMR experience can
be demonstrated. This one week training course will be held several times a year or
whenever there is sufficient demand.
Faculty, staff, and students who have undergone user training and/or certification may
operate the instruments without direct supervision, provided:
1. Financial responsibility is implicitly agreed to as a result of this use (see below).
2. Such use of the Center falls within the guidelines for sponsored research at the in-
house rates for UCHSC research. The associated charges must be charged to a
valid UCHSC account.
3. The only instrumental techniques attempted are routine ones or are those for
which the user has received relevent instruction.
Only those who have been issued a password and told by the NMR Manager that they
may operate the instruments unsupervised may do so.
Individuals who have not undergone training and checkout may submit samples to be
run by qualified facility personnel at the in-house rates plus an additional $20/hr that
applies only to the time the personnel are setting up the data acquisition or working up
the data (minimum 1 hr charge). This option is recommended for users who have
infrequent need for NMR data, or for those who have temporary need of advanced
techniques.
Private sector clients who wish to use the NMR facility should BiSMaRC personnel,
even if they have arrangements with UCHSC personnel for the performance of non-
UCHSC research. Although some arrangements with the private sector fall under the
guidelines for "sponsored UCHSC research," more often they do not.
Financial Responsibility for Charges and Damages
Users are responsible for applicable charges and for damage that results from samples
that are explosive, pressurized, chemically corrosive, radioactive, biologically
dangerous, or that otherwise pose unusual hazards to instrumentation or personnel. In all
such cases, prior advice should be sought with regard to these special samples, but
permission does not absolve any user from responsibility for harm their samples may
cause the Center.
UCHSC researchers use the Center with the understanding that the account used may be
charged up to $5000 for damages incurred as a result of careless or negligent use of the
instrumentation. This obligation does not extend to responsibility for damage that occurs
accidentally and unavoidably during normal use.
Acknowledgements
All publications resulting from use of the NMR core facilities must acknowlege use of the core.
A suitable acknowledgement would be "The NMR core facilities are funded by the University of
Colorado Comprehensive Cancer Center and the UCHSC Program in Biomolecular Structure".
Use of the 800 MHz Spectrometer must also include the following statement. "The 800 MHz
NMR sectrometer was purchased with funds provided the W.M. Keck Foundation"
Bimolecular NMR
From: David Jones [mailto:[email protected]]
Sent: Monday, November 02, 2009 5:25 PM
a) How is the quality of your measurements evaluated – quality control?
The performance of all NMR instruments is routinely calibrated against known standard
samples that are the industry standard. Performance for all user samples is assured by
addition of internal controls that are widely recognized to be inert. Alternatively,
external standards contained within a capillary can be included in the sample. These
controls provide a set of known benchmarks for calibration and optimization of the NMR
spectrometer. The effects of sample on performance can be directly inferred from the data
from these controls.
b) What is the turn-a-round time for the service you provide?
This depends on complexity of experiments to be performed and the number of samples.
Simple 1D proton or carbon spectra can be acquired rapidly within several days. More
complex experiments, turnaround is between 1 - 2 weeks
c) Who documents the data provided and signs off on the data?
The Core Director
d) Have you had experience providing data for industry?
Yes
e) Do you have a standard operating procedure manual?
f) How will you track billing and financial aspects of your core?
Billing is tracked automatically through a program designed to capture the name of the
instrument operator, a descriptor of the project or service, and the individual to be billed
for the service. Billing accounts for actual instrument time used and operator Assistance
fees. The Financial Aspects of the Core are maintained by the Program in Structural
Biology and the University of Colorado Cancer Center and are thoroughly reviewed on
an annual basis.
Biophysics Core Facility-
The Program in Biomolecular Structure
Contacts:
Dr. Robert S. Hodges, PhD
Director
303-724-3253
[email protected]
Jackie Newnam,
Administrator and primary
contact for information
regarding The Program
including graduate studies.
303-724-3268
[email protected]
Brooke Hirsch, PhD
Facility Manager
303-724-3322
[email protected]
Website:http://biomol.uchsc.edu/cores/biophysics/
Biophysical Studies
The Biophysics Core Facility is a user facility owned and operated by The Program in
Biomolecular Structure at the University of Colorado Health Sciences Center. We opened our
doors in early 2001 and have since served a wide variety of researchers on diverse projects in
both academia and industry.
We currently have resources to study biomolecular structure and thermodynamics with Biacore
surface plasmon resonance phenomonen, CD/ORD, ITC, DSC, fluorescence spectroscopy, and
analytical ultracentrifugation (AUC). Mass spectroscopy, LC/MS/MS, HPLC, amino acid
analysis are also available.
Facility Users
The Facility provides professional collaborations, training, and instrument time to researchers
associated with both nonprofit organizations and private institutions. After a user is trained, they
may use the instruments independently. Please contact us if you would like the Biophysics Core
Staff to run or analyze your samples.
Training
The Biophysics Core Staff are available to train users on each of the instruments located in the
core. We offer one-on-one and group training to those interested in operating the instruments.
Every user must be trained on each instrument before they are allowed independent use. There
will be a one-time charge for training each individual per machine. After the user is trained,
instrument user fees will be assessed. All fees associated with training and instrument use are
listed on the Rates and Policies page.
Scheduling
All scheduling is done with the online calendar. After you are trained to operate an instrument,
you may request an account from Brooke Hirsch. Priority is generally on a first-scheduled first-
served basis. Users must sign up for an instrument at least 48 hours in advance. Similarly, users
must cancel reservations at least 48 hours in advance. If a user fails to cancel an instrument
reservation 48 hours before the reserved start time, a charge will be accessed for instrument time.
Rates
Fees for University of Colorado and Affiliated Users
Instrument
Training
Session
(cost per user)
Trained users at CU and
affiliates independent
users
Biophysics Core handles samples
for CU and affiliates
JASCO 815 CD $80 $15.00 $36.00
Fluoromax-3 $50 $9.00 $30.00
Microcal VP-
DSC
$50 $10.00 or $80 per day $40.00 or $125 per day
Microcal VP-ITC $50
$15.00 (4 hr. min.) or
$80 per day
$35.00 (4 hr. min.) or $200 per day
Biacore 3000 $150
$20.00 (4 hr. min.) or
$110 per day
$50.00 (4 hr. min.) or $200 per day
Analytical
Ultracentrifuge
$150
$20.00 (for velocity) or
$160 per day $5.00 (for
equilibrium) or $100
per day
$30.00 (for velocity) or $240 per
day $8.00 (for equilibrium) or $200
per day
Amino acid
analysis
$60 $30 per sample $40 per sample
Fees for Industry/Company Users
Instrument
Training
Session
(cost per user)
Trained
Industry/Company user
independent user
Biophysics Core handles samples
JASCO 815 CD $100 $16.00 $40.00
Fluoromax-3 $100 $12.00 $37.00
Microcal VP-
DSC
$75 $19.00 or $100 per day $43.00 or $250 per day
Microcal VP-ITC $75
$19.00 (4 hr. min.) or
$100 per day
$43.00 (4 hr. min.) or $250 per day
Biacore 3000 $200
$25.00 (4 hr. min.) or
$135 per day
$62.00 (4 hr. min.) or $250 per day
Analytical
Ultracentrifuge
$200
$25.00 (for velocity) or
$200 per day $7.00 (for
equilibrium) or $125 per
day
$37.00 (for velocity) or $300 per
day $10.00 (for equilibrium) or
$250 per day
Amino acid
analysis
$100 $37 per sample $50 per sample
Biorepository Core Facility
Contact Information:
Director
M. Scott Lucia, MD
303-724-3470
Email: [email protected]
Website: under construction
The University o f Colorado Denver Biorepository ( UCDBCF) hous ed i n t he Department of Pathology
functions as a campus-wide bi orepository facility offering a wide range of services t o the University of
Colorado Denver (UCD) research community and beyond. UCDBCF manages a l arge number of organ-
specific biorepositories i n support of research projects at UCD and its affiliated hospitals. In addition,
UCDBCF is active on a national level providing centralized biorepository and pathology services for
multi-institutional SWOG, NIH, and NIDDK r esearch networks. UCDBCF has the flexibility to offer a
full r ange of services ranging f rom pr otocol development an d p atient r ecruitment to simple sp ecimen
storage. Situated in a department that bridges basic and clinical sciences, the UCDBCF is in an ideal
position to promote and support interdisciplinary research.
Facilities
• Full Service Pathology Lab
• Automated Tissue Processing
• Automated H&E Staining
• Automated Immunostaining
• Freezer Repository
• Badge Access
• UCD Security equipment monitoring
• Network based temperature monitoring
• 4300 sq ft
• Slide and Block Repository
• Badge Access
• Environmental Control
• 1700 sq ft
• Advanced Imaging Facility
• Aperio Scanscope
• 10 terabytes of storage
• Web access to images
Services
• Protocol & SOP Development
• IRB Assistance
• Collection Kit Design
• Patient Consent
• Specimen Collection
• Phlebotomy
• Inventory Management
• Histology
• Tissue Processing
• Routine H&E
• Microtomy / Cryomicrotomy
• Immunohistochemistry
• Special Stains
• Special Processing
• Tissue Microarrays
• Laser Capture Micro dissection
• DNA/RNA/Protein Isolation
• Imaging
• Whole Slide Imaging
• Image Analysis
• Epidemiology / Biostatistics
• Molecular & Clinical Diagnostics
Experience
Our biorepository staff brings over 70 combined years
of experience in biorepository management and
coordination of multi-institutional pathology and
biorepository core operations.
Our ex tensive ex perience i ntegrating research w ith
routine c linical p ractice, specimen co llection an d
storage, and information technology has enabled us to
maximize efficiency and accuracy in all aspect of our
biorepository m anagement. Advanced p athology,
histology and laboratory expertise allow us to provide
researchers w ith hi ghly s pecific di agnostic
characteristics and r eliable d ata for t he specimens
stored in our biorepository.
Price List: 8/01/09
Detailed services: UCD External
Database query and specimen tracking $50.00 per hr $70.00 per hr
Histology of archived tissue (Includes costs of specimen maintenance):
Unstained section from block $4.10 per slide $7.00 per slide
H&E stained section from block $9.10 each $15.00 each
Immunohistochemistry $50.00 per slide $75.00 per slide
Creation of tissue microarray $665.00 $1000.00
Acquisition of serum aliquot $15.00 per aliquot $75.00 per aliquot
Acquisition of tissue sample $50.00 per hr $75.00 per hr
Biobank services
Monitor probe $300.00 per freezer N/A
Monitor relay $600.00 (up to 8 freezers) N/A
Freezer monitoring and maintenance: $1.00 per day per freezer N/A
Inventory database creation: $75.00 per hour N/A
Inventory restructure: $75.00 per hour N/A
Inventory management: $30.00 per hour N/A
Biorepository Core Facility
From: Lucia, Scott
Sent: Thursday, October 08, 2009 11:20 AM
a) How is the quality of your measurements evaluated – quality control?
We do not make measurement per se. The services provided by the biorepository
core consist of assistance in the procurement, storage, processing and distribution
of patient bi ospecimens for r esearch us e. Therefore, quality i s opt imized by 1)
proper collection and handling techniques, 2) assuring integrity of the data, and 3)
assuring p roper usage o f bi ospecimens. 1) To opt imize pr oper c ollection a nd
handling, s pecimens a re c ollected us ing s tandardized c ollection ki ts a nd
protocols. E ach s pecimen container/tube i n t he kits has a uni que barcode l abel
that links it to the c ollection kit barcode a nd uni que pa tient ID t o he lp pr event
misidentification of samples. Data collected on the accompanying tracking forms
include t he date and t ime of collection, t ime of blood f low i nterruption, time of
centrifugation, time s ample was s tored in -80, etc. At points where s amples ar e
handed ove r t o ot her p ersons, s uch a s t he t ime it i s transferred from clinic to
processing l ab, we have s ign-offs for t he person who handled t he s ample up t o
that poi nt. The da ta o n t he t racking f orm i s e ntered i nto t he bi orepository
database by a biorepository technician and r eceives a finalizing signature by t he
core d irector o r co -director i f e verything i s i n or der. If pr oblems a re f ound,
personnel that handled the specimen will be contacted for clarification.
Data en try q uality i s c hecked on w eekly b asis b y a s upervisor us ing a random
selection of previously entered forms. If errors are found, additional checking of
forms will be initiated. As previously mentioned, our freezers are monitored by
an alarm system that records temperatures in real time and has automatic dial-out
when t he t emperature exceeds a s et t hreshold. We p hysically i nspect t he
biorespository on a da ily b asis dur ing w hich e ach i ndividual c ryo unit i s
examined. Problems a nd a ctions t aken t o r esolve t he situation ar e r ecorded. In
situations where l iquid samples a re of >10 years i n s torage, evaporation may
occur due to deterioration of tube seals. In addition to visual inspection, samples
may b e monitored b y t esting f or s odium or a lbumin l evels. If t he v alues ar e
within the acceptable range, samples are considered adequate and may be released
for di stribution. Additional quality control assays will be provided i f required or
requested by individual projects. RNA and DNA concentration and integrity can
be assessed using Nanodrop or the Agilent Bioanalyzer instruments. If necessary,
the l ab ha s a de dicated ABI 7700 s equence a nalyzer f or qua ntitative r eal-time
(RT-) PCR us ing T aqman or S YBR-green t echnology t hat c an be us ed i f
additional analysis and/or quality control is needed.
A committee composed of members of t he UCD departments i ncluding but not
limited t o t he de partments of pa thology, s urgery and m edicine s erves a s a n
advisory committee, th e Tissue P rocurement Committee ( TPC) f or th e general
operation of t he B CF. T he c ommittee w ill a lso be c harged w ith r eview of
specimen requests and prioritizing studies for the utilization of materials from the
biorepository. O nce a n i nvestigator h as c ontacted t he M edical Director or
Supervising Technologist t hat he/she wishes to obtain biological materials f rom
the B CF, a que ry i s made i n t he da tabase t o a ssess w hether or not a dequate
samples f or t he research i n que stion i s available. T he i nvestigator w ill t hen
submit to the Medical Director a short (2-3 pages) proposal as t o t he nature and
importance of the study, the need for biorepository samples, and the likelihood for
success. This proposal will then be distributed to members of the TPC for review
and, if satisfactory, approval to begin distributions.
b) What is the turn-a-round time for the service you provide?
This de pends on t he na ture of t he s ervices r equested a nd t he t otal nu mber of
specimens. Collections occur on same day. Pulls and processing requests must
be preapproved (see above) and then may take up to two weeks depending on how
much labor is required.
c) Who documents the data provided and signs off on the data?
See number 1 above.
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Yes.
f) How will you track billing and financial aspects of your core?
A c ost pe r s pecimen a nd/or hour ly charge r ate a pplies f or ou r s ervices ( see
attached cost sheet). F or on-campus i nvestigators, requests for services must be
accompanied b y a s peed t ype. Industry i s di rect bi lled. E xpenses a re t racked
through the biorepository expense account set up in the Department of Pathology.
University of Colorado Cancer Center
Biostatistics and Bioinformatics
Shared Core Service
Contacts:
Anna E. Barón, PhD,
Director
303-315-7502
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/biostat/index.aspx
The University of Colorado Cancer Center Biostatistics and Bioinformatics Core provides
quantitative and information science support for the planning, design, analysis and presentation
of basic science, clinical, and epidemiological investigations by Cancer Center members.
Services
• Consultation on study design (clinical and basic science, including gene expression arrays
and proteomics experiments)
• Consultation on sample size and power
• Development of data collection, storage, and quality control procedures (basic science
and clinical studies, protocol review and monitoring)
• Data analysis, including genomic and proteomic data
• Collaboration on manuscript and oral presentation preparation, and grant proposal
development
Rather than charging users for services, we ask Cancer Center investigators to write in funding
for biostatistics and bioinformatics support on grants and contracts, then to acknowledge the
Core in any publications.
How to Use the Core
Your study's initial design and data collection strongly affect its analysis and interpretation.
Please involve us during the design phase to we can help make sure your project is successful.
Our work is usually done as part of protocol development for clinical trials or during project
design for other cancer-related research.
To get started, please contact Anna Barón, director.
• You will meet with one of our Core biostatisticians or bioinformaticians to present your
hypothesis and goals.
• We will help you put together a basic scope of work and general timeline and identify
key collaborators to include.
• We will work with you throughout your project.
No fees
Biostatistics & Bioinformatics (UCCC)
From: Baron, Anna
Sent: Thursday, November 05, 2009 12:51 PM
NONE OF THIS APPLIES TO THE Biostatistics & Bioinformatics (UCCC)
a) How is the quality of your measurements evaluated – quality control?
n/a
b) What is the turn-a-round time for the service you provide?
n/a
c) Who documents the data provided and signs off on the data?
n/a
d) Have you had experience providing data for industry?
n/a
e) Do you have a standard operating procedure manual?
n/a
f) How will you track billing and financial aspects of your core?
n/a
Cellular Systems and Analysis Core Unit (IDDRC)
Director:
K. Pfenninger, MD (cell culture and biochemical analysis of the brain)
303-724-3466
[email protected]
Associate Director:
John R. Sladek, PhD (neuroanatomy and histology)
303-724-0629
[email protected]
Mission:
The overall mission of this core is to stimulate and facilitate IDD-related research at the cellular
and tissue levels. This core also performs lymphoblast immortalization for bio-banking and
genomic analysis.
The Cell Systems and Analysis Core has two sections focused on cell culture and one on brain
tissue, respectively. This core is designed not only to advance ongoing in-vitro studies but to
assist investigators without experience in the area with the adoption of in-vitro approaches. In
addition, this core provides the technology and assistance to analyze brain tissue with
neuroanatomical and cell labeling techniques as well as with approaches of subcellular
fractionation and biochemistry.
Staffing:
Renata Collard, PhD
Barbara Blanchard, MS
Services:
Cell Culture
Services include advice and assistance with the use and analysis of in-vitro model systems and
interpretation of results. The cell culture bank stores and carries a collection of cell lines that can
be grown for research use. In addition, the cell culture core performs lymphoblast
immortalization for biobanking by the IDDRC’s Translational Nexus.
If you are interested in any of the below listed Cell Culture services for your research please
contact Dr. Karl Pfenninger at [email protected].
1. In-vitro System Consulting.
K. Pfenninger is available to IDDRC investigators for the evaluation of experimental approaches
involving in-vitro systems. Options include the possibility of culturing primary neurons or glial
cells from genetically engineered rodents, the use of wild-type rodent neurons or glial cells for
transfection, and/or the use of cell lines for a particular study. Also part of the service is advice
on the feasibility of visualizing particular functions or functional changes in cells using optical
methods or biochemical approaches. This consulting service is designed primarily for those
investigators with little or no experience with in-vitro models or neuronal/glial cultures.
2. Cell Lines and Primary Neural Cells.
The Core is a repository for a variety of cell lines and fibroblasts for IDD-related research use
(see Table, below). Investigators can order from the list, the thawing and initial culture of cell
lines for further expansion and experimentation by the investigator’s laboratory. In addition, the
core can grow newly acquired cell lines for investigators and bank them for later use. In
collaboration with the IDDRC’s Molecular Discovery Core, the Cell Systems and Analysis Core
DNA-profiles human cell lines as needed to authenticate their identity. For investigators who
wish to have many cell lines grown in large quantity, the core can provide this service if the
work load permits, but the grant supporting the investigator’s study must buy personnel time in
the core to perform this service. For pilot studies or small projects the Core provides cells at no
charge.
Species Cell Type Designation
African green
monkey
male kidney Cos-7
Drosophila Schneider S2
Hamster
Chinese hamster
ovary
CHO K1
Human
cervical cancer HeLa
glioblastoma 10-08, 13-06, U373
hepatocell. Carcinoma HEPG2
kidney (embryonic) HEK293
lung, small cell
carcinoma
SCLC H510, N-417, NC1-146, NC1-H345
melanoma WM-35, WM-1617, WM-1158
melanocytes
(epidermal, normal)
NHEM 693
prostate carcinoma LNCaP, PC3, PC3M-MM2, TSU Prl
Mouse
myoblasts C2C12
melanoma B16, B16 MC1
pheochromocytoma MPC12
Rat
pheochromocytoma PC12
prostate carcinoma At-3, Mat-Lu, Mat-LyLu
The Core also provides training and assistance with the preparation of primary neural cell
cultures. For experimentation with very limited scope or pilot studies, the Core prepares cultures
of rat or mouse cortical explants or dissociated cells. For larger studies the principal
investigator’s laboratory receives appropriate training and advice. Training also may include the
establishment of other neuron populations (those from hippocampus, cerebellum, olfactory bulb,
peripheral ganglia and others) or of glial cell types.
3. Lymphoblast Immortalization.
Immortalized lymphoblasts provide DNA in essentially unlimited quantities and enable analysis
of chromosomes, copy number variations, RNA, etc. R. Collard was trained in lymphoblast
immortalization using EBV and is now performing this function for the Translational Nexus. R.
Collard spends about half of her time on lymphoblast immortalization.
4. Other Cell Culture Services.
a) Mycoplasma Testing: The cell culture core routinely tests cells for potential mycoplasma
contamination and provides this service for cultures grown and maintained in the different
IDDRC investigator laboratories.
b) Cell Transfection: The Cell Culture Core has acquired an Amaxa Nucleofector
electroporator, which is the best currently available instrument for introducing vectors into
difficult-to-transfect cell types, including primary neurons. This equipment, and advice on how
to use it, are available to IDDRC members.
c) Cell Processing and Analysis: K. Pfenninger (with members of his laboratory) and R. Collard
provide advice and training on how to handle cultures for live-cell imaging and how to process
them for, e.g., immunolabeling or a variety of biochemical approaches.
Brain Tissue Services
If you are interested in any of the Brain Tissue services listed below for your research please
contact Dr. Karl Pfenninger at [email protected] or Dr. John Sladek at
[email protected].
1. Subcellular fractionation and biochemical analysis.
K. Pfenninger provides advice for the preparation and analysis of subcellular fractions such as
synaptosomes from adult rodent brain, growth cones from fetal rodent brain, myelin,
mitochondria, and other membrane fractions. Tools and instrumentation to perform such
analyses are readily available in the IDDRC (see Molecular Discovery Core).
2. Neuroanatomy and Histology.
J. Sladek is available to advise investigators on the optimal neuroanatomical and -histological
techniques to be used for examining the brains of experimental animals and on the interpretation
of results. B. Blanchard is in charge of the various histology services.
a) Stereotaxic implantation of cells, factors and viral vectors. The Sladek laboratory has a rodent
stereotaxic apparatus with a digital positioning manipulator that allows for a high degree of
precision and reproducibility.
b) Brain perfusions can be performed on a wide variety of animal models that include rats, mice,
guinea pigs, rabbits, and non-human primates with a range of routine to specialized fixatives
including paraformaldehyde, Bouin’s, glutaraldehyde, and others. B. Blanchard is familiar with
the advantages and disadvantages associated with a particular fixative or fixation method and can
advise the members of the IDDRC of best uses and potential obstacles depending on their
experimental needs. Expertise also is available in the perfusion of embryonic and postnatal
animals, which requires special technical skill and knowledge of the appropriate fixation
methods.
c) Neurohistochemical Preparation: B. Blanchard can produce consistent, uniform tissue
sections ranging in thickness from less than 5? to 100?m or more, with the use of different
embedding techniques, and with a rotary microtome, freezing sliding-blade microtome, cryostat,
or Vibratome (for fresh tissue).
d) Staining: Routine histological preparation of tissue sections can be done with a variety of
staining and counterstaining approaches, with dyes such as cresyl violet, methyl green,
hematoxylin, and many others depending on the structure(s) needing to be visualized.
e) Immunohistochemical staining for various neuronal and glial markers, synaptic markers,
indicators of differentiation or development, receptors, transmitters, enzymes and markers of
inflammation. This may involve the application of double-labeling techniques, with the use of
permanent dyes and chromagens, such as diaminobenzidine, nickel-enhanced diaminobenzidine,
Vector Red, Vector Blue, and others, or fluorescent conjugated markers, such as fluorescein,
rhodamine, Cy2, Cy3, Cy5, and AlexaFluors. The principal investigator’s laboratory provides
the appropriate antibodies.
User Fee Table: Under construction. For information about pricing, please contact
Dr. Karl Pfenninger.
Center for Computational Mathematics (CCM)
Jan Mandel, PhD, Professor
Director
303-556-4475
[email protected]
Russel Boice
System administrator
[email protected]
303-556-5394
http://ccm.ucdenver.edu/facilities
Facilities
The Center for Computational Mathematics and the Department of Mathematical and Statistical
Sciences provide high-end scientific computing facilities, including professional technical
support, to research projects, graduate education, and affiliated faculty.
The cost of the facilities will be allocated based on total FTEs of all users. Internal use is covered
by existing UCD internal funding. Users who are paid from externally funded projects will need
to include a Computer Services item in the proposal budget and the services will be charged to
their project based on their total FTEs worked on the project. Federal rules require that all usage
is treated consistently. Approvals are pending for exact rules and rates.
On-Site Computing Facilities
• Beowulf cluster with 72CPUs, 72GB memory, and 10Gb/s interconnect
• machine room with independent air-conditioning
• numerous Linux servers with up to 16 Cores and 64 GB RAM
• NVIDIA Tesla S1070 GPU supercomputing system (960 cores) with CUDA development tools
• Linux and Windows workstations in public areas and offices, including 10 public workstations
with 30in monitors
• multiple laser printers, including high-speed color printers
• gigabit optical fiber backbone
• scientific and software development software, including Matlab, Mathematica, compilers, and
debuggers
• disk arrays with disk-to-disk backup of users' files
The Center for Computational Mathematics and the Department of Mathematical and Statistical
Sciences has a professional full time system administrator.
Front Range Consortium Supercomputing Facilities
• IBM BlueGene/L, one rack with 2048 cores. Front end with 4 POWER 5 nodes, disk array, and
connection to NCAR's mass storage. The computer is located at the National Center for
Atmospheric Research in Boulder.
• SUN Blade Constellation, 10 racks with total 7680 cores and aggregate performance of over
100TeraFLOP/s. One of the racks accelerated by NVIDIA Tesla S1070 GPUs. Disk array with
raw capacity 768 TB. The computer is currently on order and will be located at CU Boulder.
The Front Range Consortium supercomputers are funded by joint NSF grants to UCD, CU Boulder, and
the National Center for Atmospheric Research. Their use is free, but users who require support or access
from CCM on-site facilities are subject to the Computing services fee.
*Core approval pending
Center for Computational Mathematics
From: [email protected] [mailto:[email protected]]
Sent: Thursday, October 01, 2009 7:44 PM
a) How is the quality of your measurements evaluated – quality control?
We do not measure anything.
b) What is the turn-a-round time for the service you provide?
We do not provide separate track able services. For support issues, it
is generally same or next day. Computer jobs run immediately.
c) Who documents the data provided and signs off on the data?
Not applicable. We do not provide any data.
d) Have you had experience providing data for industry?
Not applicable. We do not provide any data.
e) Do you have a standard operating procedure manual?
No.
f) How will you track billing and financial aspects of your core?
With the help of the Dean's office.
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Behavioral Medicine Core (NJH)
Mailing Address:
Room K340b Goodman
National Jewish Health
1400 Jackson Street
Denver, CO 80206
Contacts
Fred Wamboldt, MD Mary Klinnert, PhD Joshua Miller
Lab Director Core Lab Supervisor Technical Assistance
303.398.1827 303.398.1231 303.398.1710
Overview
The Behavioral Medicine Core Lab (BMCL), located at the National Jewish Health site, is part of
the UCD Colorado Clinical and Translational Sciences Institute (CCTSI) and provides a variety of
services to assist CTRC investigators with behavioral and psychological components of Adult and
Pediatric protocols.
Services Include
• Treatment Adherence Monitoring
• Generic and Illness-Specific Quality of Life and Psychosocial Questionnaires (On-Line
and Off-Line Questionnaire Service and Support)
• Structured Psychiatric Diagnostic Interviews
• Family Asthma Management System Scale
• Structured Interpersonal Assessment and Scoring
• Consultation: BMCL Members can consult on including Behavioral Medicine measures in
your research.
The BMCL strongly encourages consulting members of the lab about inclusion of behavioral
medicine measures in your research. For consultation and additional information concerning any
of our provided services, please contact the BMCL staff.
Treatment Adherence Monitoring Systems
Four objective systems are available for tracking treatment and assay adherence.
• MDILog - electronic inhaler sleeves containing a microprocessor that records and stores
medication adherence.
• Doser - used to track adherence of inhaled medications (metered dose inhalers).
• MEMs Cap - used to track adherence with oral medication (pills). It can also be used to
track at-home sample collection such as salivary cortisol samples.
• EncoreAnywhere and/or Restraxx - CPAP adherence solution for gathering and
monitoring patients' adherence data over the web.
The adherence tracking devices, except for EncoreAnywhere and Restraxx, are provided to the
investigator with technical support, including set-up, data downloading, data verification, and
delivery of complete data sets. EncoreAnywhere and Restraxx is strictly a data monitoring
service.
Structured Interpersonal Assessment and Scoring
• Five Minute Speech Sample (FMSS) – brief measure of expressed emotion (EE) derived
from a speech sample.
• Family Asthma Management System Scale (FAMSS) - assesses eight aspects of asthma
management from a family systems perspective.
Full on-site or off-site training is available for both assessments via teleconferencing. Training
includes proper administration of the interviews, rating and coding the interviews, and how to
interpret the coding system. The BMCL will also help code a sample of the interviews for your
specific protocol to help maintain reliability with the measure.
Questionnaires
The following questionnaires are provided on-line* or off-line for protocols needing Generic and/or
Illness Specific Quality of Life assessments:
• Baseline Dyspnea Index and Transitional Dyspnea Index (BDI-TDI) (off-line)
• Clarke Survey of Hypoglycemia Awareness (on-line)
• Diabetes Distress Scale (on-line)
• Dyspnea-12 Questionnaire (off-line)
• Epworth Sleepiness Scale (on-line)
• Fatigue Severity Scale (FSS) (off-line)
• GEMS Activity Questionnaire (off-line)
• Hypoglycemic Fear Survey (on-line)
• Impact of Weight on Quality of Life (IWQOL-Kids) (off-line)
• Obesity Quality of Life Questionnaire (off-line)
• Pediatric Asthma Caregiver’s QoL Questionnaire (PACQLQ) (off-line)
• Pediatric Quality of Life Questionnaire (PedsQL) (off-line)
• Pittsburgh Sleep Quality Index (PSQI) (on-line)
• SF-36 Health Survey (version1) (off-line)
• SF-36 Health Survey (version 2) (on-line)
• World Health Organization Quality of Life (WHOQOL-100) (off-line)
• Youth/Adolescent Questionnaire (YAQ) (off-line)
The following questionnaires are provided on-line or off-line for protocols needing
Psychosocial/Mental Health Domain assessments:
• Behavior Assessment System for Children (BASC-2) (off-line)
• Brief Symptom Inventory (BSI) (off-line)
• Center for Epidemiologic Studies-Depression Scale (CES-D) (on-line)
• Child Behavior Checklist (CBCL) (off-line)
• Prime MD-Generalized Anxiety Disorder (GAD-7) (on-line)
• Prime MD-Patient Health Questionnaire (PHQ-9) (on-line)
• Semi-structured Interview for DSM-IV (SCID PQ-X, computer screening version) (off-line)
• State-Trait Anxiety Inventory (off-line)
*New instruments may be developed for on-line use at the investigator’s request.
NJH CTRC Behavioral Medicine Core Lab Assay Pricing
BMCL- Procedures Name/Device
Full 100%
Pri cing
Adherence Monitoring
MDILog $42.25
-MDILog computer
-Sleeves
-Docking station
-PC Software License
Doser
-regular Doser $27.03
-Doser CT $30.70
Canister weight tracking $11.40
MEMs Cap
-Mems Track Cap $25.00
-Mems Smart Cap $30.50
-Mems Smart Cap 38mm CR $32.50
-Mems Track Cap 38mm CR $26.00
-Powerview software
-Plastic Bottles
Encore Anywhere CPAP monitoring $152.30
On-line questionnaire
service
Quality of Life SF-36 Health Survey (version 2) $19.25
Pediatric Quality of Life Questionnaire
(PedsQL)
$13.60
Generic Core Scales
Family Impact Module
Mental Health
Center for Epidemiologic Studies-Depression
Scale (CES-D)
$17.40
Prime MD-Patient Health Questionnaire (PHQ-
9)
$11.70
Prime MD-Generalized Anxiety Disorder (GAD-
7)
$11.70
Child Behavior Checklist (CBCL) $19.60
Sleep Epworth Sleepiness Scale $11.70
Pittsburgh Sleep Quality Index (PSQI) $17.40
Diabetes Clarke Survey of Hypoglycemia Awareness $11.70
Diabetes Distress Scale $17.40
Hypoglycemic Fear Survey $17.40
Off-line questionnaire
support
Quality of Life- general SF-36 Health Survey (version 1) $23.10
World Health Organization Quality of Life
(WHO-QOL)
$21.20
Obesity QoL
Impact of Weight on Quality of Life (IWQOL-
Kids) $22.80
Obesity Quality of Life Questionnaire
Asthma QoL
Pediatric Asthma Caregiver’s QoL
Questionnaire (PACQLQ) $24.70
Pedatric Asthma Quality of Life Questionnaire
(PAQoLQ) $26.60
Mental Health Brief Symptom Inventory (BSI) $23.33
Child Behavior Checklist (CBCL) $25.20
Semi-structured Interview for DSM-IV (SCID) $21.20
State-Trait Anxiety Inventory Intro Kit $14.80
Behavior Assessment System for Children
(BASC-2) $26.17
Sleep Fatigue Severity Scale (FSS) $11.70
Breathing BDI-TDI $15.50
Diet Youth/Adolescent Questionnaire (YAQ) $34.15
Activity GEMS Activity Questionnaire $24.70
Pubertal Development Tanner stages – Male and Female $7.60
Interpersonal
Coding/Training
Five Minute Speech Sample (FMSS)-Advanced
Training $2,810
FMSS Consensus/Reliability Coding $28.10
Family Asthma Management System Scale $1,867
System for Coding Affect Regulation in
Families
Lab Director: Fred Wamboldt, MD
Behavioral Medicine Core Laboratory Service
a)
Quality control procedures depend on the nature of the service provided. For example,
with standardized questionnaires we develop electronic surveys if possible, with multiple
checks for accurate scoring. For data collected with psychological measures we are able
to provide psychometric calculations of internal consistency, test-retest reliability, etc.
For interpersonal assessment systems, multiple staff and trainees code the data, and we
assess reliability among coders using kappas or ICCs. Data sets derived from any
procedure are examined on a pre-set schedule for complete and accurate entries.
How is the quality of your measurements evaluated – quality control?
b)
Turn-a-round times depend on the service provided. Some procedures require daily
checks while for others weekly or bi-weekly data management is sufficient. For example,
adherence monitoring involves dispensing and receiving/downloading monitoring devices
in real time as Investigators are collecting data from subjects.
What is the turn-a-round time for the service you provide?
c)
Fred Wamboldt, MD, Mary Klinnert, PhD, or Joshua Miller, Lab Tech, provide
documentation and sign-off for different procedures.
Who documents the data provided and signs off on the data?
d)
No
Have you had experience providing data for industry?
e)
We have standard operating procedure manuals for each service or procedure that we
provide.
Do you have a standard operating procedure manual?
f)
Ronnie Calzada ([email protected]), the NJH CTRC administrator, tracks services
and manages billing and financial aspects of the BMCL.
How will you track bil ling and financial aspects of your core?
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Inflammation and Immunology Core Lab (NJH)
Mailing Address:
Room A442d Smith
National Jewish Health
1400 Jackson Street
Denver, CO 80206
Contacts
Lisa Maier, MD
Core Director
3030-398-1983
Beth Canono
Lab Manager
3030-398-1658
Website:http://cctsi.ucdenver.edu/Research-Resources/Clinical-Research-
Resources/Pages/NJHCoreLab.aspx
About This Lab
The NJH Core Lab is part of the UCD Colorado Clinical and Translational Sciences Institute (CCTSI).
With rare exceptions, the NJH Core lab is unique from the TCH and UCH Core Labs. The focus here is
specialized immunologic assays relevant to immunity and inflammation and not clinical diagnostic assays.
We have access to coordinate with the NJH clinical immunology labs with in-house pricing, providing
investigators access to unique immunology and inflammation assays.
Some examples of our capabilities include:
• Immunofluorescent Cell Staining (PBMCs, lymphyocytes, RBCs, BAL and induced sputum)
• Flow Cytometry analysis (Cell quest Pro and Flojo)
• Lymphocyte Proliferation Assays (including responses to beryllium and various steroids)
• Cell Culturing +/- various stimulation
• DNA extraction from various tissues
• Cell isolations
• RNA extraction from whole blood
• ELISA (routine cytokines plus many other markers and capacity to develop new assays in
collaboration with Elisa Tech, Inc.)
We also isolate and store serum, plasma, PBMCs, BAL, catalog multiple sample types, cryopreserve and
snap free cells and perform differential cell counts.
The NJH Core Lab is a 100-percent customer-based operation. We’re here to help you do your research.
Contact us for technical consultation, developing new assays, or training.
CTRC Core Lab I - Fee Schedule
# of
Samples
Supply Cost
Net
Time
Labor
Cost
Tier 1
Direct Supply
Cost only
Tier 1
Price per
sample
Tier 2
Service Cost
A Studies
Tier 2
Price per
sample
Tier 3
Total
Service Cost
Tier 3
Price per
sample
(Net * Rate)
(Labor + Supplies
+20% Discount)
All Costs-
NO Discounts
Isolation of PBMC 13.10 30cc 0.50 29.81 13.25 34.50 43.25
Isolation of BAL 24.78 240cc 1.00 59.63 25.00 67.75 84.75
Isolation of PMN 15.00 40cc 1.00 59.63 15.00 59.75 74.75
Standard Bronchoscopy Prep 43.12 2.00 119.26 43.25 130.00 162.75
DNA Extraction (10-12cc whole blood - Promega method)) 1 20.00 1.00 59.63 20.00 20.00 63.75 63.75 79.75 79.75
DNA Extraction (10-12cc whole blood - Promega method)) 5 100.00 2.00 119.26 100.00 20.00 175.50 35.25 219.50 44.00
DNA Extraction (10-12cc whole blood - Promega method)) 10 200.00 4.00 238.51 200.00 20.00 351.00 35.25 438.75 44.00
DNA Extraction (10-12cc whole blood - Promega method)) 20 400.00 6.00 357.77 400.00 20.00 606.25 30.50 758.00 38.00
DNA Extraction (8cc whole blood - Paxgene method)) 1 17.58 1.00 59.63 17.75 17.75 62.00 62.00 77.50 77.50
DNA Extraction (8cc whole blood - Paxgene method)) 5 87.90 2.00 119.26 88.00 17.75 166.00 33.25 207.50 41.50
DNA Extraction (8cc whole blood - Paxgene method)) 10 175.80 4.00 238.51 176.00 17.75 331.75 33.25 414.75 41.50
DNA Extraction (8cc whole blood - Paxgene method)) 20 351.60 6.00 357.77 351.75 17.75 567.75 28.50 709.75 35.50
Note - an additional $1.75 per sample (one time charge) is applicable if a second tube is drawn for storage and $5 per sample per year for storage at -80 C. Storage fee applies only after the protocol is completed.
DNA Extraction (mouthwash - 20cc) 1 10.24 1.00 59.63 10.25 10.25 56.00 56.00 70.00 70.00
DNA Extraction (mouthwash - 20cc) 5 51.20 2.00 119.26 51.25 10.25 136.50 27.50 170.75 34.25
DNA Extraction (mouthwash - 20cc) 10 102.40 4.00 238.51 102.50 10.25 273.00 27.50 341.25 34.25
DNA Extraction (mouthwash - 20cc) 20 204.80 6.00 357.77 205.00 10.25 450.25 22.75 563.00 28.25
DNA extraction (buccal swab - Qiagen method) 1 5.00 1.00 59.63 5.00 5.00 51.70 51.70 64.65 64.65
DNA extraction (buccal swab - Qiagen method) 5 25.00 1.50 89.45 25.00 5.00 91.55 18.31 109.65 21.93
DNA extraction (buccal swab - Qiagen method) 10 50.00 2.00 119.26 50.00 5.00 135.40 13.54 169.26 16.93
DNA extraction (buccal swab - Qiagen method) 20 100.00 3.00 178.89 100.00 5.00 223.00 11.15 278.89 13.95
DNA extraction (skin lesion swab - Qiagen method) 1 7.50 1.00 59.63 7.50 7.50 53.70 53.70 67.15 67.15
DNA extraction (skin lesion swab - Qiagen method) 5 37.50 1.50 89.45 37.50 7.50 101.55 20.31 126.95 25.39
DNA extraction (skin lesion swab - Qiagen method) 10 75.00 2.00 119.26 75.00 7.50 155.40 15.54 194.25 19.43
DNA extraction (skin lesion swab - Qiagen method) 20 150.00 3.00 178.89 150.00 7.50 263.15 13.15 328.90 16.45
RNA Extraction (Paxgene Method-2.5ml whole blood) 1 17.00 1.25 74.53 17.00 17.00 73.25 73.25 91.75 91.75
RNA Extraction (Paxgene Method-2.5ml whole blood) 5 85.00 2.50 149.07 85.00 17.00 187.50 37.50 234.25 47.00
RNA Extraction (Paxgene Method-2.5ml whole blood) 10 170.00 3.50 208.70 170.00 17.00 303.00 30.50 378.75 38.00
RNA Extraction (Paxgene Method-2.5ml whole blood) 20 340.00 5.00 298.14 340.00 17.00 510.75 25.75 638.25 32.00
note: currently testing DNA & RNA isolation from saliva using kits from Oragene
Differential cell count 5.00 1.00 59.63 5.00 51.75 64.75
Plasma/serum isolation 2.50 0.20 11.93 2.50 11.75 14.50
Lymphocyte proliferation 35.00 3.00 178.88 35.00 171.25 214.00
Note: Ask about current pricing for the following items
Cryopreservation of cells 1.50 per vial 1.50
Cell culture Initial Set-up cost $2.00 to $8.00 - Other costs depend upon culturing variable
ELISA (non-high sensitivity) 157.00 per plate 157.00
ELISA (high sensitivity - $450 to $500 per plate) 450 to 500 per plate 450.00
Flow cytometry 58.00 per hour 1.00 58.00
Flow data analysis Labor intensive - cost is per hour 1.00 59.63 47.75 59.75
Genetic Studies variable
Immunofloursecent cell staining Will run $50 plus number and cost of antibodies used variable
PCR no Set-up, Fragment 15.00 20.00 40.00
PCR Set-up exon, Fragment 50.00 65.00 100.00
PCR Multiplier (set-up) 250.00 325.00 500.00
Sputum Processing 30.00 30.00
Notes:
Tier 1 is Direct Supply costs only for CCTSI SAC approved
Tier 2 is Direct Supply costs plus labor related for other CTSI/GCRC studies
Tier 3 is for Industry Studies
NJH CTRC Inflammation and Immunology Core Lab
a)
Appropriate positive and negative controls are run for each assay and recorded. Reagents are
routinely checked for expiration dates. Equipment is routinely cleaned. Other quality control
measures include but are not limited to annual calibration and preventative maintenance, safety
inspections and upgrading of equipment to meet the highest standards possible.
How is the quality of your measurements evaluated – quality control?
b)
Most services are completed immediately as required. For example, peripheral blood cell
separation, bronchoalveolar lavage cell isolation and induced sputum cell isolation and
processing are conducted the day that they are available. Likewise, proliferation assays and
stimulation assays requiring culture are also set up the same day as cells are available. Once
harvested the cells or supernatant may be frozen for future batch processing. Others such as
DNA, RNA extractions and Elisa assays can be batched and run in a timely manner for technical
and cost efficiency. DNA and RNA extractions are performed weekly as needed. Elisa’s are
performed as needed and as soon as the appropriate immunoassay kits are available. Usually
these are batched and run at one time to ensure comparability of data. However, if faster
turnaround is needed, our Core lab is happy to work with the investigator.
What is the turn-a-round time for the service you provide?
c)
Samples received in to the lab are logged in to a password protected ACCESS data base with
appropriate HIPAA protection, as well as in individual folders for each protocol by a study specific
identifier. The data is always stored in a de-identified manner. Data generated within the lab is
stored in the ACCESS data base and in files created for each protocol within locked file cabinets
housed in a locked office and separate from the lab. The lab manager reviews the data and, if
appropriate, is reviewed with the core lab director.
Who documents the data provided and signs off on the data?
d)
We have experience providing data for industries. For example, we have provided data for an
industrial protocol from Gambro, for protocols supported by pharmaceutical companies including
investigator initiated protocols, such as Centocor/Johnson and Johnson, and others, and also for
a collaborative protocol with Colorado State University. Procedures performed included but were
not limited to: PMBC isolation, differential cell counts, cell cryopreservation, serum and plasma
isolation, sputum tracking and storage, urine sample aliquotting and tracking, immunofluorescent
cell staining of isolated PMBC and whole blood, flow cytometry, and flow data analysis.
Have you had experience providing data for industry?
e)
We have a standard operating procedures (SOP) manual where procedures performed in the lab
are described in detail. Special procedures or those requiring variation from the standard are
also written in detail with a protocol number for reference. These SOPs include quality control
measures to ensure that the tests and procedures are run in a standard manner.
Do you have a standard operating procedure manual?
f)
This is in the process of being set up across the CTRC administrative groups. Our administrative
contact is Ronnie Calzada ([email protected]).
How will you track billing and financial aspects of your core?
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Nursing Core
Contacts
Diane Branham, RN, BSN
Clinical Nursing Director/TCH CTRC Nurse Manager
720-777-3195
Detra Bliton, RN, BSN
UCH CTRC Nurse Manager
720-848-6430
Christine Reed, RN
Perinatal CTRC Nurse Manager
720-777-4694
Debra Coady, RN
UCB CTRC Nurse Manager
303-735-3587
Trudi Madigan, RN
NJH CTRC Nurse Manager
303-398-1717
The Nursing Core provides expert clinical research support during protocol development,
implementation, and data collection. We have dedicated facilities at four sites, University of
Colorado Hospital (UCH), The Children's Hospital (TCH), University of Colorado Boulder (UCB),
National Jewish Health (NJH), and our Perinatal Nursing Team capable of accommodating visits
at these sites and additional hospitals. Some sites have specialized equipment and services,
forming a well-networked nursing service for clinical investigators. We have five well-coordinated
groups of professionals:
• Registered Nurses with extensive experience caring for participants in complex research
protocols.
• Advanced Practitioners and Physician’s Assistants who aid the Principal Investigators in
H&Ps and research procedures.
• Professional Research Assistants and Healthcare Technicians who work closely with the
nursing staff to assist with research procedures and processing of samples.
• Sonographer skilled in collection of research images
• Administrative Staff who schedule participants, assist in creating budgets, and track the flow
of all research activity.
UCH Inpatient 15 inpatient beds, all with telemonitoring capability
UCH Outpatient Clinic 14 rooms with a 5-chair infusion room and a 7-chair blood draw room
TCH Inpatient Unit 10 inpatient beds, all with telemonitoring capability
TCH Outpatient Clinic 6 exam rooms, 5 infusion rooms PLUS the ability to send staff to other areas of
the hospital to collect samples for research (example-PICU, OR, Cath lab)
NJH Clinic 5 clinic rooms
UCB Clinic 5 rooms, 1 DXA room, 1 exercise room
Perinatal Nursing Team Conducts research in Labor & Delivery (UCH, Denver Health, St. Joes)
and the NICUs (UCH, TCH, St. Joes, Denver Health)
Services and Resources
The Nursing Core has a multi-disciplinary role in the CCTSI. Their roles include:
• Clinical Expertise
• Intensive Care/Step-Down Care
• Medical /Surgical Care
• Pediatric Care
• Perinatal Care
• Healthy Volunteer Care
• Feasibility Assessments for Study Implementation/Protocol Oversight
• Consultation Services/Study Design and Consent Development
• Investigator and Study Coordinator Support
• Data and Sample Collection
Note: Specific sites have screening, enrollment, and participation follow up.
Specialized Research Services
Please note that all four sites are well-networked and your protocol needs may be met for
patients enrolled at any of the sites (site availability in parentheses).
• High and Low Risk Exercise Testing (UCH, TCH, UCB)
• Ultrasound Core with Echocardiogram Imaging (UCH, TCH)
• Complex Drug Administration (UCH, TCH, UCB, NJH)
• Allergy Testing (UCH, NJH)
• Biopsies-Muscle, Adipose, Skin (All)
• Endothelial Cell Harvesting (UCH, TCH, UCB)
• Specialized Endocrine Testing (OGTT, IVGTT, Metabolic Clamp) (UCH, TCH, UCB)
• Hemodynamic Monitoring (UCH, TCH, UCB)
• Invasive Pressure Monitoring (UCH, UCB)
• Chemotherapy Infusions (UCH)
Specialized Equipment (site availability in parentheses)
• Metabolic (RMR) Carts (PARVO/VMAX) (UCH, TCH, UCB)
• Dual Energy X-ray Absorptiometry (DXA) (UCH, TCH, UCB)
• Calorimetry Chamber (UCH)
• Exercise Testing Equipment with a Treadmill or Bike (UCH, TCH, UCB)
• Bronchoscopy (UCH, TCH, NJH)
• Sleep Laboratory (UCH, TCH, UCB)
• PCT 3000 Scanner (UCH)
• Cardiac Monitoring Equipment (All Sites)
• ECG Machines (All Sites)
• GE Vivid 9 Ultrasound Machine (TCH, Perinatal)
• GE Vivid Q Portable Ultrasound Machine (UCH, TCH, Perinatal)
• KINCOM (UCH)
• PEA Pod (UCH, TCH, Perinatal)
• BodPod (TCH)
• Faraday Cage (UCB)
CCTSI CTRC Nursing Core
a) How is the quality of your measurement evaluated-quality control?
Each site follows the Quality Control mandated by that institution.
b) What is the turn-a-round time for the service you provide?
N/A
c) Who documents the data provided and signs off on the data?
The nursing staff provides documentation to support the protocol. The protocol is reviewed by
the site which will be implementing the research.
d) Have you had experience providing data for industry?
The nursing staff at each site has developed documentation to implement the protocol.
e) Do you have a standard operating procedure manual?
Each site has operating procedure manuals specific to that institution
f) How will you track billing and financial aspects of your core?
Billing and the financial aspects of the protocol are tracked by the administrative personnel at
each specific site.
Colorado Clinical and Translational Sciences Institute (CCTSI)
Clinical Translational Research Center (CTRC)
Nutrition Core
Contacts
Janine Higgins, PhD Archana Mande Melanie Kasten
Nutrition Research Director Nutritionist, UCH (Adult) Nutritionist, TCH (Peds)
720 777-2955 720 848-6683 720 777-2994
[email protected] [email protected] [email protected]
Core Informationhttp://cctsi.ucdenver.edu/Research-Resources/Clinical-Research-Resources/Pages/Nutrition.aspx
Availability
All Nutrition Core services are available to approved CTRC and Clinical Trials Organization (CTO) protocols.
Services may be available to other protocols on a fee-for-service basis. All fee-for-service protocols must
provide a copy of current COMIRB approval.
Cost
The Nutrition Core tracks monthly usage by protocol. Billing is handled on a case-by-case basis. Prior-
payment arrangements will be made by Janine Higgins and Pat Kittelson ([email protected]).
Prices for each service (see following table) fall into two categories: 1) CTRC cost, and 2) industry/CTO
cost:
1) CTRC cost includes food/materials cost only with minimal or no labor cost as this is subsidized by the
CCTSI. This pricing is available only Scientific Advisory and Review Committee (SARC)-approved,
investigator-initiated studies. Studies in this category are generally federally-funded (e.g. NIH) although
some are funded via private foundations and non-profit institutes.
2) Industry/CTO cost is a non-subsidized fee-for-service cost. This pricing is available for SARC- approved
CTO protocols and other industry protocols. Studies in this category are generally funded by private
companies or corporations (e.g. drug companies).
Services
Item CTRC Cost Industry/CTO Cost
Weighed, Metabolic Meal $6.00 $25.00
3-Day Metabolic Diet $42.00 $122.00
Dietary Instruction/Counseling $28.00/hr $40.00/hr
3-Day Diet Diary Analysis* $28.00 $44.00
24-Hour Dietary Recall $26.00 $40.00
Food Frequency Questionnaire $24.00 $38.00
Resting Metabolic Rate (Peds only) $35.00 $50.00
* This cost is for analysis ONLY does not include instructions at issuance which would be charged at $30/hr. It is recommended that
PRAs learn how to issue the diet diary which would incur a one-time hourly instruction charge rather than an instruction charge/subject.
National Jewish Health (NJH)
Clinical Translational Research Center (CTRC)
Research Nursing and Facilities (NJH)
Contacts
Donald Leung, MD, PhD
Associate Program Director
303-398-1186
Trudi Madigan, RN
Nurse Manager
303-398-1717
The NJH CTRC is part of the UCD Colorado Clinical & Translational Sciences Institute (CCTSI). At the
NJH CTRC clinical research visits will take place at National Jewish Health, the #1 Respiratory Hospital in
America specializing in Pulmonary, Immunology, and Allergy. National Jewish is accredited by the Joint
Commission on Accreditation of Healthcare Organizations. The subjects will be consented and seen in
the CTRC outpatient clinic. The clinic consists of three exam rooms, one interview room, and one
procedure room. The clinic is staffed by a Nurse Practitioner and RNs. History and physicals, spirometry,
EKGs, skin testing, blood draws etc. are performed in the area. An adjacent laboratory is available for
handling clinical samples. The study agent will be stored and prepared for administration by the National
Jewish Health Research Pharmacy Service. A -80
0
F freezer and biosafety cabinet is available for
storage and preparation.
• Administering Questionnaires
Services
• Adverse Event Reporting
• EKG 12 Leads Restin
• Emla Administration (PEDS topical)
• Height and Weight
• History and Physical (long and short) NP
• Informed Consent/Assent
• IRB/SARC Submission
• IRB Continuing Review
• IV Insertion – IV CATHETER INSERT
• Medication administration
• Moderate Sedation/Assistance and Supplies
• Observation Hourly
• Observation Post Medication Administration
• Pharmacokinetics
• Review of Inclusion/Exclusion Criteria
• Six Minute Walk
• Skin Test Delayed – Skin Testing
• Spriometry pre and post – Spiro Clinic Pre/P
• Spirometry pre only – Spiro Clinic Flow
• Sputum Induction
• Urine Collection
• Urine Pregnancy
• Venipuncture Vital Signs
NJH CTRC
a)
Staff performances are evaluated on an annual basis to ensure quality services.
How is the quality of your measurements evaluated – quality control?
b)
Services are provided on the day subjects are scheduled for their visits.
What is the turn-a-round time for the service you provide?
c)
MD’s and RN’s
Who documents the data provided and signs off on the data?
d)
Yes
Have you had experience providing data for industry?
e)
We follow Nursing Policies and Procedures
Do you have a standard operating procedure manual?
f)
The billing and financial aspects are handled by our administrative staff. Our administrative
contact is Ronnie Calzada.
How will you track bil ling and financial aspects of your core?
Colorado Clinical and Translational Sciences (CCTSI)
Clinical Translational Research Center (CTRC)
Research Nursing and Facilities (UCB)
Contacts
Elizabeth Connick, MD
UCB Medical Director
303-724-4930
Debra Coady, RN
Nurse Manager
303-735-3587
The UCB CTRC located at the University of Colorado Boulder is part of the UCD Colorado
Clinical and Translational Sciences Institute (CCTSI) and delivers nursing care in a research
clinic utilizing a systematic approach to nursing practices incorporating assessment, planning,
implementation, and evaluation; thus providing continuing health care to research volunteers.
New clinical procedures or techniques will be incorporated into nursing core services based upon
funding and potential overall use and is dependent on SARC and IRB approvals. Training for
new procedures or techniques will be provided by the principal investigator.
Due to the unique location of the UCB CTRC on a Ph.D. driven campus, the nursing core also
provides consultation on all medical aspects of protocol design and consent form development.
Rooms
• 1 exam room
• 4 protocol rooms
• 1 DXA room
• 1 exercise physiology room
• 1 Faraday room with nerve traffic analysis system
Services
• Phlebotomy
• Medical histories
• Medication instruction
• Intravenous catheter placement
• ECG recordings and interpretation
• Endothelial harvest collection
• Assisting with arterial line placement
• Drug infusions
• Assisting with biopsies
• 24 hour nursing and physician telephone coverage
• Health and procedural instructions to students and research volunteers
UCB CTRC
a) How is the quality of your measurements evaluated – quality control?
There is on-going review of each staff’s performance maintained by the supervisor. There
is continuing review of interventional outcomes through on-going medical assessments
and tracking of adverse events through the UCB study monitoring committee.
b) What is the turn-a-round time for the service you provide?
Services provided on the day that research volunteers are scheduled.
c) Who documents the data provided and signs off on the data?
Clinical staff (registered nurses and medical doctors) sign off on all forms relating to
procedures performed.
d) Have you had experience providing data for industry?
Yes. A clinical trial was conducted by one of our principal investigators several years
ago which utilized the nursing core.
e) Do you have a standard operating procedure manual?
Yes. Policies and procedures are kept on the unit and signed off by the UCB Medical
Director, Elizabeth Connick, MD.
f) How will you track billing and financial aspects of your core?
Billing is tracked and handled by the UCB Administrative Manager.
Clinical Investigation Core
Center for Aids Research (CFAR)
Cara Wilson, MD
Core Director
303-724-4601
[email protected]
Website:http://www.uchsc.edu/ccfar/cores/clinical.htm
The goal of the Clinical Core to provide focused yet comprehensive support of human
HIV/AIDS-related studies from their conception through implementation.
The overall mission of the Clinical Investigation Core is:
• To provide comprehensive support of HIV-related clinical investigation with a special
emphasis on providing support to junior investigators, investigators new to AIDS clinical
research, and investigators new to patient-oriented research in general.
• To ensure the recruitment of HIV-1 infected persons with diverse racial, cultural, and
gender characteristics at multiple sites throughout Colorado for participation in CFAR
clinical and translational research studies.
• To provide integrated antiretroviral clinical pharmacology expertise and resources to
support the clinical and translational research by D-CFAR investigators in Colorado and
by AIDS investigators throughout the United States.
• To ensure the quality of CFAR-supported clinical investigation through training and
certification of CFAR investigators in the principles of clinical research and human
subject protections.
• To encourage collaborative interactions among laboratory-based, translational and
clinical investigators, thereby promoting the growth of cutting edge clinical HIV/AIDS
research in Colorado.
• To pro-actively identify and correct gaps in HIV/AIDS clinical investigation in Colorado
and to provide core facilities and services that will enhance interdisciplinary
collaborations and eliminate gaps.
The Clinical Investigation Core will provide three main resources to support clinical research of
CFAR investigators: a clinical research resource, a clinical pharmacology resource, and a
specimen management resource.
To request one of our services contact [email protected].
Your form will be forwarded to the Clinical Investigation Core steering committee to work out
the funding and personnel who can help you with the project. You will receive a response to your
request within 1-2 weeks.
Clinical Investigations Core
University of Colorado Cancer Center
(UCCC)
Contacts:
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/cic/index.aspx
The UCCC Clinical Investigations Core (CIC) mission is to optimize the quality and quantity of
cancer clinical trials research for UCCC. The specific objectives are to:
• Ensure the provision of exceptional patient care at UCCC sites by offering new
approaches to cancer management through cancer clinical trials
• Support of all aspects of cancer clinical investigations headed by UCCC investigators
• Provide a conduit for activation of UCCC investigator-initiated cancer clinical trials
• Ensure opportunities for clinical trials education
• Offer a final common pathway for UCCC translational research applications
Almost 70 CIC clinical, regulatory and administrative staff manage performance of more than
400 clinical studies with a total accrual of nearly 7,500 subjects.
Services We Offer
• Regulatory submission and monitoring
• Protocol Development
• Budget development and contract negotiation
• Enrollment of eligible patients
• Data collection and monitoring
• Specimen procurement and processing
• Adverse event reporting
• Coordination of patient treatment
• Training and education of clinical and regulatory staff
• Training of Phase I oncology fellows
• General Good Clinical Practice Training
• Maintenance of the UCCC Clinical Trials Database
• Quality Assurance
• Protocol Review and Monitoring
• PQASC-audit schedule & Data Safety Management Plan
Anthony Elias, MD
Associate Director for
Clinical Research
[email protected]
720-848-1622
Madeleine Kane, MD, PhD
Medical Director
[email protected]
720-848-0354
Andrea Buchmeier, CCRC
Clinical Research Director
[email protected]
720-848-0635
University of Colorado Cancer Center
Clinical Investigations CoreAnschutz
Cancer Pavilion
1665 AuroraCT, RM 3200
Mail Slop F-700
Aurora, Colorado 80045-0510 Fax:
720-848-0671
STATEMENT OF FEES-FISCAL YEAR 2009-2010
(Effective J une 1, 2009-May 31, 2010)
1. Overhead
It is the policy of the University of Colorado Denver (UCD) to obtain the appropriate, approved
facilities and administrative cost recovery rate on all sponsored programs whether they are from
private or public sources. The overhead rate applicable to clinical research at the University of
Colorado Cancer Center (UCCC) Clinical Investigations Core (CIC) is 26% established under
the F & A policy of UCD. This rate is applied to all non-patient care costs (i.e. applied only to
labor and administrative charges). The amount is taken directly from the payments received and
retained by UCD. The overhead collected is in no way applied to the compensation provided to
either the site research staff or the UCCC principle investigator. Please see the attached link for
more detailed information regarding this subject:
2. Study Start Up Feeshttp://www .uchsc.edu/ ogc/pp/fa.php
The University of Colorado Cancer Center Clinical Investigations Core assesses the
following fees to all industry-sponsored clinical trials:
a) Informatics Fee
: The Informatics administrative fee is a flat fee charged to all protocols to
cover the expenses of maintaining on-site monitor workstations, providing computer
monitors at these workstations, providing monitors with access to UCH EMR, and IT
support for this access.
1
b) Pharmacy Fee
c)
: The Pharmacy administrative fee is a flat fee charged to all protocols that
require the dispensing services of The University of Colorado Hospital Pharmacy. This
fee is in addition to the drug dispensing fee.
Laboratory Fee
d)
: The Laboratory administrative fee is a flat fee charged to any protocol
that requires specific sample handling and shipping of specimens. This fee is in addition
to specimen processing, handling, storage and shipment fees
Research Office Start Up Fee
e)
: The Research Office Start Up fee is a flat fee that covers
the costs associated with opening a clinical trial through the University of Colorado. This
process includes regulatory document preparation for protocol submission to the UCCC
Protocol Review and Monitoring Committee (reviews for scientific merit), the IRE, and
the University of Colorado Hospital Research Review Committee (reviews for
compliance and resource utilization). It covers the costs associated with budget and
contract preparation, negotiation, finalization and implementation.
University of Colorado Hospital Research Compliance Review
f)
: The University of
Colorado Hospital (UCH) Research Compliance Review is required to review any new
protocol prior to its opening. This review process typically takes 2-6 weeks.
University of Colorado Hospital Research Compliance Fast Track Review Fee
g)
: This fee is
in addition to the fee stated above. The UCH fast track review fee guarantees a 48-72 hour
turnaround time for initial review and a 24 hour turnaround if there are questions that need
addressed prior to approval. This fee assesses an additional $250 for the expedited request;
this fee is assessed only if the sponsor requests the fast track review process.
Clinical Translational Research Center CCTRC-formerly known as OCRC): This fee
supports the work associated with preparation and submission of the protocol and all
required documentation to the CTRC. The CIRC consists of both in-patient and outpatient
research units that specialize in the conduct of clinical trials. These units are used when the
research procedures cannot be carried out in the outpatient setting or during out-patient
clinic hours. For example: around the clock PK collection. This fee is only assessed if the
study requires the use of the Clinical Translational Research Center.
The CIC will consider reduction of study start up fees if the study is considered a rollover or
extension of study previously conducted in the CIC by the same sponsor. This reduction in
startup fees will be at the discretion of the CIC Director.
Study start up fee exceptions
2
3. Items Invoiced to the Sponsor:
Regulatory Affairs Fees Administrative Category
Frequency
$1800 Regulatory Continuing Review
a
Annually
$125 Regulatory Amendment
B
Per Amendment
A. The regulatory affairs continuing review fee is assessed by the CIC to cover all expense
for annual study submission to Western Institutional Review Board (WIRB). This fee
also includes yearly regulatory maintenance of the study such as safety reporting,
adverse event reporting and other protocol related duties.
B. The regulatory affairs amendment fee is assessed by the CIC to cover all expense pertaining
to each protocol amendment.
All fees listed above are subject to overhead as described in item one. The overhead
collected is not applied to compensation provided to either the clinical research staff or the
UCCC principle investigator. All fees are invoiced to the sponsor and are due upon receipt
of invoice.
Note: The above regulatory fees are subject to a late charge for payments received later
than 60 days of Invoice date, $100 will be applied to the balance for each month payment
is not received.
For studies eligible for WIRB
submission:
FEES*
Administrative Category
$3000
$825
$1800
$350 per submission
$250 per submission
WIRB Initial Review-includes (1) consent form
WIRB Six Month Review (if applicable)
WIRB Annual Continuing Review
Changes to Research Involving Consent Form Review
Changes to Research not Involving Consent Form Review
For studies not eligible for WIRB submission, such as investigator-initiated and/or studies
requiring bio-safety committee review, our local IRB (COMIRB-Colorado Multiple
Institution Review Board) will be used.
FEES*
$2000 COMIRB Initial Review
Administrative Category
$1500 COMIRB Continuing
Annual Review
*The fees listed above are not subject to overhead.
3
4. University of Colorado Hospital pricing
Every protocol that involves the use of University of Colorado facilities is sent to the
applicable department for review and pricing. The applicable department (radiology, clinical
laboratory, pharmacy) reviews the protocol and provides the CIC with a price quote for the
procedures required. The prices quoted are offered to the CIC, and subsequently to the
sponsor, at a reduced research rate. These prices are effective for a period of 12 months
following the department's initial review. The prices set by the hospital are non-negotiable. In
addition, a CIC bill processing fee in the amount of $944 (overhead to be assessed) will be
applied to the total per patient amount. This fee supports the CIC billing process assuring that
research procedures are billed appropriately, to include compliance review of all research
invoices to ensure billing remains compliant with all federal laws.
If a protocol is not open within 12 months of initial budget agreement, prices are subject to
change. If this occurs, a revised budget will be sent for review and approval.
Protocol complexity may result in additional fees as deemed necessary by CIC
administration.
Additional Fees
Additional fees such as Principal Investigator fees, RN/Coordinator fees, Research
Administration fees (general administrative oversight of study to include payments applied,
account reconciliation, invoicing, sponsor contact for query resolution, coordinator budget or
enrollment issues, study close out, contract/amendment issues; in addition, medical and clinical
director oversight of study to include review of protocol, monitoring of site, review of
monitoring letters to ensure GCP compliance, quality and assessment of training issues and
needs), data management and archive fees are included in the body of the site's budget.
4
Clinical Science PhD and MS Program
Contact:
Lisa Cicutto, PhD, RN
Program Director
University of Colorado Denver
303-398-1538
[email protected]
http://www.uchsc.edu/clinicalscience/index.htm
The Clinical Science PhD and Masters Program
This innovative program is designed for qualified individuals who are interested in obtaining
either a Ph.D. (doctoral) or Master's degree in Clinical Science. The primary applicant audience
includes those having earned a health sciences graduate degree or a health care professional
degree (e.g., physicians, MSPH graduates, biostatisticians, epidemiologists, nurses, pharmacists,
physical therapists and dentists).
The overall goal of the University of Colorado Denver (UCD) Graduate Program in Clinical
Science (CLSC) is to train Clinician Scientists by providing a formal, structured, and rigorous
educational program in Clinical Investigation (CI), Health Information Technology (HIT), or
Health Services Research (HSR).
These three fields of clinical science are important areas of study for translational research
activities in the evolving health care environment. Graduates of our program are highly qualified
and well-trained Clinician Scientists who will be nationally competitive for grant funding and
career advancement in the health sciences.
Core Personnel
Lisa Cicutto, PhD, RN (Program Director) specializes in Allergy, Asthma, COPD/Chronic
Obstructive Pulmonary Disease/Emphysema, and other Pulmonary Disease Research. She is
Associate Professor, Colorado School of Public Health and the College of Nursing and Associate
Director, Clinical Science Graduate Program.
Welcome to the Clinical Trials
Organization
Contacts:
Jill McHale
Interim Director
(720) 777-8430
[email protected]
Website;http://research.childrenscolorado.org/content/clinical-trials-organization
The Clinical Trials Organization (CTO) supports the research mission of Children’s Hospital Colorado. The CTO
provides a variety of services to researchers who conduct clinical research, including those required for study
start up and initiation, ongoing trial management and study close out. Studies range from non-interventional
database collections to more complex treatment trials using investigational agents or devices.
Please visit our links, indexed at left, to find out more about our research and clinical activities.
Clinical Trials Organization Research
The Clinical Trials Organization (CTO) supports the research mission of Children’s Hospital Colorado. The CTO
provides a variety of services to researchers who conduct clinical research, including those required for study
start up and initiation, ongoing trial management and study close out. Studies range from non-interventional
database collections to more complex treatment trials using investigational agents or devices.
If you have questions about clinical research studies at Children’s Hospital Colorado, or would like
information regarding our current studies, please call 720-777-8430 or e-mail:
[email protected].
Clinical Trials Organization Clinical Services
The Clinical Trials Organization serves the children and primary care providers of the Rocky Mountain
region by translating cutting-edge research into clinical care. Internationally recognized leaders in
pediatric health care research are involved in a variety of groundbreaking studies working towards
advancements in pediatric health care. The Clinical Trials Organization conducts studies throughout all
arenas of pediatric medicine and exists to advance the health and welfare of children through the careful
coordination of state-of-the-art pediatric clinical research.
If you have questions about clinical research studies at The Children’s Hospital, or would like information
regarding our current studies, please call 720-777-8430 or e-mail: [email protected].
Colorado Advanced Photonics Technology Center (CAPT)
Larry Scherrer
Director
303-556-4175
[email protected]
http://www.captcenter.org/about/Default.htm
The Colorado Advanced Photonics Technology (CAPT) Center has several labs with equipment
that give companies access to state of the art measurement and fabrication equipment.
Companies are welcome to come to the center and use equipment, or contract service
measurements are also available. CAPT has a 2000 square foot facility. There is also a dark room
for photolithography, a general optics and development lab, office space, and conference room.
The four major areas of concentration are:
• Optical Characterization and Metrology Lab
• Photonics and General Developmental Lab
• Prototype Packaging and Photolithography Lab
• Environmental Test and Evaluation Lab
CAPT is conveniently located in Longmont which is close to Boulder and Denver, and easily
accessible from interstate I-25 ( see map).
As a non-profit organization, the CAPT Center provides cutting-edge technical services and
human resources to its corporate and educational partners. The CAPT Center is the only
photonics resource in Colorado that can deliver: surface roughness measurements, optical testing
, contract measurement services, prototyping, precision metrology, environmental testing, use of
photonics equipment and facilities, training for current employees, and connections with future
employees.
The CAPT Center provides access to state-of-the-art facilities and equipment:
• $5 million in equipment for material characterization, prototype packaging, measuring,
inspection and environmental testing.
• 2,000 sq. ft. of support laboratories
• Design, processing, characterization, packaging and quality labs
• CAPT Incubator Program
Before you commit to purchasing expensive equipment, test your product ideas at the CAPT
Center.
How can CAPT help you?
• By providing sophisticated equipment and tools for testing, fabrication, packaging,
environmental test and design.
• By providing clean room facilities
• By assisting in use of equipment and tools
• By training your employees through photonics short courses
• By giving you access to photonics students
CAPT also offers the following services
• surface roughness measurements
• optical testing
• Contract measurement services
• component evaluation
• Contract optical testing
• photonic and optical systems engineering
Tell us what you need!
Facility Rates and Usage
You can come and use the equipment at the CAPT Center, or we offer surface roughness
measurements, optical testing , and other contract measurement services. Use of the facility
should be reserved in advance and the use of any particular item is subject to availability. Call
your CAPT representative to schedule usage and assure availability.
Equipment Cost
CAPT Facility Rates depend on three factors: the sophistication of the equipment that is being
utilized (Equipment Classification); the commitment to use the equipment over a period of time;
and CAPT Membership status. See our complete Equipment List and Classification.
CAPT Facility Rate Schedule
Equipment
Class
Hourly Rate
($/hr)#
Daily Rate
($/day)#
Weekly Rate ($/5
Days)*
Monthly Rate
($/22 days)*
A $25 $160 $720 $2,808
B $50 $320 $1,440 $5,616
C $75 $480 $2,160 $8,424
D $100 $640 $2,880 $11,232
E $150 $960 $4,320 $16,848
F $200 $1,280 $5,760 $22,464
# Terms Net 15 days with approved credit
* Payment due in advance (days use may be non-contiguous)
Non CAPT Members pay a 50% premium
Usage Discount
The CAPT Facility Rate Schedule provides discounts for long-term usage from the hourly rate. If
equipment is utilized for 1 full day (8 hours), an automatic discount of 20% will be extended to
the user.
Weekly and monthly rates are also available at substantial discounts. The benefit of these rates is
that they apply to 40 hours of usage for the weekly rate and 176 hours of usage for the monthly
rate. The usage dates do not have to be contiguous. This payment approach offers the
opportunity for long term planning and provides flexibility that standard lease programs cannot
provide. The weekly and monthly usage fees must be paid in full in advance.
Technical Assistance and Contract Measurements
CAPT will provide Engineering level and/or Technician level technical assistance at the
following rates:
Technician: $50 per hour
Engineering: $83 per hour
Payment Terms
Terms are NET 15 days upon invoice for CAPT Members.
Terms are Due on Receipt for non CAPT Members.
Colorado Biostatistics Consortium (CBC)
Contacts:
John Neal
[email protected]
Administrator
303-724-4370
Website:http://cbc.uchsc.edu/
The Colorado Biostatistics Consortium (CBC) is a unit in the Department of Biostatistics &
Informatics, Colorado School of Public Health, University of Colorado Denver (UCD). The
CBC is a shared resource for biomedical investigators at UCD, Colorado State University (CSU),
University of Northern Colorado (UNC) and other institutions. It provides biostatistical
expertise for centers, programs, departments, and individual investigators to facilitate the design
of studies, data acquisition protocols, data analysis, and the preparation of grants
and manuscripts.
Colorado Clinical and Translational Sciences Institute (CCTSI) The CBC administers the
Biostatistics, Epidemiology, and Research Design (BERD) core function of the CCTSI.
Biostatistical consultation is provided to CCTSI award/grant recipients at no charge. BERD
hosts courses and seminars in study design, data collection and results analysis for medical
researchers who desire to deepen their understanding of these topics. For more information
about the CCTSI, please visit:http://cctsi.ucdenver.edu.
Research Consulting Laboratory (RCL) Medical investigators needing a "quick question"
answered and students working on theses, dissertations and research projects can obtain support
from the CBC Research Consulting Lab. Staffed by graduate students in Biostatistics &
Informatics, and supervised by Kim McFann, PhD, the RCL provides tutoring on the design of
studies, sample size calculations, data analysis, and other biostatistical subjects. Located in
Historic Building 500, Third Floor, West Wing, Room W3132, the RCL is open during normal
business hours every weekday. Call 303-724-4619 to schedule an appointment.
How to contact the CBC:
Contact John Neal (CBC Administrator) to arrange a meeting with a senior biostatistician.
CBC Fees
Medical researchers working under the auspices of the Colorado Clinical and Translational
Sciences Institute (CCTSI) should contact the CBC regarding their biostatistical needs.
For investigators who have their own funding, there are two options for obtaining biostatistics
support, provided that the CBC has the resources and expertise to meet the client’s needs:
1. Agreement
For ongoing, long-term grants or departmental support requiring a variety of services.
? A monthly retainer for a specified time period for the anticipated work involved.
? To be negotiated on a case-by-case basis with the Director of the CBC.
2. Hourly Rates
For one-time, short-term projects requiring specific services within a limited time frame.
? $125 per hour for University departments and affiliated organizations or institutions.
? For non-affiliated organizations, the hourly rate will be negotiated, depending on scope of
work, plus travel costs, if incurred.
Frequently Asked Questions:
1. Why would I use the CBC instead of hiring my own biostatistician?
? Rather than relying on a single person’s education and background, you would have access to
a range of levels (MS / junior to PhD / senior level biostatisticians), as well as taking advantage
of the wide array of expertise within the CBC collaborative pool of colleagues. See Faculty for
details.
? Consortium statisticians are mentored by senior faculty, providing a depth of shared
experience that cannot be found in a single individual.
? You avoid the management responsibility and facilities expense associated with a “regular”
employee, while having the flexibility to obtain part-time or short-term support as needed.
? You can control the specific costs associated with a project or grant.
? You can secure intellectual collaboration on short notice, without undergoing a time-
consuming hiring process.
? The CBC works with you to help structure your research and analyses. As a collaborative
partner, the CBC can assist you in preparing grant proposals, designing studies, analyzing their
results – all the way through to helping you write manuscripts, reports to funding agencies, and
presentations of findings.
2. What do the hourly rates include?
? Support for staff salaries and benefits.
? Support for the CBC infrastructure, including computer hardware/software, professional
development, administrative and financial management.
? Built-in “capacity” to respond to and collaborate on new projects as they arise.
4. Do I have to pay the CBC if I just have a quick question?
? No. We are happy to share our expertise with the University community by addressing quick
biostatistical questions or providing short consultations at no charge.
? The CBC also includes a “Research Consulting Lab” which offers walk-in statistical
consultation at no charge. This is primarily targeted toward students. However, faculty
investigators are welcome to utilize this service as well, although they may be referred to the
CBC for more in-depth collaboration.
? If the question isn’t really “quick” and requires comprehensive analysis or treatment, the CBC
will work with you to structure a longer term collaboration. 5.
How do I incorporate the CBC into my research?
? Contact John Neal, Administrator: 303-724-4370 or [email protected]
? We will set up an initial meeting to discuss your project. (Note: There is no charge for the
initial meeting.)
Core Facility
Contacts
Directors
Karen Swisshelm, PhD, FACMG
(303) 724-5701
[email protected]
Loris McGavran, PhD, FACMG
(303) 724-5701
[email protected]
Genetic Counselors
Janine Gessner, MS
(303) 724-5723
[email protected]
Michelle Springer, MS, CGC
(303) 724-5710
[email protected]
Client Services
Susan Mountain-Morgan
(303) 724-5701
[email protected]
Website: www.coloradogeneticslab.com
CAP #2182823
CLIA # 06D0644362
Colorado Genetics Laboratory
About Colorado Genetics Laboratory
Colorado Genetics Laboratory (CGL) is nationally recognized for excellence and strives to provide the
highest quality cytogenetic testing. Based in Denver and serving the Rocky Mountain region, CGL
specializes in prenatal, postnatal, and cancer cytogenetics; fuorescence in situ hybridization (FISH); and
microarray (cytogenomic) technologies. With decades of experience, our cytogenetic technologists
are outstanding in the feld. Certifed genetic counselors are on staf to aid in test interpretation and
answer your questions. We provide the most up-to-date information on chromosome abnormalities
and microarray fndings. Client services representatives are available to assist with transport of samples,
copies of reports and other special requests.
1) How is the quality of your measurements evaluated - quality control?
Colorado Genetics Laboratory (CGL) is accredited by Clinical Laboratory Improvement Amendments (CLIA) and the College of
American Pathologists (CAP). Internal quality controls are performed and evaluated to ensure our services are superior. CGL
participates in the Children’s Oncology Group, the Eastern Cooperative Oncology Group (ECOG) and the Southwest Oncology
Group peer-reviewed cytogenetic cancer studies.
2) What is the turn around time for the service you provide?
Turn around times are accommodated to meet your research and clinical trial needs. Please contact CGL at (303) 724-5701 to
discuss your testing timeline.
3) Who documents the data provided and signs of on the data?
Our certifed cytogenetic technologists analyze and document their fndings in a written report. The report is reviewed and
signed by the laboratory directors.
4) Have you experience providing data for industry?
Colorado Genetics Laboratory has been working with private industry for over 14 years.
5) Do you have a standard operating procedure manual?
Colorado Genetics Laboratory is accredited by CLIA and CAP. Our operating procedure manual is annually reviewed and
updated as required by these regulators.
6) How will you track billing and fnancial aspects of your core?
Billing and expenses are tracked though CGL administration. Please contact our Business Manager, Kathy Taylor, at
(303) 724-5705, to discuss pricing for your specifc cytogenetic testing needs.
Services
Chromosomal Microarray (CMA)
• High-resolution DNA
array containing 180,000
oligonucleotide clones
• Follows International
Standards for Cytogenomic
Array in chip design
• Clones spaced ~16 Kb
along the backbone
• Increased
coverage in disease regions
• Targeted coverage of 500+ disease genes, microdeletion/
duplication syndrome regions, and subtelomeres
• Abnormalities detected at a resolution of 100-200 Kb
• Two diferent software platforms available for analysis
to increase overall accuracy and for quality control.
• Confrmation studies performed on abnormal cases
• Autism referrals cross-referenced with current autism
databases for the most up-to-date copy number
associations
Cancer Cytogenetics
• Chromosome analysis of bone marrow, blood, lymph node
and solid tumor
• FISH for chromosomal abnormalities common in cancers
• FISH for brain cancer
• FISH on parafn-embedded specimens
Constitutional Cytogenetics
• Standard and high-resolution analysis available
• Analysis done on peripherial blood, fbroblasts, amniotic
fuid, chorionic villius samples and other tissue types,
including human stem cells
Flourescence in situ Hybridization (FISH)
• Cancer abnormalities
• Chimerism in transplant patients
• Trisomy screening
• Microdeletion/duplication syndromes
• Identifcation of marker, derivative or structural aberrations
Cell Line Verifcation
• Karyotype analysis
• FISH verifcation
Additional Services
• Research services
• Tissue culture
• Cryopreservation
• Alpha-fetoprotein & acetylcholinesterase
analysis on amniotic fuid samples
Colorado Genetics Laboratory
CANCER SPECIMENS
TEST REQUEST FORM
3055 Roslyn Street, Suite 200
Denver, Colorado 80238
(303) 724-5701
(888) 659-4932 Toll Free
(303) 322-1052 FAX
PLEASE CALL PRIOR TO SENDING SPECIMEN(S)
PATIENT INFORMATION
Colorado Genetics Laboratory
Patient Last Name _______________________________________ First Name ___________________________ Middle Initial _____ Sex: M F
Date of Birth __________________________ Hospital/ID Number ______________________________ INPATIENT OUTPATIENT
REFERRED BY
PHYSICIAN ___________________________________________________
Address __________________________ ___________________________
City ______________________________ State: _______ Zip: ________
Telephone ______________________ Fax ___________________
FACILITY _____________________________________________________
Address __________________________ ___________________________
City ______________________________ State: _______ Zip: ________
Telephone ______________________ Fax ___________________
BILLING
BILL CHARGES TO: Patient Insurance Hospital Physician/Clinic (provide billing information on reverse side of form)
SIGNS, SYMPTOMS, NARRATIVE DIAGNOSIS AND ICD9 CODES
Required for specimen processing (PLEASE DO NOT USE “RULE OUT”)
ICD9 _____
ICD9 _____
ICD9 _____
In addition to the studies requested below, the
Colorado Genetics Laboratory is authorized to
perform FISH (fluorescence in situ hybridization)
if indicated by the patient’s clinical history or
cytogenetic results.
_____________________________________
Physician Signature
SPECIMEN COLLECTION
Date Collected: ___________________ Time: __________ AM PM Amount Collected: ____________________
PATIENT STAMP HERE
PRENATAL & TISSUE SPECIMENS
Gestation by ultrasound on date specimen
collected _________________________
LMP ____________________________
G ___ P ____ SAB ____ TAB ____
Fetal sex (if known): M F
Specimen Type
?Amniotic Fluid
?Chorionic Villus
?Percutaneous umbilical blood
?Products of conception
?Placenta
?Fetal Tissue
?Skin Biopsy
?Other
Studies Requested
?Chromosome analysis
?Trisomy screen by FISH and
chromosome analysis
?Alpha-fetoprotein? Yes No
?Acetylcholinesterase (AchE)
?FISH for:
?Culture and freeze for future studies
?Culture for molecular or biochemical
studies:*
*Please attach “Information for Referral
Specimens” form
?CML
?AML
?ALL
?Myeloma
?Diagnostic
?Myelodysplasia
?B-cell Lymphoma
?T-Cell Lymphoma
?CLL
?Post Transplant
Sex of Donor:
M F
Specimen Type
?Bone marrow aspirate
?Bone marrow core biopsy
?Peripheral blood
?Lymph Tumor
?Solid Tumor:
?Other:
Studies Requested
?Chromosome analysis
Fish Studies for:
?BCR/ABL t(9;22)
?MLL (11q23)
?PML/RARA t(15;17)
?ALL Panel
?AML Panel
?CLL Panel
?MDS Panel
?Myeloma Panel
?Chimerism (for BMT patients)
?Screen for prior abnormal clone
?Other
Additional FISH studies available.
Please call the laboratory.
CONSTITUTIONAL BLOOD SPECIMENS
?Peripheral blood
?Cord blood
?Other:
Studies Requested
?High resolution chromosome analysis
?Routine chromosome analysis
?STAT trisomy screen by FISH and routine
chromosome analysis
(Call before ordering)
?FISH for:
?Chromosomal Microarray (CMA)
?Parental FISH follow-up for abnormal array
?Fragile X Panel
(Includes FMR1 and routine chromosome
analysis)
specify
specify
specify
specify
source
specify
specify
specify
specify
Patient's accession number
Revised July, 2010 Continued on Reverse Side
Disease FISH Probes Included in Panel
Acute Myelogenous Leukemia (AML)
Chronic Lymphocytic Leukemia (CLL) 12, 13q14, TP53, ATM
Chronic Myelogenous Leukemia (CML) BCR/ABL
Diagnostic Acute Lymphoblastic Leukemia (ALL) - Pediatric 4, 10, 17, 21, TEL/AML, BCR/ABL, MLL, p16 deletion
Diagnostic Acute Lymphoblastic Leukemia (ALL) - Adult 4, 10, 17, 21, p16 deletion, BCR/ABL, MLL
Lymphoma - see individual probes below
Multiple Myeloma (MM) 1q21, 11q23, 13q14, TP53, IGH
Reflex for Positive IGH IGH/FGFR3, IGH/CCND1, IGH/MAF
Myelodysplastic Syndrome (MDS) 5/5q31, 7/7q31, 8, 20q12, MLL
Neuroblastoma MYCN, 1p36, ATM, 17qtel
FISH Probe Chromosome(s) Disease
1p36 deletion 1 Neuroblastoma
1p36/19q13 deletion 1, 19 Brain tumors
1q21 enumeration 1 Multiple myeloma
4 enumeration 4 ALL
4q12 (PDGFRA) 4 Hypereosinophilia
5/5q31 enumeration Loss of 5q AML, MDS
7/7q31 enumeration Monosomy 7 AML, MDS
8 enumeration Trisomy 8 AML, MDS
9p21 deletion (p16, CDKN2A) 9 ALL
10 enumeration 10 ALL
12 enumeration Trisomy 12 CLL
13q14 (D13S319) enumeration 13q14.3 CLL, Multiple myeloma
17 enumeration 17 ALL
17qtel enumeration iso 17q Neuroblastoma, brain tumors
20q12 deletion 20 MDS
21 enumeration 21 ALL
ALK 2p23 Lymphoma, ALCL
AML1 (RUNX1) 21q22 ALL, AML
AML1/ETO t(8;21) AML
API2/MALT1 t(11;18) MALT lymphoma
ATM 11q22.3 CLL, Neuroblastoma
BCL3 19q13 Lymphoma
BCL6 3q27 Lymphoma
BCR/ABL t(9;22) ALL, AML, CML
Chimerism XX/XY Post transplant
CBFB 16q22 AML
CHOP (DDIT3) 12q13 Myxoid liposarcoma
C-MYC amplification 8q24 Brain tumors
E2A 19p13 ALL
EGFR enumeration 7p12 Brain tumors
ETV6 (TEL) 12p13 ALL, AML
EVI1 3q26 Myeloid malignancies
EWS 22q12 Ewing sarcoma
FKHR (FOX01A) 13q14 Rhabdomyosarcoma
IGH 14q32 Lymphoma, Myeloma
IGH/BCL2 t(14;18) Follicular lymphoma, DLBCL
Acute Promyelocytic Leukemia (APL)
5/5q31, 7/7q31, 8; AML1/ETO, MLL, CBFB (BCR/ABL on request)
PML/RARA - Reflex to AML Panel for Negative PML/RARA
ONCOLOGY FISH PROBES
Brain Tumors 1p36/19q13 deletion, EGFR, PTEN, amplification C-MYC, MYCN
FISH TEST LIST
Please remember to check off "Chromosome Analysis" on the
Cytogenetics Request form and attach it to this form.
Patient Name:_______________________________________________________________
ONCOLOGY FISH PANELS
Colorado Genetics Laboratory
FISH Probe Chromosome(s) Disease
IGH/CCND1 t(11;14) Mantle cell lymphoma, Multiple myeloma
IGH/CCND3 t(6;14) Multiple myeloma, DLBCL
IGH/FGFR3 t(4;14) Lymphoma, Multiple myeloma
IGH/MAF t(14;16) Multiple myeloma
IGH/MAFB t(14;20) Multiple myeloma
IGH/MALT1 t(14;18) MALT lymphoma
IGH/MYC t(8;14) Burkitt lymphoma, DLBCL
IGK 2p11.2 Immunoglobulin kappa
IGL 22q11 Immunoglobulin lambda
MALT1 18q21 MALT lymphoma
MLL 11q23 ALL, AML, MDS
Monosomy 22 22q Brain tumors, ATRT, Ependymoma, Meningioma
MYB 6q23 ALL
MYC 8q24 Lymphoma, DLBCL
MYCN amplification 2p23-p24 Neuroblastoma
PDGFRB 5q33 Myeloid neoplasm, Eosinophilia
PML/RARA t(15;17) APL
p16 deletion 9p21 ALL
PTEN 10q23 Brain tumors
Post Transplant XX/XY Post transplant chimerism
RB1 13q14 Retinoblastoma
SYT (SS18) 18q11 Synovial sarcoma
TEL/AML t(12;21) ALL
TP53 deletion 17p13.1 CLL, Multiple myeloma
Previous clone Specify:
Enumeration for individual chromosome Specify:
Microdeletion / Duplication Syndrome
1p36 Deletion 1p36
4p16.3 Wolf-Hirschhorn
5p15.2 Cri-du-Chat
5q35 Sotos
7q11.2 Williams
15q11.2 Prader-Willi / Angelman / 15q duplication
17p11.2 Smith Magenis
22q11.2 DiGeorge / VCFS
Xp22.3 Kallmann 1
Xp22.32 Steroid Sulfatase
Identification
Centromere enumeration probes Specify:
Whole chromosome paint probes Specify:
Aneuploid Interphase Screen Chromosomes
Prenatal Trisomy Screen
Postnatal Trisomy Enumeration
Postnatal Gender Determination
Tissue Trisomy Enumeration
CONSTITUTIONAL FISH PROBES
X, SRY
X, Y, 13, 15, 16, 18, 21, 22
X, Y, 13, 18, 21
X, Y, 13, 18, 21
Cytogenetics Request form and attach it to this form.
FISH TEST LIST
Please remember to check off "Chromosome Analysis" on the
Patient Name:_______________________________________________________________
ONCOLOGY FISH PROBES CONTINUED
Colorado Genetics Laboratory
Colorado Health Outcomes Program (COHO)
Contacts:
David West, PhD
Director
Tel: 303-724-1170
[email protected]
Allison Kempe, MD, MPH
Director, Children’s
Outcomes Research
Director, Primary Care
Research Fellowships
Professor, Pediatrics
Tel: 303-724-1176
[email protected]
Kyle Osborn, COHO/COR
Administrator
Tel: 303-724-1177
[email protected]
Lou Moss
Program Assistant/IRB
Coordinator
Tel: 303-724-1171
[email protected]
http://www.uchsc.edu/coho/
The core function and mission of The Colorado Health Outcomes Program (COHO) is to conduct and
evaluate interventions which improve population health and the overall quality of health care. COHO is
committed to expanding partnerships not just with academic researchers at national universities, but also
within community organizations that deliver health care, public and private payers that finance it, and the
many organizations dedicated to developing innovative health care technologies, services, and delivery
systems. The Colorado Health Outcomes Program (COHO) is dedicated to conducting clinical and
systems health services research. Four methodological “core” areas are the focus of the program: 1)
Primary Care Research; 2) Comparative Effectiveness and Safety Research; 3) Systems Redesign of
Healthcare Systems to improve quality and efficiency; and 4) the application of clinical informatics to
improve the quality of care.
The health care system in the United States today faces many difficult questions. What are the best ways
to measure a person's health status and quality of life and to assess the impact of health care on such
outcomes? How should health care delivery be organized to optimize care for individuals with chronic
health conditions? How can disparities in health and health care for vulnerable populations be reduced?
Questions such as these prompted the formation of COHO.
COHO shares its mission, faculty, staff, and offices with the Children's Outcomes Research (COR)
program.
Our investigators currently consult to and collaborate with on a variety of investigators and agencies on
grant and contract-funded projects.
COHO is not a typical technical core. Rather, we are a Center for Health Services Research.
Colorado Multiple Institutional Review
Board (COMIRB) Review Fees
Marie Wade, Office Manager
Phone: 303-724-1053
Fax: 303-724-0990
E-mail: [email protected]
Website:http://comirbweb.uchsc.edu/portal/
Full Board Initial Review
$ 2,000
Full Board Continuing Review $ 1,500
Expedited Initial Review $ 950
Expedited Continuing Review No Charge
Exempt Initial Review No Charge
Exempt Continuing Review N/A
Amendments and Updates No Charge
Western Institutional Review Board
(WIRB) Review Fees
Effective July 1, 2008
Full-Board Initial Review $3,000
Full-Board Annual Continuing Review $1,800
COMIRB
From: Lakin, Alison
Sent: Monday, November 02, 2009 6:12 PM
Unfortunately, due to the transition to a new database, I do not have the capability to provide
some of the data at this time.
Below is my response to the questions asked.
Sorry
Alison
Alison Lakin RN, LL.B, LL.M, Ph.D
a. How is the quality of your measurements evaluated – quality control?
We do internal quality assurance
b. What is the turn-a-round time for the service you provide?
This data is not currently available
c. Who documents the data provided and signs off on the data?
Protocol review is conducted by 5 panels headed by two co-chairs. The co-chairs have
signature authority for approvals. Any reports generated via the COMIRB database are
handled by Greg Olender, IT Manager.
d. Have you had experience providing data for industry?
COMIRB reviews industry sponsored protocols but most of its current volume is review
of grant funded protocols.
e. Do you have a standard operating procedure manual?
COMIRB Policies and Procedures are available on the COMIRB website.
f. How will you track billing and financial aspects of your core?
Marie Wade, Office Manager, is responsible for billing and tracking finances
The Program in Biomolecular Structure
Computational Biology Core
Contact:
Robert Hodges, PhD
303-724-3253
[email protected]
Website:http://biomol.uchsc.edu/
The Program is an interdepartmental graduate training program
offered within the School of Medicine at the University of Colorado at
Denver and Health Sciences Center Fitzsimons campus in Aurora,
Colorado. Student training places a major emphasis on research
experiences, both in lab rotations and thesis projects, and includes a
range of coursework in biochemistry; drug design; pharmacology;
cellular, molecular and structural biology.
The Program encourages students to engage in collaborative projects
and provides shared mentoring that can include faculty from outside
The Program. Such interactions are geared towards fostering
interdisciplinary training.
Faculty research activities cover a range of structural and computational
techniques including NMR Spectroscopy, X-Ray Crystallography,
Mass Spectrometry and Proteomics, Biophysics, and Peptide/Protein
Chemistry that are focused on a diversity of biological targets such as
signaling molecules, transmembrane proteins, RNA, genome
bioinformatics, lipids, and oligosaccharides.
The Program In Biomolecular Structure
University of Colorado Denver
12801 E. 17
th
Avenue, Mail Stop 8101
Aurora, Colorado 80045
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
Jackie Newnam, Administrator and primary contact for information regarding The Program
including graduate studies.
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9118
[email protected]
Core Facilities Contact Information
Biophysics
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
Brooke Hirsch, Facility Manager
Phone: 303-724-3322
Fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
Computational Biology
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
David Farrell, Systems Administrator
Phone: 303-724-3320
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
Fees vary must contact David Farrell
Mass Spectrometry / Proteomics
Dr. Mark Duncan, Director
Phone: 303-724-3343
12801 E. 17
th
Avenue, Mail Stop 8119
[email protected]
Dr. Kirk Hansen, Facility Manager
Phone: 303-724-3325
12801 E. 17
th
Avenue, Mail Stop 8119
[email protected]
Nuclear Magnetic Resonance
Dr. David Jones, Director/Facility Manager
Phone: 303-724-3600
Fax: 303-724-3663
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Dr. Geoffrey Armstrong, Operational Specialist
800/900 MHz NMR
Phone: 303-724-3331
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Peptide/Protein Chemistry
Dr. Robert S. Hodges, Director
voice: 303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
Office: Fitzsimons, RC-1 South Tower, Room 9121
[email protected]
Dziuleta Cepeniene, Operations Specialist
Voice: 303-724-3336
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
X-Ray Crystallography
Dr. Mair Churchill, Director
Phone: 303-724-3670
Fax: 303-724-3663
12801 E. 17
th
Avenue, Mail Stop 8303
[email protected]
Sarah Roemer, Facility Manager
Phone: 303-724-3672
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
University of Colorado Cancer Center
Cytogenetics Core
Contacts:
Marileila Varella-Garcia, PhD
Director
[email protected]
303-724-3147
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/cytogenics/index.aspx
FISH
Aneusomies for EGFR (red) and centromere 7 (green) sequences detected in formalin-fixed,
paraffin embedded lung cancer tissue sections
The UCCC Cytogenetics Core Laboratory provides classic and molecular cytogenetics services,
including fluorescence in situ hybridization (FISH). We have experience with commercially
available and researcher-provided probes, such as:
• chromosome enumeration probes
• painting probes
• translocation probes
• single copy or locus-specific probes
• nick-translated DNA fragments
We also provide consulting services and training for non-assisted lab use.
Our Services
Single and dual color fluorescence in situ hybridization (FISH) assays
• Differentiation of mammalian chromosomes or DNA sequences translocated to rodent
chromosomes and monitoring established cell lines using human genomic or Cot-1 DNA
probes.
• Identification of specific aneuploidies in metaphase spreads and interphase nuclei, in
preparations from diffuse or solid tissues using satellite and locus-specific DNA probes.
• Identification of particular human chromosomes or chromosome fragments in complex
rearrangements and/or marker chromosomes using whole chromosome-specific painting
probes (WCP) or a region-specific probe (Partial Chromosome Probes). WCPs are used
also for identification of human chromosomes in hybrid cells.
• DNA clone mapping (phage, cosmid, P1, PAC, BAC, and YAC) on metaphase
chromosomes of human, rat, mouse and hamster cells.
• Investigation of genomic deletion, duplication or amplification in metaphase and in
interphase nuclei in fresh or preserved biological preparations using DNA clones.
• Detection of chromosome translocations in metaphase or interphase cells using probes
encompassing or closely associated with the breakpoints.
Multicolor-FISH assay
• Simultaneous hybridization of several probes to extended chromatin to determine the
orientation and overlap of the tested sequences.
• Analysis of multiple probes in a given cell for more accurate definition of its genomic
status.
Spectral Karyotyping
Spectral karyotype of a cell representative of the small cell lung carcinoma cell line
UMC19.
Comparative Genomic Hybridization (CGH) assay
• Analysis of DNA sequence copy numbers of cultured or uncultured human, mouse and
rat specimens.
• Multicolor Karyotyping using spectral karyotyping in human, mouse and rat specimens
(SKY) and multiplex-FISH (M-FISH) in human specimens.
Unbanded chromosome analysis
• Breakage evaluation.
• Cell proliferation index (mitotic index).
• Ploidy evaluation
Giemsa-trypsin (GTG) banded chromosome analysis
• Karyotype characterization of human, mouse, rat, and hamster specimens or cell lines in
metaphase or prometaphase cells.
• Determination of cell line homogeneity and evolution using metaphase analysis.
• Identification of parental species in hybrid cell lines.
Additional procedures
Tissue culture
Initiation, maintenance, harvest, and freezing of cell cultures for cytogenetic purposes.
Establishment of immortal cell lines from lymphocytes
DNA labeling by nick-translation for FISH assays
Lab staff performs nick translation labeling. DNA fragments may be genomic DNA, cDNA or
vector DNA. Due to sensitivity limitations of our current instrumentation, we need unique
sequence probes larger than 2.5 kb for mapping studies. If the probe is known to be amplified,
we can use probes >1.0 kb.
How to Use This Core Lab
Testing and instrumentation are available by appointment only. Turnaround time is highly
dependent on the specimen or project. Please contact Dr. Varella-Garcia to schedule your project
and discuss turnaround times.
Prices
We offer discounts for University of Colorado Cancer Center members. All prices listed are
estimated based on special conditions. Please contact Dr. Varella-Garcia for specific pricing for
your project.
Test Description
Member
Base
Non-Member
Base
Cell culture and harvesting $89 $165
EBV transformation of lymphocytes $463 $727
Slide making $20 $38
Ploidy Evaluation $97 $173
Classical Karyotyping $444 $797
DNA Cloning $751 $1,229
DNA Labeling $103 $170
FISH assays – probe A (homebrew) $367 $619
FISH assays – probe B (commercial) $356 $624
Multicolor Karyotyping $1,546 $2,248
Comparative Genomic Hybridization $1,088 $1,603
Consulting $174 $233
Prices 07/01/2008-06/30/2009
Cytogenetics Core
From: Garcia, Marileila
Sent: Tuesday, November 03, 2009 9:57 AM
a) How is the quality of your measurements evaluated – quality control?
We follow standard guidelines required by CAP-CLIA and FDA.
b) What is the turn-a-round time for the service you provide?
It is very much depending on the test. Some tests are reported in 3 days, some may take
one month.
c) Who documents the data provided and signs off on the data?
The technologists document the data provided and the reports are signed by the Core
Director.
d) Have you had experience providing data for industry?
Yes, we have many contracts with pharmaceutical and biotech companies in the last 8
years.
e) Do you have a standard operating procedure manual?
Yes, exactly as required by CAP-CLIA and FDA regulation.
f) How will you track billing and financial aspects of your core?
The Cancer Center requires annual cost study, which is submitted and approved by the
University officials. The Core generate an invoice and the Cancer Center Administrative
Office assists with all financial issues.
Developmental Core
Center for Aids Research (CFAR)
Contacts:
Myron Levin, MD,
Core Director
303-724-2451
[email protected]
Linda Van Dyk, Ph.D.
Core Co-Director
303-724-4207
[email protected]
Website:http://www.uchsc.edu/ccfar/cores/development.htm
The primary purpose of the Developmental Core is to allocate resources to augment AIDS
research efforts at component institutions. Emphasis is placed on support for interdisciplinary
projects and infrastructure investments that will have a broad impact on AIDS research
capabilities by recruiting new investigators, providing transitional funding to Junior Faculty, and
facilitating the conduct of pilot studies.
The Developmental Core has three Specific Aims:
1. To make major infrastructure or programmatic investments that will broadly facilitate
interactions, capabilities, and/or efficiencies of the AIDS research community at the
component institutions.
2. To recruit outstanding new investigators with AIDS expertise to the faculties of the
institution from outside institutions or from training programs within the institution.
3. To provide initial funding for pilot and feasibility studies.
These funds might be used by junior investigators, by established investigators to explore novel
areas of AIDS research, or by experienced investigators not previously involved in AIDS
research.
The CFAR Research Development Fund provides support for three types of
projects:
New Initiative Grant
To facilitate the recruitment of new faculty or investment in major new programs or
infrastructure related to HIV research. In the case of new recruitments these grants can be
used as matching funds with other institutional or philanthropic support. Funds may be
used for salary support, supplies, and/or equipment. Preference will be given to proposals
that involve multiple investigators and/or will facilitate new HIV-related research
collaborations among productive groups.
Grants will be at the level of $60,000 for one year with the potential for renewal under
certain circumstances.
Junior Faculty Grant
To facilitate the transition of trainees to faculty status. Funds may be used for salary
supplementation, technical support, and/or supplies.
Grants will be at the level of $50,000 for one year with the potential for a second year
under certain circumstances.
Pilot Project Grant
To support pilot or feasibility projects that will open a new area of investigation in an
HIV-research laboratory or initiate HIV research in additional laboratories. These awards
should be used to generate sufficient preliminary data to enable investigators to acquire
external funding in the future.
Grants will be at the level of $30,000 for one year.
No Fees
The Diabetes and Endocrinology Research Center (DERC) at the University of Colorado Denver
on the Anschutz Campus in Aurora, Colorado brings together the collective experience of basic
and clinical scientists from different faculty and research backgrounds to enhance the
productivity and the quality of diabetes and endocrinology research within the University of
Colorado Denver Health Sciences Center community.
DERC Program Directors:
J ohn Hutton, PhD
Program Director, Barbara Davis Center for Childhood Diabetes, UCD.
Professor, Departments of Pediatrics, Cellular & Structural Biology.
Phone: 303-724-6836
George Eisenbarth, MD, PhD
Program Deputy Director, Barbara Davis Center for Childhood Diabetes, UCD.
Professor, Departments of Pediatrics, Cellular & Structural Biology.
Phone: 303-724-6837
Website:http://www.uchsc.edu/misc/diabetes/DERC/index.htm
UCD DERC Molecular Biology Services
Automated DNA Sequencing
• Dye-terminator sequencing on ABI 3130xl and ABI 3100-Avant capillaries
• Online sample submission and results retrieval
• 24-36 hour turnaround time
- Next business day for samples submitted before 12pm
• See Sample Submission Guidelines for details and requirements
Automated Fragment Analysis
• Microsatellite analysis
• SNP detection
• Determination of STR or VNTR number
Real Time PCR
• Roche LC480 and AB 7000 SDS
• High Resolution Melt Capable
• Genotyping
• Gene Quantification and Expression analysis
in-situ hybridization probe synthesis
• Full scale hybridization from gene of interest selection to imaging and analysis
• Preparative work underway to build probe library for islet related targets (insulin,
glucagon, slc30a8, etc)
• In conjunction with the DERC Histology Core
Basic Molecular Biology Services
• Nucleic acid purification
• Cloning and expression of genes of interest in bacterial systems
• Plasmid DNA preparation (small-large scale)
• Site directed mutagenesis
• Restriction digestion and analysis
• RT-PCR
• PCR and PCR product purification
• Recombinant protein expression and purification
Custom Services
• Please contact [email protected] or [email protected] for
inquiries regarding your project.
The purpose of this website is to provide some basic information about the DERC cores
including contact information and links to on-line services where they are available. If you have
questions about the UCD DERC please contact us (email or phone: 303.724.6836).
Diabetes & Endocrinology Research Center
Molecular Biology Core Facility (DERC MBCF) Price List
DERC Members
Non-DERC or
UCD Affiliate
DNA Sequencing
Data Collection Only $5.10 $6.35
Reaction Plus Data Collection $8.90 $9.90
Fragment Analysis
Genomic DNA Preparation $1.90 $2.30
PCR - ABI True $0.56 $0.67
PCR - Epicentre $1.00 $1.20
SNP Analysis $3.80 $4.55
Injection on 3100 Avant $5.10 $6.10
Analysis $25/hour $35.00/hour
Real Time PCR Machine Usage
Real Time PCR Session $22.00 $24.00
Allelic Discrimination (Pre/Post Read) $10.00 $12.00
Laboratory Services*
Mouse Model Identification (MMI) - per sample $6.25 $7.50
Bulk MMI (20+samples) $5.00 $6.00
Plasmid Maxi Prep (single) $28.15 $33.80
Plasmid Maxi Prep (5+samples) $24.20 $29.00
Plasmid Mini Prep (single) $3.30 $4.00
Plasmid Mini Prep (10+samples) $2.75 $3.30
RNA Isolation - Mini Prep (single) $8.85 $10.60
Cloning/Transformation PCR product $25.00 $30.00
in situ Probe Generation $167 min. $225 min.
*Cost of materials/reagents included
We offer many common molecular biology related laboratory techniques for services.
Please contact us for pricing/quotes for your project!
Manager: Randy Wong, phone: 303.724.6825
Prices current thru J une 2009.
The purpose of this website is to provide some basic information about the DERC cores
including contact information and links to on-line services where they are available. If you have
questions about the UCD DERC please contact us (email or phone: 303.724.6836).
Barbara Davis Center – Page 1 of 7
Diabetes & Endocrinology Research Center (DERC)
Barbara Davis Center for Childhood Diabetes at UCD
From: Powell, Mary, Cc: Hutton, John
Sent: Friday, October 09, 2009 2:09 PM
The Barbara Davis Center (BDC) is the home for the NIH Diabetes Endocrinology Research
Center (DERC) that provides funding for seven distinct cores. These cores provide services to
principal investigators within the BDC researching type 1 or childhood diabetes and other
principal investigators throughout campus wide scientific projects. Core facilities at the BDC are
BioResources (animal and islet), Autoantibody Measurement, Flow Cytometry, Histology and
Molecular/Vector.
In addition, the BDC is the home of the Juvenile Diabetes Research Foundation (JDRF)
Autoimmunity Prevention Center. Another of the facilities funded by the JDRF Center grant
provides Lymphocyte Analysis core.
Responses to your queries are below and identified by each core.
Each core has described their response to question f). A general statement applies to all. The
core operates as a service center with an auxiliary university account and the UCD Finance
Office approves charges on an annual basis. Requests are submitted online and monthly billing
is performed through the same portal to preapproved account holders and speed types.
BioResources Core (Animal and Islet Preparation)
The core focuses on animal models of autoimmune diabetes (particularly the NOD mouse) and
derived strains eg. NOD Scid, NOD Rag -/-, NOD Ins 1 -/-, NOD Ins 2 -/-.
a) How is the quality of your measurements evaluated – quality control?
Animal: Basic evaluation of diabetes such as glucose tolerance testing and disease monitoring is
performed a Veterinary Technologist with 20+ years experience. She performs all the hands-on
animal work that allows us to offer a high standard of care and competence, and there is
continuous researcher feedback for assessing the quality and timeliness of the work performed.
The Animal Core work is done in the University’s AALAC-certified Center for Comparative
Medicine, and thus we must operate at a high standard commensurate with their rules and
regulations.
Islet: Each new lot of digestive enzyme is tested for optimal concentration and pancreas
digestion time, and the islets produced are functionally tested by transplantation into diabetic
mice. Additionally, there is continuous researcher feedback of islet viability and quality.
b) What is the turn-a-round time for the service you provide?
Animal: Animal procedures are normally scheduled a week in advance.
Maintenance of researchers’ breeding colonies is an ongoing process.
Islet: Islet preparations are normally booked about one week in advance.
Barbara Davis Center – Page 2 of 7
c) Who documents the data provided and signs off on the data?
Animal: The BDC Animal Core Vet. Tech. performs all animal procedures, breeding colony
maintenance, and maintains all appropriate records. The core manager oversees all animal core
work.
Islet: The core manager maintains a notebook, detailing each islet harvest, which is monitored by
the core director.
d) Have you had experience providing data for industry?
No, for both animal and islet services.
e) Do you have a standard operating procedure manual?
Yes, for animals and both mouse and rat islet harvesting.
f) How will you track billing and financial aspects of your core?
Animal: The Animal Core produces a comprehensive annual cost analysis, which must be
evaluated and approved by the University’s finance department. The Vet. Tech. records and
collates all animal procedure and breeding colony maintenance charges. From this information,
the core manager generates monthly invoices, and the BDC administrative staff reallocates the
charges to the appropriate speed types.
Islet: The Islet Core produces a comprehensive annual cost analysis, which must be evaluated
and approved by the University’s finance department. The core manager records and collates all
islet harvesting data. From this information, he generates monthly invoices, and the BDC
administrative staff reallocates the charges to the appropriate speed type.
Autoantibody Measurement Core
The core performs standardized measurements of circulating autoantibodies including insulin
AA, 1A2A, GADA, ZnT8A, 2104A, TPO A, TG 2A.
a) How is the quality of your measurements evaluated – quality control?
CLIA inspection by state. Internal quality control of assays with standard samples with results
within set ranges and Shewhart plots. External quality control where existing, in particular CDC
and Immunology of Diabetes Society coded workshops (DASP). External quality control UCLA
for molecular HLA typing. Internal: Shewart Plot for each assay is plotted all time. External:
DASP autoantibody workshop organized by CDC and IDS every 18 months. Blinded split
duplicate programs by each NIH project we involved.
b) What is the turn-a-round time for the service you provide?
Less than one week. Routinely one week, maximum two weeks.
Barbara Davis Center – Page 3 of 7
c) Who documents the data provided and signs off on the data?
Liping Yu and Roberto Gianani and for specific research projects George Eisenbarth
Liping Yu documents all the data and signs off the report and George Eisenbarth double checks
the data and sign off all consent forms.
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Yes, we have SOP for each autoantibody assay.
f) How will you track billing and financial aspects of your core?
Auxiliary University account established and Cost Center analysis.
Liping Yu and Kathy Barriga report the numbers of assays to Luciana Smith every month.
Luciana generates bill to each internal speed type and keep the records.
Flow Cytometry Core
The BDC core maintains and operates two flow cytometers used principally for research studies
of autoimmunity in humans and animal models.
a) How is the quality of your measurements evaluated – quality control?
The core’s two cytometers are maintained on Preventive Maintenance/service contracts from the
manufacturer. The core manager runs daily QC/calibration programs on both instruments.
b) What is the turn-a-round time for the service you provide?
Open blocks of times are usually available to reserve for the following day, although booking
more is advance is prudent. Use of both cytometers is by an on-line reservation system, with
BDC researchers having first priority.
c) Who documents the data provided and signs off on the data?
The researchers and their staffs run their own samples and collect/collate their own data.
Technical assistance/training for core users is available from the core Monday – Friday, 8AM to
5PM.
d) Have you had experience providing data for industry?
No.
e) Do you have a standard operating procedure manual?
Barbara Davis Center – Page 4 of 7
Yes, for both cytometers.
f) How will you track billing and financial aspects of your core?
The Cytometry Core produces a comprehensive annual cost analysis, which must be evaluated
and approved by the University’s finance department. Researchers record their usage and
provide an appropriate speed type on line (dnaLIMS program). From this information, the core
manager generates monthly invoices, and the BDC administrative staff reallocates the charges.
Histology Core
The core performs standard histopathological analyses based on light microscopy and
immunohistochemistry.
a) How is the quality of your measurements evaluated – quality control?
The quality of our data is measured by using control tissues to ensure that proper staining has
occurred. Stains and alcohol solutions are replaced on a regular basis to ensure that stains are of
the highest quality.
b) What is the turn-a-round time for the service you provide?
The average turn-a-round time for the service that we provide is about 2-3 days.
c) Who documents the data provided and signs off on the data?
Researchers and their staff provide and sign off on the data from our service.
d) Have you had experience providing data for industry?
No.
e) Do you have a standard operating procedure manual?
The histology core has a standard operating procedure manual that is stored in the facility. It
contains the protocols for all of the staining/embedding that the core provides and is updated as
new procedures and stains are added. Additionally we have operating manuals on hand for the
Leica tissue processor, microtome, and cryotome.
f) How will you track billing and financial aspects of your core?
Billing for the core is tracked online using the dnaTools web site. Customers place their order via
the website and upon submitting their order they are quoted the price. Monthly accounting
reports are created the first of the month and are submitted for billing. The histology core keeps a
copy of these records in the core.
Lymphocyte Analysis Core
Barbara Davis Center – Page 5 of 7
This core supported by the JDRF Center grant provides high-quality services for lymphocyte
subset purification and phenotypic and functional analyses. Lymphocytes are a fundamental
requirement for a wide variety of studies addressing the role of T and B cells in pathogenesis of
type 1 diabetes.
a) How is the quality of your measurements evaluated – quality control?
ELISPOT BioReader
In addition to the routine maintenance service performed as part of the service contract with the
Biosys ELISPOT Reader, Core personnel run reference plates twice a month for instrument
calibration to insure accurate readings.
AutoMacs Cell Sorter
1) To ensure maximum performance of the AutoMACS Separator over time, technical service is
provided by Miltenyi Inc. The service contract includes technical support and annual preventive
maintenance such as thorough cleaning, replacing o-rings, tubing, valves, and syringes.
2) AutoMACS columns are replaced every two weeks.
3) Routine clean programs – see SOP.
4) SAFE Program - The SAFE Clean Program (programmed into the AutoMACS by Miltenyi)
should is performed on the AutoMACS sorter at least once per week or after 2.4E+09 cells have
been passed through a single sorting column, whichever occurs first.
Bioplex
Instrument calibration is done monthly using a kit containing beads to standardize daily signal
output and ensure unit-to unit reproducibility of the reader. Instrument validation is performed
prior to analysis run, using a kit containing beads to validate the operational specifications of the
reader, including accuracy, linearity, dynamic range, slope, fluidics, and optical alignment.
b) What is the turn-a-round time for the service you provide?
Depending on the work load between 4-7 days
c) Who documents the data provided and signs off on the data?
The PRA documents the data and the Core’s director signs off on the data
d) Have you had experience providing data for industry?
No.
e) Do you have a standard operating procedure manual?
Yes.
f) How will you track billing and financial aspects of your core?
At this point we are not charging for our service and will adopt the standard systems in place for
the DERC and UCD Finance department.
Barbara Davis Center – Page 6 of 7
Molecular/Vector Core
This core is a centralized resource for automated DNA sequencing, genotyping, fragment
analysis, quantitative PCR, production of recombinant adenoviruses, and provision of certified
specific reagents.
a) How is the quality of your measurements evaluated – quality control?
Molecular: The MBCF’s two DNA sequencing instruments are maintained on service contracts
from the manufacturer. Inclusive in the service contracts are bi-annual instrument maintenance,
spectral calibration, and cleaning. Positive control standards are run with each reaction set, which
are run twice daily. Additionally, our LIMS system and instrument manufacturer software
analysis program provides universal quality scoring.
Vector: What quality control. The quality control of the vector core most often comes from
titer’s generated with the final product and a specific Supernatant Rescue assay. Additional
assays can be ordered to analyze whether the virus does what it was designed to do such as
Western blotting or PCR analysis.
b) What is the turn-a-round time for the service you provide?
Molecular: For DNA sequencing, the MBCF provides results within 24-36 hours after sample
submission. For genotyping services, the MBCF strives to provide results within 3-5 days.
Vector: The turn-a-round time depends on the specific service requested and ranges from about 3
days to 6 weeks. Due to the past customer level, most requests can be started immediately.
c) Who documents the data provided and signs off on the data?
Molecular: The MBCF provides data archival/retrieval through a LIMS (Laboratory Information
Management System), which is housed on an internal server. For all other services,
documentation is recorded by all staff for all techniques performed, similar to a laboratory
notebook documentation. All procedures are documented and disseminated to all recipients of
services.
Vector: The sole employee, vector core manager, documents all data produced from the work
done in the core.
d) Have you had experience providing data for industry?
Molecular: Yes, the MBCF currently services at least four external Non-University entities.
Vector: No
e) Do you have a standard operating procedure manual?
Molecular: Yes the MBCF maintains an internal standard operating procedure manual. These
SOPs apply mainly to routine high-throughput services. For more variable services (custom
projects), the MBCF utilize generally accepted/published methodology.
Barbara Davis Center – Page 7 of 7
Vector: Yes, we have a standard operating procedure for most of the procedures we use to
produce Adenovirus.
f) How will you track billing and financial aspects of your core?
Molecular: Monthly invoicing is created by the MBCF Core Manager with service orders
recorded online through the LIMS system and direct service requests. The MBCF produces a
comprehensive annual cost study (evaluated and approved through the UCD finance department)
that determines unit costs for all products and services. All invoices are emailed to each user.
Summary invoicing is sent to our Administrative Core where all charges are reallocated to each
requestor’s Speed Type.
Vector: The vector core tracks all billing and financial aspects with the use of spreadsheets that
have been designed for filling in monthly accounting.
DNA Diagnostic Laboratory
Introduction
The UCD DNA Diagnostic Laboratory at the University of Colorado Denver is a clinical
molecular genetics laboratory offering full service nucleic acid-based testing. Established as a
national and regional resource for the medical and genetics communities, the laboratory performs
testing for a variety of genetic diseases utilizing state of the art techniques.
Clinical and Laboratory Staff
Elaine B. Spector, PhD
Director, DNA Diagnostic Laboratory
303-724-3801
[email protected]
Website:http://www.uchsc.edu/dnalab/
Accreditation
The laboratory is licensed by the College of American Pathologists (#211828-31) and
acknowledged by the Clinical Laboratories Improvement Act (#06D0644348). The laboratory
voluntarily participates in quality assurance programs.
University of Colorado DNA Diagnostic Laboratory: Testshttp://www.uchsc.edu/dnalab/tests.html 7/11/2007
UCDHSC DNA Diagnostic Laboratory
We offer the following tests:
Ashkenazi Jewish Panels: FGFR3, Fibroblast Growth Factor Receptor 3
Ashkenazi Panel 1 Achondroplasia
Tay Sachs Disease (Hexosaminidase A Deficiency) Hypochondroplasia
Canavan Disease Thanatophoric Dysplasia, Types I and II
Fanconi Anemia (FANCC-Related) Nonsyndromic Craniosynostosis Syndromes
Familial Dysautonomia Muenke Syndrome
Ashkenazi Panel 2 Crouzon Syndrome with Acanthosis Nigricans
Niemann-Pick, Type A/ B (Sphingomyelinase Deficiency) Hereditary Hemochromatosis
Mucolipidosis, Type IV Limb / Heart Disorders
Bloom Syndrome Holt-Oram Syndrome, TBX5 – sequence * SOON
Glycogen Storage Disease, Type Ia (Von Gierke Dis.) Duane Radial Ray Syndrome, SALL4 – sequence * NEW
Ashkenazi Panel 3
Townes-Brock Syndrome, SALL1 – sequence * SOON
Gaucher Disease Liver Disease, UGT1A1 * NEW
CFTR-Related Disorders (41 mutations) Crigler-Najjar Syndrome, Gilbert Syndrome
Cystic Fibrosis Hyperbilirubinemia, Transient Familial
CBAVD (Congenital Bilateral Absence of Vas Deferens) Chemotherapy Dosage Test * SOON
Cardiomyopathy Disorders Metabolic Disorders
Danon Disease (Glycogen Storage IIB) * NEW ANT, Antiquitin – Pyridoxine-Responsive Neonatal Seizures * NEW
Lamin A/C (LMNA) GA I, Glutaric Acidemia Type 1 – Sequence GCD
LMNA-Related Cardiomyopathy GA II (MADD) – Sequence ETFDH/ ETF-QO * NEW
Emery-Dreifuss Muscular Dystrophy, Autosomal GA II (MADD) – Sequence ETFA and ETFB * NEW
Limb-Girdle Muscular Dystrophy (LGMD), Type 1B Homocystinuria due to CBS Deficiency * NEW
Charcot-Marie-Tooth Neuropathy, Type 2B1 LCHAD, Long Chain 3-Hydroxy-Acyl-CoA Dehydrogenase Def. –
Hutchinson-Gilford Progeria Syndrome Common Mutation
Mandibuloacral Dysplasia MCAD, Medium Chain Acyl-CoA Dehydrogenase Deficiency –
Clotting Disorders Common Mutation
Factor V Leiden Thrombophilia MCAD, Full Sequence * SOON
Prothrombin G20210 Thrombophilia (Factor II) NKH, Non-Ketotic Hyperglycinemia – Sequence AMT, GLDC
MTHFR, A233V: C677T (Thermolabile Variant) NKH, Non-Ketotic Hyperglycinemia – Sequence GCSH
MTHFR, E429A: A1298C * NEW Propionic Acidemia due to PCCA or PCCB Deficiency * NEW
Warfarin Dosage Test * NEW VLCAD, Very Long Chain Acyl-CoA Dehydrogenase Def. * NEW
DNA Isolation MCC, Maternal Cell Contamination Study
Deafness / Nonsyndromic Hearing Loss Pigmentation Disorders
Connexin 26, GJ B2-Related DFNB 1 HPS, Hermansky-Pudlak Syndrome, Type 1
Connexin 30, GJ B6-Related DFNB 1 * NEW OCA1, Oculo-Cutaneous Albinism, Type 1a/ 1b * NEW
FMR-1
OCA2, Oculo-Cutaneous Albinism, Type 2 * NEW
Fragile X Syndrome WT-1 Related Disorders – sequence * NEW
FXTAS: Adult-Onset Tremor Ataxia Syndrome Denys-Drash Syndrome, Isolated Diffuse Mesangial Sclerosis,
POF: Premature Ovarian Failure Familial Wilms Tumor, Frasier Syndrome
Please contact the laboratory for prices: 303-724-3801
Send samples with Consent Form and Request Form, to shipping address: RC-1 North, Rm P18-4404J, 12800 E. 19th Ave, Aurora, CO 80045
Mailing address: UCDHSC DNA Diagnostic Laboratory, Mail Stop 8313, PO Box 6511, Aurora, CO 80045
University of Colorado (Old name: UCHSC DNA Diagnostic Laboratory)
UCD DNA Diagnostic Laboratory: Tests Offered
?? Each Sample Needs a Completed Request Form AND Consent Form AND Fax Form, and This Checklist ??
Lab director: [email protected]; 303-724-3801 Mailing address for correspondence: Mail Stop 8313, PO Box 6511, Aurora, CO 80045
Genetic counselor: [email protected]; 303-724-1572 Shipping address for samples: 12800 E. 19th Ave, Rm P18-4404J, Aurora, CO 80045
www.uchsc.edu/DNALab, Fax: 303-724-3802 1 of 3 3/11/2009
Test # (5% prepay discount for all testing; parents free for some.) Prices CPT Codes
1 DNA Isolation $75 1 x 83891; 1 x 83912
2 Shipping: $50 plus all shipping costs $50 +
3 Carrier test (for many disorders listed): 2 known mutations NEW REDUCED PRICE $250 1 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 1 x 83912
4 Carrier test (for many disorders listed): 1 known mutation $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
5 Prenatal test (for many disorders listed): 2 known mutations $800 2 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 2 x 83912
6 Prenatal test (for many disorders listed): 1 known mutation $500 2 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 2 x 83912
7 MCC, Maternal Cell Contamination Study (for all prenatal testing) $200 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
Ashkenazi Panels + Cystic Fibrosis
8 Ashk 1 + Ashk 2 + Ashk 3 + CF $525 1 x 83891; 4 x 83894; 4 x 83898; 2 x 83896; 2 x 83900; 80 x 83901; 4 x 83912
9 Ashkenazi Panel 1: Tay Sachs; Canavan; Fanconi; Familial Dysautonomia $200 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
10 Ashkenazi Panel 2: Niemann-Pick; Mucolipidosis; Bloom; Glycogen Storage Dis. Ia $200 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
11 Ashkenazi Panel 2, ordered with other ASHK $100 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
12 Ashkenazi Panel 3: Gaucher Disease $200 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
13 Ashkenazi Panel 3, ordered with other ASHK $100 1 x 83891; 1 x 83894; 1 x 83898; 1 x 83912
100 Ashkenazi Panel 4: MSUD, Maple Syrup Urine Disease – COMING SOON (Test is in development)
101 Ashkenazi Panel 4, ordered with other ASHK – COMING SOON (Test is in development)
14 Cystic Fibrosis, CFTR-Related Disorders $250 1 x 83891; 2 x 83896; 2 x 83900; 80 x 83901; 1 x 83912
15 Cystic Fibrosis, CFTR-Related Disorders, ordered with ASHK panel(s) $125 1 x 83891; 2 x 83896; 2 x 83900; 80 x 83901; 1 x 83912
Cardiomyopathy Disorders
16 ARVD comprehensive, Panels A+B ordered together $2,000 1 x 83891; 106 x 83894; 106 x 83898; 106 x 83904; 4 x 83912
17 ARVD Panel A: ARVD9, PKP2 $1,400 1 x 83891; 34 x 83894; 34 x 83898; 34 x 83904; 1 x 83912
18 ARVD Panel B, ARVD8+10+11, ordered together $1,400 1 x 83891; 72 x 83894; 72 x 83898; 72 x 83904; 3 x 83912
19 ARVD8, DSP, ordered alone $525 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
20 ARVD10, DSG2, ordered alone $1,000 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
21 ARVD11, DSC2, ordered alone $1,060 1 x 83891; 32 x 83894; 32 x 83898; 32 x 83904; 1 x 83912
22 Danon Disease (LAMP2, Glycogen Storage IIB) $650 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
23
Lamin A/C (LMNA): LMNA-Related Dilated Cardiomyopathy; Autosomal Emery-Dreifuss
Muscular Dystrophy; Limb-Girdle Muscular Dystr. 1B; Familial Partial Lipodystrophy Dunnigan
type; Charcot-Marie-Tooth 2B1; Hutchinson-Gilford Progeria; Mandibuloacral Dysplasia
$750 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
Clotting Disorders
24 FV, Factor V (five) Leiden Thrombophilia $150 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83908; 1 x 83912
25 MTHFR-AV, A233V: C677T (Thermolabile Variant) $175 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83898; 2 x 83908; 1 x 83912
26 MTHFR-EA, E429A: A1298C $75 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83898; 2 x 83908; 1 x 83912
27 PT, Prothrombin G20210 Thrombophilia (Factor II, FII or F2) $125 1 x 83891; 1 x 83893; 2 x 83896; 2 x 83908; 1 x 83912
28 Warfarin Dosage Test-Discontinued $325
Deafness / Hearing Loss
29 Connexin 26, GJB2-Related DFNB1, sequence $450 1 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 1 x 83912
30 Connexin 30, GJB6-Related DFNB1, common deletion $350 1 x 83891; 3 x 83894; 3 x 83898; 1 x 83912
31 Pendred Syndrome, SLC26A4 $1,100 1 x 83891; 36 x 83894; 36 x 83898; 36 x 83904; 1 x 83912
32 Waardenburg Comprehensive: all 4 genes ordered together $2,400 1 x 83891; 68 x 83894; 68 x 83898; 68 x 83904; 4 x 83912
University of Colorado (Old name: UCHSC DNA Diagnostic Laboratory)
UCD DNA Diagnostic Laboratory: Tests Offered
?? Each Sample Needs a Completed Request Form AND Consent Form AND Fax Form, and This Checklist ??
Lab director: [email protected]; 303-724-3801 Mailing address for correspondence: Mail Stop 8313, PO Box 6511, Aurora, CO 80045
Genetic counselor: [email protected]; 303-724-1572 Shipping address for samples: 12800 E. 19th Ave, Rm P18-4404J, Aurora, CO 80045
www.uchsc.edu/DNALab, Fax: 303-724-3802 2 of 3 3/11/2009
Test # (5% prepay discount for all testing; parents free for some.) Prices CPT Codes
33 Waardenburg syndrome 1, 3, CDHS: PAX3, ordered alone $650 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
34 Waardenburg syndrome 2, Tietz: MITF, ordered alone $1,000 1 x 83891; 30 x 83894; 30 x 83898; 30 x 83904; 1 x 83912
35 Waardenburg syndrome 4: SOX10, ordered alone $400 1 x 83891; 6 x 83894; 6 x 83898; 6 x 83904; 1 x 83912
36 Waardenburg-Shah syndrome, EDNRB, ordered alone $600 1 x 83891; 14 x 83894; 14 x 83898; 14 x 83904; 1 x 83912
Disorders of Sex Development
37 AIS Panel (Androgen Insensitivity Syndrome): AR+SRY+WT1 ordered together $1,500 1 x 83891; 42 x 83894; 42 x 83898; 42 x 83904; 3 x 83912
38 AR: Androgen Receptor, sequence $1,000 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
39 SRY: XY Gonadal Dysgenesis, Y-linked $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
40 WT1-Related Disorders: Denys-Drash; Frasier; Wilms Tumor; Nephrotic Syndrome $750 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
FGFR3, Fibroblast Growth Factor Receptor 3
41 Achondroplasia; Hypochondroplasia $400 1 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 1 x 83912
42 Thanatophoric Dysplasia, Types I and II $400 1 x 83891; 10 x 83894; 10 x 83898; 10 x 83904; 1 x 83912
43 Muenke Syndrome (Exon 7) $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
44 Crouzon Syndrome with Acanthosis Nigricans (Exon 10) $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
45 Saddan (Exon 15) $250 1 x 83891; 2 x 83894; 2 x 83898; 2 x 83904; 1 x 83912
46
Fragile X, FMR-1: Fragile X Syndrome; FXTAS: Adult-Onset Tremor Ataxia
Syndrome; POF: Premature Ovarian Failure
$300
1 x 83891; 2 x 83892; 4 x 83894; 1 x 83896; 1 x 83897;
4 x 83898; 4 x 83904; 1 x 83912
Iron Storage Disorders
47 Hereditary Hemochromatosis $150 1 x 83891; 3 x 83892; 3 x 83894; 4 x 83898; 1 x 83912
Limb / Heart Disorders
48 SALL1, Townes-Brock Syndrome $950 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
49 SALL4, Duane Radial Ray Syndrome $950 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
50 TBX5, Holt-Oram Syndrome $950 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
Liver Disorders
51 UGT1A1: Gilbert Syndr.; Transient Familial Hyperbilirubinemia; Ristocetin Chemo Dosage Test $300 1 x 83891; 1 x 83893; 4 x 83896; 4 x 83898; 4 x 83904; 1 x 83912
Metabolic Disorders
52 3MCC Panel, 3-Methylcrotonyl-CoA Carboxylase Def.: 3MCC A+B ordered together $1,500 1 x 83891; 34 x 83894; 34 x 83898; 34 x 83904; 2 x 83912
53 3MCC-A (3MCCC1), ordered alone $900 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
54 3MCC-B (3MCCC2), ordered alone $800 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
55 ANT, Antiquitin, Pyridoxine-Dependent Neonatal Seizures, ALDH7A1 $1,500 1 x 83891; 34 x 83894; 34 x 83898; 34 x 83904; 1 x 83912
56 GA I, Glutaric Acidemia Type 1, GCD $525 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
57 GA II comprehensive, Glutaric Acidemia Type II, all three genes $2,400 1 x 83891; 54 x 83894; 54 x 83898; 54 x 83904; 3 x 83912
58 GA II (MADD), ETFDH (also known as ETF-QO) $1,000 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
59 GA II (MADD), ETFA $850 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
60 GA II (MADD), ETFB $550 1 x 83891; 12 x 83894; 12 x 83898; 12 x 83904; 1 x 83912
61 HCS, Holocarboxylase Synthetase Deficiency $725 1 x 83891; 20 x 83894; 20 x 83898; 20 x 83904; 1 x 83912
62 Homocystinuria due to CBS Deficiency $1,200 1 x 83891; 30 x 83894; 30 x 83898; 30 x 83904; 1 x 83912
63 LCHAD, Long Chain 3-Hydroxy Acyl-CoA Dehydrogenase Deficiency, common mut. $250 1 x 83891; 1 x 83892; 1 x 83894; 2 x 83898; 1 x 83912
University of Colorado (Old name: UCHSC DNA Diagnostic Laboratory)
UCD DNA Diagnostic Laboratory: Tests Offered
?? Each Sample Needs a Completed Request Form AND Consent Form AND Fax Form, and This Checklist ??
Lab director: [email protected]; 303-724-3801 Mailing address for correspondence: Mail Stop 8313, PO Box 6511, Aurora, CO 80045
Genetic counselor: [email protected]; 303-724-1572 Shipping address for samples: 12800 E. 19th Ave, Rm P18-4404J, Aurora, CO 80045
www.uchsc.edu/DNALab, Fax: 303-724-3802 3 of 3 3/11/2009
Test # (5% prepay discount for all testing; parents free for some.) Prices CPT Codes
64 MCAD, Medium Chain Acyl-CoA Dehydrogenase Deficiency, common mutation $250 1 x 83891; 2 x 83898; 2 x 83904; 1 x 83912
65 MCAD, Medium Chain Acyl-CoA Dehydrogenase Deficiency, full sequence $1,000 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
66 MMA, Methylmalonic Acidemia, Panel 1: MUT + A + B $1,500 1 x 83891; 52 x 83894; 52 x 83898; 52 x 83904; 3 x 83912
67 Methylmalonic Acidemia, MMA-MUT, ordered alone $960 1 x 83891; 24 x 83894; 24 x 83898; 24 x 83904; 1 x 83912
68 Methylmalonic Acidemia, MMA-A, ordered alone $480 1 x 83891; 12 x 83894; 12 x 83898; 12 x 83904; 1 x 83912
69 Methylmalonic Acidemia, MMA-B, ordered alone $640 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
70 MMA, Methylmalonic Acidemia, Panel 2: C + E $500 1 x 83891; 14 x 83894; 14 x 83898; 14 x 83904; 2 x 83912
71 Methylmalonic Acidemia, MMA-CHC, ordered alone $320 1 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 1 x 83912
72 Methylmalonic Acidemia, MCEE, ordered alone $240 1 x 83891; 6 x 83894; 6 x 83898; 6 x 83904; 1 x 83912
73 NKH Tier 1, Non-Ketotic Hyperglycinemia, AMT + GLDC $2,400 1 x 83891; 60 x 83894; 60 x 83898; 60 x 83904; 2 x 83912
74 NKH, only AMT $800 1 x 83891; 12 x 83894; 12 x 83898; 12 x 83904; 1 x 83912
75 NKH, only GLDC $1,600 1 x 83891; 48 x 83894; 48 x 83898; 48 x 83904; 1 x 83912
76 NKH Tier 2, Non-Ketotic Hyperglycinemia, GCSH $400 1 x 83891; 10 x 83894; 10 x 83898; 10 x 83904; 1 x 83912
77 Propionic Acidemia A+B $1,800 1 x 83891; 76 x 83894; 76 x 83898; 76 x 83904; 2 x 83912
78 Propionic Acidemia due to PCCA Deficiency $1,100 1 x 83891; 48 x 83894; 48 x 83898; 48 x 83904; 1 x 83912
79 Propionic Acidemia due to PCCB Deficiency $700 1 x 83891; 28 x 83894; 28 x 83898; 28 x 83904; 1 x 83912
80 SPR, Sepiapterin Reductase Deficiency $400 1 x 83891; 6 x 83894; 6 x 83898; 6 x 83904; 1 x 83912
81 Trimethylaminuria, TMAU (coming soon, not available now) $500 1 x 83891; 14 x 83894; 14 x 83898; 14 x 83904; 1 x 83912
82 VLCAD, Very Long Chain Acyl-CoA Dehydrogenase Deficiency, ACADVL $725 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
Pigmentation Disorders
83 HPS1, Hermansky-Pudlak Syndrome Type 1, common mutation only $250 1 x 83891; 1 x 83894; 2 x 83898; 1 x 83912
84 HPS package, sequence HPS1+HPS4 $2,500 1 x 83891; 56 x 83894; 56 x 83898; 56 x 83904; 2 x 83912
85 HPS1, Hermansky-Pudlak Syndrome Type 1, sequence $1,700 1 x 83891; 28 x 83894; 28 x 83898; 28 x 83904; 1 x 83912
86 HPS4, Hermansky-Pudlak Syndrome Type 4, sequence $1,700 1 x 83891; 28 x 83894; 28 x 83898; 28 x 83904; 1 x 83912
Albinism Panel: max price for all OCA1-4 + OA testing needed by patient $2,500 It varies
87 OCA1, Oculo-Cutaneous Albinism, Type 1a/1b, TYR sequence $1,000 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
88 OCA2, Oculo-Cutaneous Albinism, Type 2, P-gene sequence $1,500 1 x 83891; 46 x 83894; 46 x 83898; 46 x 83904; 1 x 83912
89 OCA2, Oculo-Cutaneous Albinism, Type 2, P-gene deletion $350 1 x 83891; 2 x 83894; 4 x 83898; 1 x 83912
90 OCA3, Oculo-Cutaneous Albinism, Type 3, TYRP1 sequence $1,000 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
91 OCA4, Oculo-Cutaneous Albinism, Type 4, MATP sequence $1,000 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
92 OA1, X-linked Ocular Albinism, GPR143 sequence $800 1 x 83891; 18 x 83894; 18 x 83898; 18 x 83904; 1 x 83912
Aicardi-Goutieres Syndrome
93 AGS Comprehensive: Aicardi-Goutieres Syndrome (all 4 genes ordered together) $1,650 1 x 83891; 50 x 83894; 50 x 83898; 50 x 83904; 4 x 83912
94 AGS Tier 1, AGS 1,5+2: TREX1 + RNASEH2B together (65% of mutations) $900 1 x 83891; 26 x 83894; 26 x 83898; 26 x 83904; 2 x 83912
95 AGS Tier 2, AGS 3+4: RNASEH2C + RNASEH2A ordered together $900 1 x 83891; 24 x 83894; 24 x 83898; 24 x 83904; 2 x 83912
96 AGS Type 1,5: TREX1-Related Aicardi-Goutieres Syndrome, ordered alone $450 1 x 83891; 4 x 83894; 4 x 83898; 4 x 83904; 1 x 83912
97 AGS2, RNASEH2B-Related, Type 2, ordered alone $650 1 x 83891; 22 x 83894; 22 x 83898; 22 x 83904; 1 x 83912
98 AGS3, RNASEH2C-Related, Type 3, ordered alone $500 1 x 83891; 8 x 83894; 8 x 83898; 8 x 83904; 1 x 83912
99 AGS4, RNASEH2A-Related, Type 4, ordered alone $600 1 x 83891; 16 x 83894; 16 x 83898; 16 x 83904; 1 x 83912
DNA SEQUENCING SERVICES
Contacts:
Chr istopher Korch, Efang Li,
Todd Pitts, Har r y Dr abkin
303-724-3167
303-724-3889
DNA.Cor [email protected]
Web Site:http://loki.uchsc.edu/
1. Overview of DNA Sequencing Services
2. Premium Full-Service Standard Single-Pass DNA Sequencing
3. Normal Mid-Level Standard Single-Pass DNA Sequencing
4. High Through-put Mid-Level Single-Pass DNA Sequencing
Budget Single-shot DNA Sequencing
1. Overview of DNA Sequencing Services
The primary function of the CU-Cancer Center DNA Sequencing Core is to sequence DNA
samples brought to us as purified DNA. We can also purify DNA from bacterial colonies for
sequencing. However, we highly recommend that the customer confirm that the E. coli
transformant does in fact bear the correct plasmid before submitting it for DNA purification and
sequencing.
We offer several levels of sequencing service - from our Premium Full-Service Single-Pass
Sequencing to budget "Single-Shot" sequencing, where the customer performs the sequencing
reaction themselves and submits the reaction products ready for electrophoresis on one of our
automated sequencers. The Core's two capillary ABI fluorescent sequencing instruments can
provide between 650 and 950 bp of reliable DNA sequence per AmpliTaq FS cycle sequencing
reaction with dRhodamine and BigDye labelled dye-terminators.
Sequencing results will only be delivered electronically as follows: customers will receive an
email informing them that their results are ready. In the message, there will be a link to our
website from where the results can be downloaded, using the customer's name and password.
The data will be available on the server for one month from date of posting; afterwards
customers will need to contact the Core directly for the data. We will no longer print
electropherograms of sequencing results.
On this website customers will have access to the text files (.seq), electropherogram files (.ab1),
and .pdf files of the electropherograms. The electropherogram (.ab1) files will be editable, but
the .pdf files will not. Viewing the .ab1 files you will need to download either Editview (for
MACs) or Chromas (for PCs). Both are free of charge and available at the following websites:
Editview:http://www.appliedbiosystems.com/support/software/dnaseq/installs.cfm
Chromas:http://www.technelysium.com.au/chromas.html
Xplorer Lite:http://www.dnatools.com/download.html
2. Premium Full-Service Standard Single-Pass DNA Sequencing
This is the highest level of sequencing service, which includes performance and processing of
the sequencing reaction, loading the products on a sequencing instrument, and preparing and
troubleshooting the results for the customer. The DNA samples should be quantified by the
customer using agarose gel electrophoresis and be submitted to the Core at the following
concentrations:
Premium Service DNA and Primer Concentrations
Type of DNA
DNA Concentration
(nanograms / microliter)
Primer Concentration
(micromolar)
Plasmid DNA
150. 5.
Uncloned PCR Product
15. 5.
DNA restriction fragment
15. 5.
Lambda, PAC, BAC, Cosmid
DNA 500.
100.
The DNA and primers should be submitted in 1.5-1.7 mL microfuge tubes and the labels on the
tubes must be exactly as that submitted through the on-line ordering system. To estimate the
concentration and purity (i.e., presence of RNA and genomic DNA) of your DNA samples, we
recommend that you electrophorese your samples on an agarose gel and compare the intensity of
the ethidium bromide bands of your DNA sample against that of the bands present in a ladder of
mass standards. Three commercially available mass standards that can be used are: PGC
Scientifics Gene Choice DNA Ladder I (Cat. No. 62-6108-00), which we sell and you thereby
avoid paying shipping costs. New England Biolabs (NEB) also have a 1KB Ladder (Cat. No.
N32325), which is available in the NEB freezer in the UCHSC School of Medicine Room 5626.
Inter-Mountain Scientific Company (ISC Bioexpress) sells the Gene Mate Quanti-Maker 1 kb
Ladder (Cat. No. C-5087-200), which is very similar to the mass ladder from PGC Scientifics.
When it comes to DNA concentration, more is not always better. Too much DNA or too
concentrated primer solutions can give results with high background or appear to be a mixture of
sequences. We will assume the concentration of your sample is the one appropriate for your
samples (see above table) and will run the reactions accordingly. If the reaction fails because of
a possible error on the part of Core personnel, the reaction will be repeated at no extra charge.
We can provide several standard sequencing primers (M13 Forward, M13 Reverse, SP6
promoter, T3 promoter, T7 promoter primer, and T7 terminator, see section below for primer
sequences) at no additional cost to the customer. We also have the primer T7neo, which is
specific for the mammalian expression vectors derived from the pCIneo and pSI vectors. The
customer may also bring their own primer for sequencing their DNA samples. We can sequence
different types of DNAs: plasmids, PCR fragments, restriction fragments, cosmid, PAC, and
lambda phage. The Core will provide the customer with the sequencing results as an electronic
copy of the text file, and a printout of the electropherogram.
3. Normal Mid-Level Standard Single-Pass DNA Sequencing
For EACH reaction, the customer should mix the below specified amounts of DNA and the
desired primer made up in a total volume of 17.0 microliters using either water or 10 mM Tris-
HCl (pH 8) in a labelled 1.5 -1,7 mL microcentrifuge tube (Please note tube size!).
Mid-Level Service DNA and Primer Quantities
Type of DNA DNA Quantity (nanograms) Primer Quantity (picomoles)
Plasmid DNA
1250 10
Uncloned PCR Product
50 10
DNA restriction fragment
50 10
Lambda, PAC, BAC, Cosmid
DNA
3000 100
Do not use TE, because the EDTA will inhibit the reaction. The Core does not supply any
primers for this level of service. Instructions for labelling the tubes are found below and on the
order form specific for this service. The Core will add an aliquot of this mixture to a tube
containing the sequencing reagents, perform and process the cycle-sequencing reactions, load the
samples on a gel, and provide the customer with the sequencing results as described above. Only
failures clearly due to an error of the sequencers will be repeated.
4. High Throughput Mid-Level Single-Pass DNA Sequencing
These options include running and analysis of sequencing reactions and emailing of electronic
copies of the data. The customer mixes specific amounts of DNA and primer (see below) and we
do the rest. No repeats unless due to Core error. Turn-around time approximately 1-2 working
days.
In order to offer these inexpensive sequencing options, we must specify how the samples are
brought to the Core. The samples must be a minimum of 47 samples and pre-loaded in an
Applied Biosystems MicroAmp Optical 96-well Reaction plate (Part Number N801-0560 which
can be purchased through the ABI Freezer Program in the DNA Core; currently $40.70 per box
of 10 plates). The wells must be covered with either strips of 8 caps (ABI part # N801-0535
currently $55.50 for 300 strips of 8 caps) or with optical adhesive cover sheets (AB part #
4311971; currently $122.00 for package of 100 cover sheets). Each of the wells must contain one
sample of DNA mixed with a single primer in the amounts below, depending on the type of
DNA. The last well in the batch ( H12) should be left empty for the addition of a control
template provided by the Sequencing Core. The DNAs and primers must be dissolved in water.
We suggest quantifying the DNAs using a mass ladder as described above.
High-Through-put Mid-Level Service DNA and Primer Quantities
Type of DNA DNA Quantity
(nanograms)
Primer Quantity
(picomoles)
Total Volume
(microliters)
Plasmid (3 - 20 kb)
150 5 10
PCR Fragment (Purified,
i.e., not cloned
15 5 10
DNA Restriction
Fragment (Purified, i.e.,
not cloned
15 5 10
BAC (bacterial artificial
chromosome)
600 100 10
Lambda phage DNA,
Cosmid DNA (> 30 kb)
600 100 10
We suggest that DNAs with unusual features that can make them difficult to sequence (e.g., very
GC rich regions, known hairpins structures) be submitted for Premium Full Service Sequencing
instead of attempting to sequence them by any of the Mid-Level DNA sequencing services and
that the customer inform the Core personnel of these potential problems.
Budget Single-shot DNA Sequencing
The customer performs the sequencing reactions with either of the ABI dye-terminator cycle
sequencing ready reaction kits: the dRhodamine (ABI part number 403044 or 403045) or
BigDye dye-terminator kit (ABI part number 4303149 or 4303150). The customer must
perform and process the cycle-sequencing reactions per instructions from ABI and from the
Core. Instructions for labelling the tubes are on the order form specific for this service. Core
personnel will electrophorese the reaction products on on the appropriate automated DNA
sequencing instrument and provide the customer with the sequencing results as described above.
Results will only be repeated if due to a failure of the automated sequencers.
Please specify on the order form which ABI sequencing chemistry kit was used!!
DNA SEQUENCING & ANALYSIS CORE PRICES
FOR SERVICES
Effecti ve July 1, 2005
Price List For Cancer Center Members Only
DNA Sequencing
Premium Full Service Single-Pass Sequencing Reaction
Core quantifies DNA and performs sequencing reaction. Use of standard
sequencing primers included: M13 Forward, M13 Reverse, SP6, T7, T7-neo, and
T3. Repeats included, if fault due to Core
$ 12.50
Normal Mid-Level Single-Pass Sequencing Reaction
Customer mixes DNA and desired primers at specified DNA
and primer concentrations. Core does not provide any sequencing
primers. Core performs sequencing reaction. No repeats.
$ 9.00
High Through-put Mid-Level Single-Pass Sequencing Reaction
Batches of 48+ Samples (price per sample)
$ 8.00
Budget Single-shot Sequencing
The Core runs customer's processed sequencing reaction on its automated
sequencers. No repeats.
$ 4.00
DNA Profiling - Identification of Cell Lines
PCR Amplification and Fragment Analysis $ 40.00
Template Preparation
Plasmid Minipreps (from colonies or liquid cultures)
High Copy Number Plasmids
Low - Medium Copy Number Plasmids
$ 15.00
$ 20.00
Purification of PCR Products from Reaction Mixtures $ 10.00
Semiautomatic, High-Throughput Plasmid Minipreps
Price per 96 cultures
$500.00
Quantification of Templates of Unknown Concentration $ 5.00
Miscellaneous Services (e.g., dilution of primer) $ 5.00
Hybridization Filters
High Density Hybridization Filters for Screening DNA Libraries
2 copies
3-7 copies
$180.00
$200.00
DNA Analysis Available on request.
Please call for quotation.
Additional Services
Available on request. Please call for quotation for Primer Walking, Large-scale Preps of
Sequence Quality Plasmid DNA, Preparation of Lambda or Cosmid DNA Templates,
Construction and Screening of DNA Libraries (In vitro Transposon Libraries in Plasmids
and Cosmids), Preparation of Sequence Submissions.
DNA SEQUENCING & ANALYSIS CORE PRICES
FOR SERVICES
Effecti ve July 1, 2005
Price List For Academic and Non-Profit Institutions
DNA Sequencing
Premium Full Service Single-Pass Sequencing Reaction
Core quantifies DNA and performs sequencing reaction. Use of standard
sequencing primers included: M13 Forward, M13 Reverse, SP6, T7, T7-neo, and
T3. Repeats included, if fault due to Core
$ 15.00
Normal Mid-Level Single-Pass Sequencing Reaction
Customer mixes DNA and desired primers at specified DNA
and primer concentrations. Core does not provide any sequencing
primers. Core performs sequencing reaction. No repeats.
$ 11.00
High Through-put Mid-Level Single-Pass Sequencing Reaction
See brochure or separate description for details on sample preparation for this
procedure.
Batches of 47+ Samples (price per sample)
$ 9.00
Budget Single-shot Sequencing
The Core runs customer's processed sequencing reaction on its automated
sequencers. No repeats.
$ 4.50
DNA Profiling - Identification of Cell Lines
PCR Amplification and Fragment Analysis $ 50.00
Template Preparation
Plasmid Minipreps (from colonies or liquid cultures) $ 15.00
High Copy Number Plasmids
Low-Medium Copy Number Plasmids
$ 20.00
Purification of PCR Products from Reaction Mixtures $ 10.00
Semiautomatic, High-Throughput Plasmid Minipreps
Price per 96 cultures
$500.00
Quantification of Templates of Unknown Concentration $ 5.00
Miscellaneous Services (e.g., dilution of primer) $ 5.00
Hybridization Filters
High Density Hybridization Filters for Screening DNA Libraries
2 copies
3-7 copies
$180.00
$200.00
DNA Analysis Available on request.
Please call for quotation.
Additional Services
Available on request. Please call for quotation for Primer Walking, Large-scale Preps of
Sequence Quality Plasmid DNA, Preparation of Lambda or Cosmid DNA Templates,
Construction and Screening of DNA Libraries (In vitro Transposon Libraries in Plasmids
and Cosmids), Preparation of Sequence Submissions.
DNA SEQUENCING & ANALYSIS CORE PRICES
FOR SERVICES
Effecti ve July 1, 2005
Price List For Industrial and For-Profit Customers
DNA Sequencing
Premium Full Service Single-Pass Sequencing Reaction
Core quantifies DNA and performs sequencing reaction. Use of standard
sequencing primers included: M13 Forward, M13 Reverse, SP6, T7, T7-neo, and
T3. Repeats included, if fault due to Core
$ 16.00
Normal Mid-Level Single-Pass Sequencing Reaction
Customer mixes DNA and desired primers at specified DNA
and primer concentrations. Core does not provide any sequencing
primers. Core performs sequencing reaction. No repeats.
$ 12.00
High Through-put Mid-Level Single-Pass Sequencing Reaction
Batches of 48-Samples (price per sample)
$ 10.00
Budget Single-shot Sequencing
The Core runs customer's processed sequencing reaction on its automated
sequencers. No repeats.
$ 6.00
DNA Profiling - Identification of Cell Lines
PCR Amplification and Fragment Analysis $ 60.00
Template Preparation
Plasmid Minipreps (from colonies or liquid cultures) $ 22.00
$ 27.00
High Copy Number Plasmids
Low Medium Copy Number Plasmids
Purification of PCR Products from Reaction Mixtures $ 15.00
Semiautomatic, High-Throughput Plasmid Minipreps
Price per 96 cultures
$600.00
Quantification of Templates of Unknown Concentration $ 5.00
Miscellaneous Services (e.g., dilution of primer) $ 5.00
Hybridization Filters
High Density Hybridization Filters for Screening DNA Libraries
2 copies
3-7 copies
$270.00
$300.00
DNA Analysis Available on request.
Please call for quotation.
Additional Services
Available on request. Please call for quotation for Primer Walking, Large-scale Preps of
Sequence Quality Plasmid DNA, Preparation of Lambda or Cosmid DNA Templates,
Construction and Screening of DNA Libraries (In vitro Transposon Libraries in Plasmids
and Cosmids), Preparation of Sequence Submissions.
The Evaluation Center
Contact:
Bonnie Walters
Director
The Evaluation Center
School of Education and Human Development
University of Colorado Denver
Campus Box 106; P.O. Box 173364
Denver, CO 80217-3364
303-315-4967
General Email: [email protected]
http://www.ucdenver.edu/academics/colleges/SchoolOfEducation/CentersPartnerships/Evaluation/Pages/E
valuation.aspx
Vision:
Powered by a commitment to cutting edge evaluation methodologies, we strive to make program
evaluation a widely accepted and valued practice.
Mission:
As a collaborative enterprise, it is our mission to use rigorous, innovative evaluation processes to inform
and promote evidence-based programs, practices and policies in schools, institutions of higher education,
health care and in our communities.
Goals:
•
To promote the use of evaluation by diverse stakeholders;
•
To help institutions and organizations become effective consumers of evaluation data;
•
To provide a setting where Ph.D. and master's degree students can further develop quantitative
and qualitative evaluation expertise by working on real life evaluation projects; and
•
To become a resource for informing health, education, and social policiesAll trademarks are
About Us
The Evaluation Center is a distinct division of the university whose purpose is to promote
evidence-based practices and policies through inquiry-based evaluation processes to non-profit
agencies. The Evaluation Center provides credible, scholarly, and objective formative and
summative evaluation. Our staff has experience in providing large-scale evaluation services
having worked with projects funded by the National Science Foundation, the University
Corporation for Atmospheric Research, the Danforth Foundation, the National Education
Association, and the US Department of Education.
Resources
Collaborative Process Initiation Flowchart
Frequently Asked Questions
Useful Links to Other Sites
•
Digital Resources for Evaluators
Links to online evaluation tools, texts, and other resources.
•
The Online Evaluation Research Library
This site, funded by the National Science Foundation, provides evaluation plans, instruments, and
reports for NSF projects that can be used as examples by Principal Investigators, project evaluators, and
others outside the NSF community as they design proposals and projects.
•
Research Methods Knowledge Base
This page is an introduction to basic ideas, types, and questions about evaluation.
•
Resources for Methods in Evaluation and Social Research
This page lists FREE resources for methods in program evaluation and social research. The focus is on
"how-to" do evaluation research and the methods used: surveys, focus groups, sampling, interviews, and
other methods.
Flow Cytometry and Cell Sorting Facility
Contacts:
Brent Palmer, PhD
Director
303-724-7203
[email protected]
Website:http://www.uchsc.edu/clinimmune/flowcytometry/index.htm
General Information about Flow Cytometry
Flow cytometry is a multi faceted technique for characterizing and delineating cell populations
via size, shape, surface and intracellular protein expression, which yields valuable information
on both phenotype and cell expression. Flow cytometry is unique in its ability to rapidly analyze
and sort thousands of cells per second while simultaneously providing data on distinctive cell
populqations resolved at the single cell level. Flow cytometry can be used as a tool to identify
novel cell populations based on the expression of cell surface markers through intracellular
staining. It can also be used to examine antigen specific T cells, gene expression, or qualify the
proliferative capacity of different cell populations. In addition it is a technique that can be
performed using any cell sample suspension, e.g., blood cells, collagen digested or disaggregated
tissue (e.g. lung, liver, and spleens cells), stem cells and cultured cells.
The BD FACSAria is a cell sorter that is capable of rapid, simultaneous purification of
phenotypically distinct populations of cells. Up to four different cell populations can be purified
simultaneously from the same sample.
The Immunohistopathology Unit provides CFAR members with the following tools and services:
• Cryostat for cutting frozen infectious tissue for HIV-1-related research
• Leica DMR – Light microscope capable of color imaging and associated with
quantitative image analysis software
• Leica DM5000B – Fluorescent microscope capable of imaging fluorescently stained
specimens (4 colors)
• Immunostaining and assay development including software programming for image
analysis, for HIV-1-related projects
• Identification of HIV-1-producing cells by in situ hybridization
• Technical expertise in design and implementation of immunohistochemical or
immunofluorescent staining studies
• Training in immunostaining techniques and use of microscopy equipment and software
Please note our services, equipment and pricing below:
CFAR
Member Rate
Non-CFAR
Member Rate
Non-Academic
Industry Rate
CELL Analysis
FACScan (1-3
colors)**
$35 $40 $60
FACSCalibar (1-4
colors)**
$40 $50 $75
LSR II (1-13
colors)**
$55 $80 $100
FACSAria (1-13
colors)
$77 $99 $125
Cell Sorting
FACSAria (1-13
colors)*
$99 $125 $150
Data Analysis
FlowJO, Diva, Cell
Quest
Free Free Free
Training and
Consultation
Free Free Free
* The price for cell sorting (FACSAria) includes technician time.
* Please add $40/hour to the price of the FACScan, FACSCalibur and LSR II if the samples are
run by Flow Lab personnel.
The facility's technical director, Brent Palmer Ph.D., and staff help design experiments, develop
and implement new applications as well as collaborate scientifically with users. The staff provide
full service flow cytometry assistance, including sample preparation, staining, and data
acquisition and analysis. We currently perform immunophenotyping for a number of clinical
trials, including CD4/CD8 immunophenotyping for the Adult Clinical Trials Group (ACTG).
Please contact Brent Palmer PhD ([email protected]) if you have additional questions
about our services.
Flow Cytometry & Immunology Core
From: Palmer, Brent
Sent: Thursday, October 08, 2009 9:32 AM
a) How is the quality of your measurements evaluated – quality control?
Our flow cytometry laboratory follows CLEA guild lines and is certified by the College of American Pathologist
(CAP). Everyday our flow cytometers are QC’ed using standard bead-based methods.
b) What is the turn-a-round time for the service you provide?
We have online scheduling for the use of our flow cytometer (potentially immediate access) and all of the clinical
tests we provide have 24 hour or less turn around time.
c) Who documents the data provided and signs off on the data?
All clinical flow cytometry tests are CAP certified and all tests are signed off by the technical director (Brent
Palmer) of the lab.
d) Have you had experience providing data for industry?
We have provided service to multiple biotech companies in the Denver-Boulder area
e) Do you have a standard operating procedure manual?
Yes
f) How will you track billing and financial aspects of your core?
Billing is carefully tracked by our personal and billing is done by sending invoices to all user. Lab Manager
(Prosoft) data-base is use to track clinical samples and flow cytometer usage is determined by tracking log on and
log off time on the flow cytometers. Flow cytometry billing is done in 15 minutes increments. Billing is done
monthly.
Flow Cytometry Services at the
University of Colorado Cancer Center
Contacts:
Christopher J. Hogan, PhD
Director
303-724-3145
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/flowcytometry/index.aspx
The Flow Cytometry Core at the University of Colorado Cancer Center offers services to
Cancer Center members, Charles C. Gates Regenerative Medicine and Stem Cell Biology
Program members, academic non-members and private industry researchers. CC and RMSCB
Members receive scheduling priority and a discounted rate for services. Learn more about
becoming a UCCC member or a RMSCB member .
Our experienced staff can analyze your samples for you or train you to run the analysis
equipment for all services except cell sorting. Core staff performs all cell sorting.
Flow Cytometry Analysis Services
We have three main analyzers, each best for different types of analysis. You may use the
machines yourself or ask us to analyze your samples for you.
Becton Dickinson FACSCalibur
• 2 lasers: 488 and 635
• 4 color analysis
• Suggested fluors: FITC , PE , PECy7, APC
Beckman Coulter FC500
• High through-put
• 2 lasers: 488 and 635
• 5 color analysis
• Suggested fluors: FITC , PE , PE-Texas Red, APC, PECy7, PI
Cyan
• Analysis rate of 50,000 events/second
• 100 million event data files
• New 40mW red diode laser for enhanced APC and APC-Cy7 detection
• 9-color analysis
• 9 colors
Cell Sorting Services
We have two cell sorting machines with different capabilities. Core staff performs all cell sorts.
Moflo
• 3 lasers: 488, 635 and tunable Krypton
• Many laser lines for optimizing fluorescent protein detection
• Plate sorting
• 7 color capability
Moflo XDP
• Optimized for rare events
• Plate sorting
• 4 lasers: UV, 405, 488, 635
• 9 color capability
• Sort rate of 70,000 events per second
• 5 decade data resolution
• Plate sorting for any size plate
• 4-way sorting
Luminex Multiplex Bead Assays
This analysis measures cytokines, chemokines, phosphoproteins and apoptosis markers.
Also available
• ViCell Cell Counter
• Victor Multilabel Counter (self-service only in RC-1 South, Room 4215)
• Cytospin microscope slide centrifuge
Prices
Service Description
Cancer
Center
Member Rate
Stem Cell
Member
Rate
Non Cancer
Center
Member Rate
Stem Cell Non
Cancer
Center Rate
Commercial
Rate
Research Flow
Analyzers
$78 $66 $229 $216 $251
Research Flow
Analyzers - Self-
Run/Consult
$51 $39 $99 $87 $109
Research Flow Sorts $122 $99 $242 $219 $267
Wallac Plate Reader $17 $17 $57 $57 $63
Vicell Cell Counter $2.66 $2.66 $3.56 $3.56 $3.91
• Prices effective July 1, 2008-June 30, 2009
Flow Cytometry & Immunology Core (UCCC)
From: Hogan, Chris
Sent: Monday, November 09, 2009 5:01 PM
a) How is the quality of your measurements evaluated – quality control?
Instrument quality control is performed daily to verify alignment and sensitivity.
b) What is the turn-a-round time for the service you provide?
Turn-a-round t ime probably doesn’t really apply, but scheduling l ead t ime does.
Time is u sually a vailable o n th e a nalyzers within 1 -2 da ys a nd l ead t ime f or
scheduling the sorters is 3-4 days.
c) Who documents the data provided and signs off on the data?
We have a staff of three, all of whom are highly experienced in Flow Cytometry
and have at l east 10 years of experience. All of the staff participates i n national
and international flow cytometry training workshops and conferences.
d) Have you had experience providing data for industry?
Yes, several private industry organizations routinely use our services.
e) Do you have a standard operating procedure manual?
We have standard operating procedure manuals for each instrument that relate to
instrument maintenance and operation. The staff consults on a n i ndividual basis
with i nvestigators c oncerning t he pr oper c ontrols a nd s pecimen pr eparation f or
their individual assays.
f) How will you track billing and financial aspects of your core?
Flow Cytometry services ar e ch arged o n a t ime-used b asis. E ach i nstrument
automatically l ogs t he t ime u sed f or ea ch i nvestigator. Invoices ar e p repared
monthly f or t he pr evious m onth’s c harges. A cost s tudy i s p erformed yearly
through t he U niversity finance de partment t o e nsure t hat pr icing i s f air a nd
reasonable.
University of Colorado Cancer Center
Gene Expression, Microarray and PCR Core
Contacts:
Mark Geraci, MD
Core Director
[email protected]
303-315-0398
Bifeng Gao, PhD
Microarray Core Manager
[email protected]
303-724-3367
Bryan Haugen, MD
Core Co-Director
PCR Director
[email protected]
303-724-3921
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/gene-
expression/index.aspx
HNSCC and NSCLC cell lines with similar
gefitinib response sort together.
The Gene Expression Core is dedicated to providing state-of-the-art facilities and technical support and
services for analysis of gene expression, which will allow UCCC members to be on the cutting edge of
cancer research.
The Gene Expression Core is comprised of:
• Microarray Core
• PCR Core
Core Objectives
• Analyze gene expression using both pre-made and custom designed oligonucleotide arrays
• Facilitate gene discovery
• Accurately quantitate gene expression using real time PCR and GenomeLab GeXP technology
• Provide support for data analysis and bioinformatics by our data mining tool and our data
analysis capabilities
• Remain committed to using a variety of approaches for expression analysis
• Provide consultation and educational services to help those members with limited knowledge
on microarray technology and to bring the Core customers up to date as technology advances
The Gene Expression Core was established in response to the technological advances in gene array, as
well as the demand for high throughput expression analysis and genomic investigation to investigate
pathogenesis, therapeutics, genetic susceptibility and gene discovery in cancer research. The informatics
aspect is of paramount importance, and five distinct analysis programs, as well as a network, are used to
store, share and analyze the data.
To date, the Core is one of the highest volume Affymetrix microarray facilities in academia in the
country, having performed more than 10,900 microarrays including test arrays over seven years for
nearly 250 investigators. On average, 85% of the users are UCCC members.
Contacts:
Mark W. Geraci, M.D.
Director
[email protected]
Office: 303-724-6040
Bifeng Gao, PhD
Assistant Professor
Core Manager
303-724-6048
[email protected]
Website:http://microarray.uchsc.edu/index.php
Microarray Core
The Microarray Core Facility at University Of Colorado Health Sciences Center (UCHSC) is an
advanced, state-of-the-art Microarray Technology Center providing crucial research support for
investigators interested in using Affymetrix GeneChips®, CombiMatrix CustomArray™ Chips or the
Nanogen NanoChip®. We also host rtPCR with the Bio-Rad iCycler. Our team is dedicated to
providing high-quality microarray laboratory instruction, service, and consultation to the research and
clinical community affiliated with UCHSC and other research institutions in the region.
Affymetrix Nanogen CombiMatrix iCycler Agilent
Nucleic Acid Isolation Call or Email Dr. Gao
The quality of the nucleic acid is essential to the overall success of the
microarray analysis. Since the most appropriate protocol for the isolation of
RNA or DNA is source dependent, we recommend using a protocol that has
been established for the tissues or cells being used. In the absence of an
established protocol, we recommend using one of the commercially available
kits designed for nucleic acid isolation.
Nucleic acid analysis via the Agilent Bioanalyzer 2100. Price
The 2100 bioanalyzer is Agilent's highly successful microfluidics-based
platform for the analysis of DNA, RNA, proteins and cells. As the first
commercial, analytical instrument based on lab-on-a-chip technology the
Agilent 2100 bioanalyzer has proven to be an excellent alternative to messy
and labor-intensive gel electrophoresis techniques; delivering fast,
automated, high quality digital data instead of the subjective, time-consuming
results associated with gels.
The process only takes 35 ~ 40 minutes for 12 samples: Load samples, run
chip, view output.
Nucleid acid analysis and concentration determination via the
NanoDrop® ND-1000.
Free for
Array Customers
The NanoDrop® ND-1000 UV-Vis Spectrophotometer enables highly
accurate analyses of extremely small samples with remarkable
reproducibility. The patented sample retention system eliminates the need for
cuvettes and capillaries which decreases the measurement cycle time. The
ND-1000 is designed for 1-2 ul undiluted samples.
RNA Sample Labeling Price
• 1 to 5 µg of total RNA required for Affymetrix labeling protocol
• 5 to 10 µg of total RNA required for ENZO Biosciences labeling
protocol
• 1st and 2nd strand cDNA synthesis from total RNA
• Generation of biotin-labeled cRNA
• Quantification and quality check
• cRNA fragmentation
Small Amount RNA Sample Labeling (5-200ng of total RNA is
required)
Price
• Total RNA quality assessment
• 1st and 2nd strand cDNA synthesis from total RNA
• in vitro transcription (IVT)
• Second round 1st and 2nd strand cDNA synthesis
• IVT with biotin
• Quantification and quality check
• cRNA fragmentation
Genomic DNA Sample Labeling for Genotyping Call or Email Dr. Gao
• 0.25 µg of genomic DNA is required
• Restriction digestion of DNA
• Cleanup, and QC for the restriction digest
• Ligation
• PCR
• Fragmentation
• End-labeling
GeneChip® Processing Price
• Samples are loaded on to an expression or mapping array and
hybridized overnight.
• The samples are removed to microfuge tubes,
• The arrays are then processed through the GeneChip® Fluidics
Station 450.
• Each array is then scanned on the Affymetrix GeneChip® Scanner
3000.
Combimatrix CustomArray™ Chips Call or Email Dr. Gao
CombiMatrix Corporation's CustomArray™ is a high quality, completely
customizable array format that provides a cost effective and timely solution
for microarray users. Oligonucleotide probes can be defined and designed by
the user and supported by the open source CombiMatrix probe design
system at no additional cost. CustomArray™ uses a specially modified
"CMOS" semi-conductor to direct the molecular assembly of a specific
sequence of DNA bases in response to a digital command. The 12,000
feature CustomArray™ chip available in 1 × 3 inch format to fit most spotted
microarray scanners.
SNP / STR Detection via Nanogen NanoChip® MBW Call or Email Dr. Gao
The NanoChip® Molecular Biology Workstation is an automated multi-purpose
instrument that facilitates detection of known sequences, such as in the
analysis of Single Nucleotide Polymorphisms (SNPs) and Short Tandem
Repeats (STRs) using the NanoChip® Electronic Microarray. The unique,
open-architecture design permits us to define, select and build our own test
panels or use predefined analyte specific reagent packs (ASR's).
Data analysis service Call or Email Dr. Gao
Basic Data Analysis: the core will run a pairwise comparision analysis (e.g.,
control vs. experimental) using Affymetrix GCOS data analysis software.
Extended Data Analysis: the core analyst will provide an indepth analysis of
multivariate experiment data (e.g., 3 or more treatments, time-course
experiment, etc.).
Pricing
Core lab service cost
Affymetrix GeneChip® price list attached for UCHSC
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
GeneChip® Arrays & Reagents
GeneChip ® arrays are analysed with GeneChip ® instruments and software systems only
Expression Anal ysis
Human Arrays
Part Product Name Contents Per Array Total Price
900366 GeneChip® Human Genome U133A Array contains 5 arrays $1,875 $375
900367 GeneChip® Human Genome U133A Array contains 30 arrays $11,250 $375
900470 GeneChip® Human Genome U133 Plus 2.0 contains 2 arrays $850 $425
900466 GeneChip® Human Genome U133 Plus 2.0 contains 6 arrays $2,550 $425
900467 GeneChip® Human Genome U133 Plus 2.0 contains 30 arrays $12,750 $425
900471 GeneChip® Human Genome U133A 2.0 contains 2 arrays $550 $275
900468 GeneChip® Human Genome U133A 2.0 contains 6 arrays $1,650 $275
900469 GeneChip® Human Genome U133A 2.0 contains 30 arrays $8,250 $275
900368 GeneChip® Human Genome U133B Array contains 5 arrays $1,875 $375
900369 GeneChip® Human Genome U133B Array contains 30 arrays $11,250 $375
900370 GeneChip® Human Genome U133 Set contains 5 U133A and 5 U133B human arrays $3,750 $375
900444 GeneChip® Human Genome U133 Set contains 30 U133A and 30 U133B human arrays $21,000 $350
900377 GeneChip® Human Genome Focus Array contains 5 arrays $1,000 $200
900376 GeneChip® Human Genome Focus Array contains 30 arrays $6,000 $200
900649 GeneChip® Human Exon 1.0 ST Array contains 2 arrays $1,050 $525
900650 GeneChip® Human Exon 1.0 ST Array contains 6 arrays $3,150 $525
900651 GeneChip® Human Exon 1.0 ST Array contains 30 arrays $15,750 $525
900653 GeneChip® Human Exon 1.0 ST Array Training Kit each $9,050
900654 GeneChip® Human Exon 1.0 ST Array Starter Pack each $28,700
Rat Arrays
900404 GeneChip® Rat Expression Array 230A contains 5 arrays $1,750 $350
900405 GeneChip® Rat Expression Array 230A contains 30 arrays $10,500 $350
900505 GeneChip® Rat Genome 230 2.0 Array contains 2 arrays $800 $400
900506 GeneChip® Rat Genome 230 2.0 Array contains 6 arrays $2,400 $400
900507 GeneChip® Rat Genome 230 2.0 Array contains 30 arrays $12,000 $400
900406 GeneChip® Rat Expression Array 230B contains 5 arrays $1,750 $350
900407 GeneChip® Rat Expression Array 230B contains 30 arrays $10,500 $350
900408 GeneChip® Rat Expression Set 230 contains 5 230A and 5 rat 230B arrays $3,500 $350
900442 GeneChip® Rat Expression Set 230 contains 30 230A and 30 rat 230B arrays $19,500 $325
Mouse Arrays
900412 GeneChip® Mouse Expression Array 430A contains 5 arrays $1,875 $375
900413 GeneChip® Mouse Expression Array 430A contains 30 arrays $11,250 $375
900495 GeneChip® Mouse Genome 430 2.0 contains 2 arrays $850 $425
900496 GeneChip® Mouse Genome 430 2.0 contains 6 arrays $2,550 $425
900497 GeneChip® Mouse Genome 430 2.0 contains 30 arrays $12,750 $425
900498 GeneChip® Mouse Genome 430A 2.0 contains 2 arrays $550 $275
900499 GeneChip® Mouse Genome 430A 2.0 contains 6 arrays $1,650 $275
900500 GeneChip® Mouse Genome 430A 2.0 contains 30 arrays $8,250 $275
900414 GeneChip® Mouse Expression Array 430B contains 5 arrays $1,875 $375
900415 GeneChip® Mouse Expression Array 430B contains 30 arrays $11,250 $375
900416 GeneChip® Mouse Expression Set 430 contains 5 430A and 5 430B mouse arrays $3,750 $375
900443 GeneChip® Mouse Expression Set 430 contains 30 430A and 30 430B mouse arrays $21,000 $350
Arabidopsis Arrays
900385 GeneChip® Arabidopsis ATH1 Genome Array contains 5 arrays $1,500 $300
900386 GeneChip® Arabidopsis ATH1 Genome Array contains 30 arrays $9,000 $300
Bovine Arrays
900561 GeneChip® Bovine Genome Array contains 2 arrays $550 $275
900562 GeneChip® Bovine Genome Array contains 6 arrays $1,650 $275
900563 GeneChip® Bovine Genome Array contains 30 arrays $8,250 $275
Canine Arrays
900725 GeneChip® Canine Genome 2.0 Array contains 2 arrays $800 $400
900726 GeneChip® Canine Genome 2.0 Array contains 6 arrays $2,400 $400
900727 GeneChip® Canine Genome 2.0 Array contains 30 arrays $12,000 $400
900489 GeneChip® Canine Genome Array contains 5 arrays $1,375 $275
900490 GeneChip® Canine Genome Array contains 30 arrays $8,250 $275
C. elegans Arrays
900383 GeneChip® C. elegans Genome Array contains 5 arrays $1,500 $300
900384 GeneChip® C. elegans Genome Array contains 30 arrays $9,000 $300
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
Chicken Arrays
Part Product Name Contents Per Array Total Price
900590 GeneChip® Chicken Genome Array contains 2 arrays $800 $400
900591 GeneChip® Chicken Genome Array contains 6 arrays $2,400 $400
900592 GeneChip® Chicken Genome Array contains 30 arrays $12,000 $400
Drosophila Arrays
900531 GeneChip® Drosophila Genome 2.0 Array contains 2 arrays $550 $275
900532 GeneChip® Drosophila Genome 2.0 Array contains 6 arrays $1,650 $275
900533 GeneChip® Drosophila Genome 2.0 Array contains 30 arrays $8,250 $275
900335 GeneChip® Drosophila Genome Array contains 5 arrays $1,500 $300
900336 GeneChip® Drosophila Genome Array contains 30 arrays $9,000 $300
E. coli Arrays
900550 GeneChip® E. coli Genome 2.0 Array contains 2 arrays $350 $175
900551 GeneChip® E. coli Genome 2.0 Array contains 6 arrays $1,050 $175
900552 GeneChip® E. coli Genome 2.0 Array contains 30 arrays $5,250 $175
900381 GeneChip® E. coli Antisense Genome Array contains 5 arrays $1,500 $300
900382 GeneChip® E. coli Antisense Genome Array contains 30 arrays $9,000 $300
Maize Arrays
900614 GeneChip® Maize Genome Array contains 2 arrays $550 $275
900615 GeneChip® Maize Genome Array contains 6 arrays $1,650 $275
900616 GeneChip® Maize Genome Array contains 30 arrays $8,250 $275
Medicago Arrays
900734 GeneChip® Medicago Genome Array contains 2 arrays $850 $425
900735 GeneChip® Medicago Genome Array contains 6 arrays $2,550 $425
900736 GeneChip® Medicago Genome Array contains 30 arrays $12,750 $425
P. aeruginosa Arrays
900339 GeneChip® P. aeruginosa Genome Array contains 5 arrays $1,500 $300
900340 GeneChip® P. aeruginosa Genome Array contains 30 arrays $9,000 $300
Plasmodium/Anopheles Arrays
900511 GeneChip® Plasmodium/Anopheles Genome Array contains 2 arrays $600 $300
900512 GeneChip® Plasmodium/Anopheles Genome Array contains 6 arrays $1,800 $300
Poplar Arrays
900728 GeneChip® Poplar Genome Array contains 2 arrays $850 $425
900729 GeneChip® Poplar Genome Array contains 6 arrays $2,550 $425
900730 GeneChip® Poplar Genome Array contains 30 arrays $12,750 $425
Porcine Arrays
900623 GeneChip® Porcine Genome Array contains 2 arrays $550 $275
900624 GeneChip® Porcine Genome Array contains 6 arrays $1,650 $275
900625 GeneChip® Porcine Genome Array contains 30 arrays $8,250 $275
Rhesus Macaque Arrays
900655 GeneChip® Rhesus Macaque Genome Array contains 2 arrays $850 $425
900656 GeneChip® Rhesus Macaque Genome Array contains 6 arrays $2,550 $425
900657 GeneChip® Rhesus Macaque Genome Array contains 30 arrays $12,750 $425
Rice Arrays
900599 GeneChip® Rice Genome Array contains 2 arrays $850 $425
900600 GeneChip® Rice Genome Array contains 6 arrays $2,550 $425
900601 GeneChip® Rice Genome Array contains 30 arrays $12,750 $425
Soy Arrays
900525 GeneChip® Soy Genome Array contains 2 arrays $850 $425
900526 GeneChip® Soy Genome Array contains 6 arrays $2,550 $425
Sugar Cane Arrays
900626 GeneChip® Sugar Cane Genome Array contains 2 arrays $350 $175
900627 GeneChip® Sugar Cane Genome Array contains 6 arrays $1,050 $175
900628 GeneChip® Sugar Cane Genome Array contains 30 arrays $5,250 $175
Test Arrays
900341 GeneChip® Test3 Array contains 5 arrays $500 $100
900342 GeneChip® Test3 Array contains 30 arrays $3,000 $100
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
Tomato Arrays
Part Product Name Contents Per Array Total Price
900737 GeneChip® Tomato Genome Array contains 2 arrays $350 $175
900738 GeneChip® Tomato Genome Array contains 6 arrays $1,050 $175
900739 GeneChip® Tomato Genome Array contains 30 arrays $5,250 $175
V. vinifera Arrays
900509 GeneChip® V. vinifera Genome Array contains 2 arrays $550 $275
900510 GeneChip® V. vinifera Genome Array contains 6 arrays $1,650 $275
Wheat Arrays
900558 GeneChip® Wheat Genome Array contains 2 arrays $850 $425
900559 GeneChip® Wheat Genome Array contains 6 arrays $2,550 $425
900560 GeneChip® Wheat Genome Array contains 30 arrays $12,750 $425
Xenopus Arrays
900491 GeneChip® Xenopus Genome Array contains 5 arrays $1,500 $300
900492 GeneChip® Xenopus Genome Array contains 30 arrays $9,000 $300
Yeast Arrays
900553 GeneChip® Yeast Genome 2.0 Array contains 2 arrays $350 $175
900554 GeneChip® Yeast Genome 2.0 Array contains 6 arrays $1,050 $175
900555 GeneChip® Yeast Genome 2.0 Array contains 30 arrays $5,250 $175
900256 GeneChip® Yeast Genome S98 Array contains 5 arrays $1,500 $300
900285 GeneChip® Yeast Genome S98 Array contains 30 arrays $9,000 $300
Zebrafish Arrays
900487 GeneChip® Zebrafish Genome Array contains 5 arrays $1,500 $300
900488 GeneChip® Zebrafish Genome Array contains 30 arrays $9,000 $300
Made-to-Order: Select Custom Expression Arrays
900513 GeneChip® B.subtilis Genome Array contains 6 arrays $1,800 $300
900514 GeneChip® S.aureus Genome Array contains 6 arrays $1,650 $275
900515 GeneChip® Barley Genome Array contains 6 arrays $1,800 $300
900516 GeneChip® Human X3P Array contains 6 arrays $2,550 $425
Made-to-Order Array Program
Part Product Name Number of Arrays Per Array Price
510429 GeneChip® Arabidopsis Genome Array (previous generation) 40 +/- 5 arrays $300
510051 GeneChip® E. coli Genome Array (Sense) 40 +/- 5 arrays $300
510332 GeneChip® Human Cancer G110 Array 90 +/- 5 arrays $300
510137 GeneChip® HuGeneFL Array 40 +/- 5 arrays $375
510559 GeneChip® Human Genome U95Av2 Array 40 +/- 5 arrays $375
510462 GeneChip® Human Genome U95B Array 40 +/- 5 arrays $375
510463 GeneChip® Human Genome U95C Array 40 +/- 5 arrays $375
510464 GeneChip® Human Genome U95D Array 40 +/- 5 arrays $375
510465 GeneChip® Human Genome U95E Array 40 +/- 5 arrays $375
510243 GeneChip® Mu11KsubA Genome Array 40 +/- 5 arrays $375
510244 GeneChip® Mu11KsubB Genome Array 40 +/- 5 arrays $375
510318 GeneChip® Tag 3 Probe Array 90 +/- 5 arrays $300
510424 GeneChip® Rat Neurobiology U34 Array 160 +/- 5 arrays $250
510330 GeneChip® Rat Toxicology U34 Array 160 +/- 5 arrays $250
510338 GeneChip® Rat Genome U34A Array 40 +/- 5 arrays $350
510339 GeneChip® Rat Genome U34B Array 40 +/- 5 arrays $350
510340 GeneChip® Rat Genome U34C Array 40 +/- 5 arrays $350
510568 GeneChip® Murine Genome U74Av2 Array 40 +/- 5 arrays $375
510570 GeneChip® Murine Genome U74Bv2 Array 40 +/- 5 arrays $375
510571 GeneChip® Murine Genome U74Cv2 Array 40 +/- 5 arrays $375
GeneChip® Custom Expressi on™ Array Design 100-2187
Part Product Name Number of Arrays Total Price
000356 CustomExpress Design Fee for 90 array order 90 +/- 5 arrays $10,000
000357 CustomExpress Design Fee for 180 array order 180 +/- 10 arrays $7,500
000358 CustomExpress Design Fee for 360 array order 360 +/- 15 arrays $5,000
000359 CustomExpress Design Fee for 540 or greater array order 540 +/- 20 arrays $0
000390 CustomExpress Array - 11um features each $150
000455 Custom Tiling Array - 11um features each $125
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
GeneChip® Custom Expressi on™ Array Design 100-3660
Part Product Name Number of Arrays Total Price
000321 CustomExpress Design Fee for 90 array order 90 +/- 5 arrays $20,000
000322 CustomExpress Design Fee for 180 array order 180 +/- 10 arrays $15,000
000323 CustomExpress Design Fee for 360 array order 360 +/- 15 arrays $10,000
000324 CustomExpress Design Fee for 540 or greater array order 540 +/- 20 arrays $0
000391 CustomExpress Array - 11um features each $230
000454 Custom Tiling Array - 11um features each $200
GeneChip® Custom Expressi on™ Array Design 49-5241
Part Product Name Number of Arrays Total Price
000372 CustomExpress Design Fee for 40 array order 40 +/- 5 arrays $40,000
000373 CustomExpress Design Fee for 80 array order 80 +/- 10 arrays $30,000
000374 CustomExpress Design Fee for 160 array order 160 +/- 15 arrays $20,000
000375 CustomExpress Design Fee for 240 or greater array order 240 +/- 20 arrays $10,000
000395 CustomExpress Array - 11um features each $345
000453 Custom Tiling Array - 11um features each $300
GeneChip® Custom Expressi on™ Array Design 49-7875
Part Product Name Number of Arrays Total Price
000364 CustomExpress Design Fee for 40 array order 40 +/- 5 arrays $50,000
000365 CustomExpress Design Fee for 80 array order 80 +/- 10 arrays $40,000
000366 CustomExpress Design Fee for 160 array order 160 +/- 15 arrays $30,000
000367 CustomExpress Design Fee for 240 or greater array order 240 +/- 20 arrays $20,000
000396 CustomExpress Array - 11um features each $375
000452 Custom Tiling Array - 11um features each $325
GeneChip® Custom Expressi on™ Array Design 400
Part Product Name Number of Arrays Total Price
000407 CustomExpress Design Fee for 380 array order 380 +/- 5 arrays $110,000
000408 CustomExpress Design Fee for 760 array order 760 +/- 10 arrays $105,000
000409 CustomExpress Design Fee for 1520 array order 1520 +/- 15 arrays $95,000
000410 CustomExpress Design Fee for 2280 or greater array order 2280 +/- 20 arrays $85,000
000393 CustomExpress Array - 11um features each $150
000451 Custom Tiling Array - 11um features each $125
GeneChip® Custom Expressi on™ Array Design 169
Part Product Name Number of Arrays Total Price
000415 CustomExpress Design Fee for 155 array order 155 +/- 5 arrays $120,000
000416 CustomExpress Design Fee for 310 array order 310 +/- 10 arrays $115,000
000417 CustomExpress Design Fee for 620 array order 620 +/- 15 arrays $100,000
000418 CustomExpress Design Fee for 930 or greater array order 930 +/- 20 arrays $90,000
000392 CustomExpress Array - 11um features each $175
000450 Custom Tiling Array - 11um features each $150
GeneChip® Custom Expressi on™ Array Design 100
Part Product Name Number of Arrays Total Price
000411 CustomExpress Design Fee for 90 array order 90 +/- 5 arrays $130,000
000412 CustomExpress Design Fee for 180 array order 180 +/- 10 arrays $120,000
000413 CustomExpress Design Fee for 360 array order 360 +/- 15 arrays $105,000
000414 CustomExpress Design Fee for 540 or greater array order 540 +/- 20 arrays $90,000
000397 CustomExpress Array - 11um features each $275
000449 Custom Tiling Array - 11um features each $225
GeneChip® Custom Expressi on™ Array Design 64
Part Product Name Number of Arrays Total Price
000403 CustomExpress Design Fee for 55 array order 55 +/- 5 arrays $140,000
000404 CustomExpress Design Fee for 110 array order 110 +/- 10 arrays $125,000
000405 CustomExpress Design Fee for 220 array order 220 +/- 15 arrays $110,000
000406 CustomExpress Design Fee for 330 or greater array order 330 +/- 20 arrays $95,000
000389 CustomExpress Array - 11um features each $400
000448 Custom Tiling Array - 11um features each $350
GeneChip® Custom Expressi on™ Array Design 49
Part Product Name Number of Arrays Total Price
000399 CustomExpress Design Fee for 40 array order 40 +/- 5 arrays $150,000
000400 CustomExpress Design Fee for 80 array order 80 +/- 10 arrays $135,000
000401 CustomExpress Design Fee for 160 array order 160 +/- 15 arrays $115,000
000402 CustomExpress Design Fee for 240 or greater array order 240 +/- 20 arrays $95,000
000394 CustomExpress Array - 11um features each $425
000447 Custom Tiling Array - 11um features each $375
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
NimbleExpress Arrays
511298 NimbleExpress Array each $650
000469 NimbleExpress Design Fee $2,500
Expression Anal ysis Reagents
Part Product Name Contents Total Price
900542 GeneChip® DNA Labeling Reagent, 7.5 mM sufficient for 30 reactions $300
900585 GeneChip® Blood RNA Concentration Kit sufficient for 30 reactions $120
900586 GeneChip® Globin-Reduction RNA Controls sufficient for 12 reactions $120
900433 GeneChip® Eukaryotic Poly-A RNA Control Kit sufficient for approx. 100 reactions $300
900371 GeneChip® Sample Cleanup Module sufficient for 30 reactions $225
900375 GeneChip® T7-Oligo(dT) Promoter Primer Kit sufficient for 150 reactions $975
900301 Control Oligo B2, 3nM (also included in 900454 and 900457) sufficient for 30 reactions $75
900449 IVT Labeling Kit sufficient for 30 reactions $1,440
900547 IVT cRNA Cleanup Kit sufficient for 30 reactions $120
900431 One-Cycle cDNA Synthesis Kit sufficient for 30 reactions $1,650
900432 Two-Cycle cDNA Synthesis Kit sufficient for 30 reactions $2,400
900686 GeneChip® HT One-Cycle Target Labeling and Control Kit sufficient for 96 reactions $10,120
900687 GeneChip® HT One-Cycle cDNA Synthesis Kit sufficient for 96 reactions $5,280
900688 GeneChip® HT IVT Labeling Kit sufficient for 96 reactions $4,610
900493 GeneChip® Expression 3' Amplification One-Cycle Target Labeling and
Control Reagents
$3,300
900494 GeneChip® Expression 3' Amplification Two-Cycle Target Labeling and
Control Reagents
$4,145
900454 GeneChip® Expression 3' Amplification Reagents - Hybridization
Controls
sufficient for 30 reactions $300
900457 GeneChip® Expression 3' Amplification Reagents - Hybridization
Controls
sufficient for 150 reactions $1,350
900720 GeneChip® Hybridization Wash and Stain Kit sufficient for 30 reactions $625
900721 Stand-alone Wash Buffer A $105
900722 Stand-alone Wash Buffer B $75
Expression Anal ysis WT Reagents
900652 WT Target Labeling and Control Reagents sufficient for 30 reactions $3,900
900673 WT cDNA Synthesis and Amplification Kit sufficient for 30 reactions $1,650
900671 WT Terminal Labeling Kit sufficient for 30 reactions $1,950
900812 WT Double-Stranded DNA Terminal Labeling Kit sufficient for 30 reactions $950
900813 WT Double-Stranded cDNA Synthesis Kit sufficient for 30 reactions $1,900
900672 WT cDNA Synthesis and Amplification Kit sufficient for 10 reactions $580
900670 WT Terminal Labeling Kit sufficient for 10 reactions $685
900811 WT Amplified Double-Stranded cDNA Synthesis Kit sufficient for 10 reactions $2,100
Expression Anal ysis Accessories
900223 Expression Analysis Technical Manual $65
DNA Analysis
GeneChip® Human Mapping 10 K System
Part Product Name Contents Per Array Total Price
900540 GeneChip® Human Mapping 10K 2.0 Xba Array contains 30 arrays $5,550 $185
900446 GeneChip® Human Mapping 10K Xba 131 Array contains 30 arrays $10,500 $350
900441 GeneChip® Human Mapping 10K 2.0 Xba Assay Kit sufficient for 30 reactions $1,500
900534 Affymetrix PCR Primer 001 sufficient for 100 reactions $100
900548 GeneChip® Human Mapping 10K 2.0 Training Kit $2,900
000386 GeneChip® Human Mapping 10K Training $2,500
GeneChip® Human Mapping 100K System
900518 GeneChip® Human Mapping 50K Xba Array contains 30 arrays $6,300 $210
900523 GeneChip® Human Mapping 50K Hind Array contains 30 arrays $6,300 $210
900520 GeneChip® Human Mapping 50K Xba Assay Kit sufficient for 30 reactions $1,500
900521 GeneChip® Human Mapping 50K Hind Assay Kit sufficient for 30 reactions $1,500
900549 GeneChip® Human Mapping 50K Xba Training Kit $3,800
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
GeneChip® Human Mappi ng 500K System
Part Product Name Contents Per Array Total Price
900768 GeneChip® Human Mapping 250K Nsp Array contains 30 arrays $14,100 $470
900770 GeneChip® Human Mapping 250K Sty Array contains 30 arrays $14,100 $470
520330 GeneChip® Human Mapping 250K Nsp Array min. 200 array order, each $470
520331 GeneChip® Human Mapping 250K Sty Array min. 200 array order, each $470
900765 GeneChip® Human Mapping 250K Sty Assay Kit sufficient for 30 reactions $1,650
900766 GeneChip® Human Mapping 250K Nsp Assay Kit sufficient for 30 reactions $1,650
900753 GeneChip® Human Mapping 250K Nsp Assay Kit sufficient for 100 reactions $5,500
900754 GeneChip® Human Mapping 250K Sty Assay Kit sufficient for 100 reactions $5,500
900786 GeneChip® Mapping 500K Nsp Training Kit $4,800
GeneChip® CustomSeq™ Resequencing Arrays
Part Product Name Contents Total Price
000527 CustomSeq Resequencing 50kb Array Design Fee for 1 wafer order 155 arrays $10,000
000528 CustomSeq Resequencing 50kb Array Design Fee for 2 wafer order 310 arrays $7,500
000529 CustomSeq Resequencing 50kb Array Design Fee for 4 wafer order 620 arrays $4,500
000530 CustomSeq Resequencing 50kb Array Design Fee for 6 wafer order 930 arrays $0
511445 CustomSeq Resequencing 50KB Array (1st Lot) each $150
000505 CustomSeq Resequencing 100kb Array Design Fee for 1 wafer order 90 arrays $15,000
000506 CustomSeq Resequencing 100kb Array Design Fee for 2 wafers order 180 arrays $10,000
000507 CustomSeq Resequencing 100kb Array Design Fee for 4 wafers order 270 arrays $5,000
000508 CustomSeq Resequencing 100kb Array Design Fee for 6 wafers order 540 arrays $0
511336 CustomSeq Resequencing 100KB Array (1st Lot) each $225
000509 CustomSeq Resequencing 300kb Array Design Fee for 1 wafer order 45 arrays $20,000
000510 CustomSeq Resequencing 300kb Array Design Fee for 2 wafers order 90 arrays $15,000
000511 CustomSeq Resequencing 300kb Array Design Fee for 4 wafers order 180 arrays $10,000
000512 CustomSeq Resequencing 300kb Array Design Fee for 6 wafers order 270 arrays $0
511337 CustomSeq Resequencing 300KB Array (1st Lot) each $325
900447 GeneChip® Resequencing Reagent Kit sufficient for 30 reactions $850
520016 GeneChip® SARS Resequencing Array each $300
511300 GeneChip® Mitochondrial Resequencing 2.0 Array each $150
Instrument and Software Systems
GeneChip® Instrument Systems
High Throughput Scanner
00-0172 GeneChip® HT Scanner $325,000
Complete Instrument System
Part Product Name Contents Total Price
00-0185 GCS 3000 MegAllele System, NA $279,000
00-0212 GeneChip® Scanner 3000 7G System, NA $199,000
00-0217 GCS 3000 7G w/Workstation and AutoLoader, NA $219,000
00-0162 GeneChip® Array Station, NA $250,000
Scanner System wi th Workstation
00-0211 GeneChip® Scanner 3000 7G w/Workstation $146,000
00-0214 GA2500 to GCS3000 7G Upgrade $120,000
00-0215 GCS 3000 7G w/Workstation and AutoLoader $165,000
GeneChip® System Components
00-0183 GCS 3000 MegAllele Genotyping 7G Upgrade $75,000
00-0205 GCS 3000 7G Field Upgrade $10,000
00-0206 GCS 3000 7G MegAllele Genotyping 4C Upgrade $65,000
00-0210 GeneChip® Scanner 3000 7G $140,000
00-0223 GCS 3000 MegAllele Genotyping Upgrade for S/N ?547 $65,000
QC Toolbox
00-0225 QC Toolbox Software Kit, Version 2 $2,500
Node System
00-0104 GCS 3000 Node U.S./Canada $69,000
Fluidics Station 450
00-0079 Fluidics Station 450 $55,500
00-0081 Fluidics Station 450 Upgrade U.S./Canada $20,000
Hybridization Oven 640
800138 Hybridization Oven 640 (110V) $7,500
800139 Hybridization Oven 640 (220V) $7,500
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
Effective: Jan 2006
US Dollar
Academic Tier 3
Affymetrix Price Sheet
Probe Array Cartri dge Carriers
Part Product Name Contents Total Price
90-0356 GeneChip® Probe Array Cartridge Carriers Red (qty 2) $69
90-0357 GeneChip® Probe Array Cartridge Carriers Green (qty 2) $69
90-0358 GeneChip® Probe Array Cartridge Carriers Purple (qty 2) $69
90-0359 GeneChip® Probe Array Cartridge Carriers White (qty 2) $69
AutoLoader
Part Product Name Total Price
00-0179 2D Handheld Barcode Reader $975
00-0093 External Barcode Reader Holder $275
00-0094 AutoLoader Carousel $975
00-0111 Uninterruptible Power Supply, NA $2,900
00-0129 AutoLoader Upgr w/EBR-GCS 3000 S/N 502 $25,000
00-0090 AutoLoader Upgrade with EBR & Holder $25,000
Affymetrix® Software Solutions
Software Solutions
Acquisition and Analysis
Part Product Name Description Total Price
690025 Microarray Suite-Software License (5.1) 1 seat, perpetual license $4,200
690037 Full Application Package annual licenses $4,000
690038 Genotyping Application Package annual licenses $2,000
690039 Expression Application Package annual licenses $2,200
00-0126 Full Application Package with Computer annual licenses $8,000
00-0127 Genotyping Application Package with Computer annual licenses $6,000
00-0128 Expression Application Package with Computer annual licenses $6,200
Management Storage Soluti ons
690035 GeneChip® Operating Software Server Basic Package annual licenses $45,000
800143 LIMS Server Hardware Standard $32,000
900328 MicroDB™ Software 1 seat, perpetual license $5,600
Data Mining Soluti ons
690043 Data Mining Tool 3.1 (GCOS) annual license $2,200
690045 Data Mining Tool 3.1 (GCOS) 1 seat, perpetual license $5,600
690004 Data Mining Tool 3.0 (MAS) 1 seat, perpetual license $5,600
External Developer Program
Part Product Name Description Total Price
690050 Commercial Software Developer's Kit geographic license annual subscription $10,000
690033 GCOS Development Server Software geographic license annual subscription $9,800
690034 GCOS Development Client Software $1,000
000349 Software Consulting Services per hour $300
000350 Software Training per hour $300
Software Manual s
700293 Microarray Suite User's Guide $65
700338 LIMS Installation and Administration Guide $65
700339 LIMS User's Guide $65
700233 Data Mining Tool User's Guide $65
700480 MicroDB User's Guide $50
Software Combi nation Packages
Software Combi nation Packages
Desktop Packages
00-0180 Dual Processor Instrument Control Workstation with GCOS $6,500
Prices subject to change without notice. Prices do not include value added tax or other sales taxes. National delivery costs are not included
PCR core facility
Contacts:
Mark Geraci, MD
Core Director
[email protected]
303-315-0398
Bryan Haugen, MD
Core Co-Director
PCR Director
[email protected]
303-724-3921
Umarani Pugazhenthi
Core Manager
Phone: 303-724 -3965
[email protected]
How to use our core facility……
1. Send the mRNA sequence for the target of interest, marking the exon borders
(if known) to [email protected] via email.
2. We will design the primers/probe and send you the optimal set for real time PCR. You then blast the
probe sequence for specificity.
4. We will place the order and notify you by email when it is received (approximately 7~10 days from
ABI). Pl will provide the speed type for charging.
5. You will need to provide one of the following in order to optimize the primers/probe and to set up a
standard curve for your assay:
a) Quantitated riboprobe (absolute standard)
b) RNA from source with known expression of gene (relative standard)
c) DNA (absolute PCR standard)
6. When your test samples (RNA in water ~ 1 ug/ul) are ready, contact Uma @ 303-724 3965 to set up a
date and time for sample drop off.
7. The results of your experiment include the following: Plots showing the amplification of target and
normalizing genes, the standard curve and quantities of target genes normalized to control genes.
8. Please send a copy of your publications for our record.
Pricing :
Effective 07-01-2008
Cancer Center Non member
Member Pricing Pricing
RNA Duplicate $13 $17
DNA Duplicate $ 9 $13
rRNA Control $17 $23
Standard Curve $110 $174
Optimization $123 $ 205
Plate Run $ 91 $170
RNA Extraction-5 samples $157 $284
RNA Extraction-10 samples $188 $341
RNA Extraction-15 samples $218 $396
RNA Extraction-20 samples $248 $ 452
Gene Expression, Microarray & PCR (UCCC)
From: Geraci, Mark
Sent: Monday, November 02, 2009 11:02 AM
a) How is the quality of your measurements evaluated – quality control?
Standard “best Practices for Microarray” criteria
b) What is the turn-a-round time for the service you provide?
About one week, depending on the project size
c) Who documents the data provided and signs off on the data?
Core Manager, Dr. Bifeng Gao
d) Have you had experience providing data for industry?
Yes, extensive
e) Do you have a standard operating procedure manual?
Yes
f) How will you track billing and financial aspects of your core?
Cancer Center support
Gene-Targeting/Viral Vector Core
Contact:
Mark Dell'Acqua, PhD
Core Director
[email protected]
http://www.uchsc.edu/neuroscience/Program/cores.htm
This core has two components:
1. Generation of Gene-Targeted/Transgenic Mouse Constructs (Mark Dell'Acqua, Core B
Director; Brain Parr, Coordinator; Wallace Chick; Research Associate). Neuroscience
Program members interested in generating transgenic, knock-out and knock-in mice
should contact Mark Dell'Acqua. Due to the highly specialized nature of the work only a
small number of gene-targeted/transgenic mouse projects will be under taken at any given
time. Selection of these projects will be based on proposals from investigators that will be
evaluated by the Core B advisory panel (Wallace Chick, Brian Parr, Trevor Williams,
Mark Dell'Acqua, and Diego Restrepo). Please contact Core B director Mark Dell'Acqua
for more details.
2. Generation of Viral Vectors for Infection of Neurons/Glia (Jerry Schaack, Coordinator).
This aspect of the core is open for business. Individuals should contact Jerry (Jerry
Schaack).
This core is not open to the general university community at this time (it is open only
Neuroscience Program members on a case-by-case basis). This core provides very specialized,
low throughput, time intensive services on a project-by-project basis so the questions in the
questionnaire are not really applicable. Nonetheless, here is the link to our website:
Grants & Contracts
Contacts:
General Information please call 303-724-0900
Pamela J. Jones Ph.D., Director
303-724-0096
Contracts/Policy
Christine Ahearn, JD
Assistant Director
303-724-0245
[email protected]
PreAward/IS
Jennifer Silverthorne, MPA
Assistant Director
303-724-0093
[email protected]
PostAward/Accounting
Pam Vincent, BS
Assistant Director
303-724-0019
[email protected]
Website:http://www.uchsc.edu/ogc/index.php
About Grants and Contracts
Mission
The mission of Grants and Contracts (G&C) is to provide service to principal investigators and
administrators, for the purpose of obtaining and administering extramural funds in compliance
with University and sponsor guidelines.
Services
Grants and Contracts assists University of Colorado Denver faculty in their efforts to secure
external support for their instructional, research, public service, and scholarly activities. This
includes:
a. budget development;
b. grant application and contract proposal review;
c. contract proposal development, negotiation, and acceptance;
d. subrecipient agreement development, negotiation, and acceptance; and
e. providing advice on sponsor and University requirements.
Grants and Contracts is also responsible after award for compliance with non-technical sponsor
requirements which include:
a. financial reporting and standard invoicing (e.g. does not include non-governmental
clinical trial invoicing which is done by academic departments);
b. providing advice on sponsor and University requirements;
c. acting as a liaison with sponsor contract/financial representatives;
d. managing cash; and
e. acting as a liaison for audits of sponsored activity.
OGC also has responsibility for various systems required by the federal government, for
providing management reports, and for keeping abreast of major grant/contract regulations
changes.
No fees
Can charge for these fees
1. Invoicing contracts
2. Contract Negotiations
3. Training
4. Info Ed
5. All business operations for research administration
6. Research Services
Grants & Contracts
From: J ones, Pamela J
Sent: Friday, November 06, 2009 2:48 PM
a) How is the quality of your measurements evaluated – quality control?
OGC has operating standards that are monitored for all aspects of the three core areas.
These operating standards incorporate general operations standards, General Accounting
Standards Board requirements, National Research Compliance Standards and internal
control/ procedural standards.
b) What is the turn-a-round time for the service you provide?
Turn-Around times are established by type of service, institutional requirements or
business standards
General Operational Service Standards for OGC include but are not limited to:
Proposal Review – paper – 5 days electronic – 12 days
Contract Negotiation – primary and subs – depending upon complexity – 6-8 weeks is the
average
Project Set-Up – average is 5-10 business days after receipt of award unless there are
problems with the award
On-time FSR submissions
c) Who documents the data provided and signs off on the data?
Director, Assistant Directors and Managers
d) Have you had experience providing data for industry?
Yes – to the compliance and sponsor industries
e) Do you have a standard operating procedure manual?
Yes – see website
f) How will you track billing and financial aspects of your core?
OGC is funded via Fund 10 and F&A from sponsored projects – we do not bill for our
services.
High-Throughput Genome Sequencer
Contact:
David Pollock, PhD
Department of Biochemistry & Molecular Genetics
Mail Stop 8101
Research Complex 1 South
12801 17th Ave., Room #10111
PO Box 6508
Aurora, CO 80045
[email protected]
http://www.evolutionarygenomics.com/CCG/CCG.html
The Lab:
Protein sequence, structure, and functional evolution; Evolutionary genomics; Adaptive co
evolution and ancestral reconstruction; Evolution of mitochondrial genomes; Evolutionary
theory; Testing evolutionary predictions through mutagenesis and directed evolution
Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories by
A. P. Jason de Koning, Wanjun Gu and David D. Pollock, Molecular Biology and Evolution
(available online September 2009). Complex models, way fast. Check it out.
New:
We have developed a code package called PLEX (Phylogenetics, Likelihood, Evolution, and
compleXity), written by Jason de Koning, Wanjun Gu, and David Pollock. The approach is
described in the above paper. Code is under continued development, with versions available
upon request.
Evidence for an ancient adaptive episode of convergent molecular evolution, Todd A. Castoe, A.
P. Jason de Koning, Hyun-Min Kim, Wanjun Gua, Brice P. Noonan, Gavin Naylor, Zhi J. Jiang,
Christopher L. Parkinson and David D. Pollock, PNAS, 2009
See PNAS commentary by Scott Edwards, "Natural Selection and Phylogenetic Analysis"
(May/June 2009).
Convergence/Divergence code from Castoe et al 2009 for use with codeml
See addendum/commentary by Castoe, de Koning, and Pollock (preprint available upon request)
We're looking for postdoc applicants for computational biology fellowships working on protein
evolution (Pollock) or transcription factor binging site (TFBS) evolution (Pollock and Kechris).
Please contact David Pollock for details. This is an ongoing search for excellent candidates.
List of Services & Fees:
In house pricing for a full plate of FLX or Titanium sequencing costs $10,000. Please contact us
for additional services and pricing.
High-Throughput Sequencing Core
From: Pollock, David
Sent: Monday, October 12, 2009 9:13 AM
Information for Dick Traystman r.e. High-Throughput Sequencing Core (HTSC run by
the Consortium for Comparative Genomics within the UCCC DNA Sequencing Core)
a) How is the quality of your measurements evaluated – quality control?
All sequencing runs include an internal set of quality control sequences which are
evaluated in each run. Also, the sequencing output (number, length, and sequence
quality scores) of the empirical data provide a measure of the quality of each
sequencing run
b) What is the turn-a-round time for the service you provide?
The turn-a-round time for a sample submitted according to the requirements
outlined in the HTSC core guidelines and sequenced on a full plate of Titanium or
FLX, with no major problems arising, is 2-3 weeks. If a shotgun library is needed,
an additional week should be added to the turn-a-round time. If sequencing is
requested on a smaller scale, i.e. 1/8 plate, ¼ plate or ½ plate, the timing will
depend not only on the sample submitted but also the rest of the samples that are
needed to fill the plate. Any delays in filling the plate translate to delays in
sequencing. We plan according to the samples that are being submitted and delays
due to unfilled plates should be low.
c) Who documents the data provided and signs off on the data?
The HTSC saves all sequencing data from the 454 sequencing process. The data
files are labeled, and sent to HTSC users. An internal record is kept of each
sample sequenced, the date the data is sent to the customer, invoicing and
payment details, and the name and storage location of the data file.
d) Have you had experience providing data for industry?
Yes, we have provided sequencing services to industrial organizations.
e) Do you have a standard operating procedure manual?
We follow the Roche GS FLX & Roche GS FLX Titanium Sequencing Method
Manuals. If library creation is needed, follow the GS FLX Shotgun DNA Library
Preparation Method Manual or the GS FLX Titanium 20kb and 8kb Span Paired
End Library Preparation Method Manual.
f) How will you track billing and financial aspects of your core?
We have a dedicated accountant from the University of Colorado Cancer Center
who tracks the spending, billing and revenue for the HTSC. We have contact with
him, and are updated regularly on the financial status of our facility. In addition to
this, we keep our own internal records of all financially related aspects of the
HTSC.
List of Services & Fees:
In house pricing for a full plate of FLX or Titanium sequencing costs $10,000.
Please contact us for additional services and pricing.
Website:http://www.evolutionarygenomics.com/CCG/CCG.html
HLA (Histocompatibility) Testing and
Umbilical Cord Blood Bank
ClinImmune Labs and the University of Colorado Cord Blood Bank
ClinImmune Labs, located i n t he B ioscience P ark C enter ne xt t o t he U niversity o f C olorado
Anschutz M edical C ampus i n A urora, C olorado, i s a hi ghly efficient a cademic bus iness t hat
integrates th e h ighest quality la boratory s ervices a nd p roducts w ith its s cholarly mis sion to
contribute t o t he s cience o f an d education ab out s tem cel l t herapy. Our co mpany v iews a v ery
important c omponent of i ts bus iness a s c onsultative. O ur s taff p rovides e ducation and t echnical
advice t o t he r esearch a nd m edical c ommunity on s tem c ell processing a nd s torage,
histocompatibility analysis and sequencing issues.
As an acad emic-based bi otechnology c ompany, ClinImmune Labs is c ommitted to p roviding th e
highest quality s ervice t o our clinical customers bot h i n Denver and t hroughout t he world, t o our
research faculty at the University of Colorado Anschutz and Boulder campuses, stem cell biologists
throughout the U.S, and to the biotechnology companies that reside in the Rocky Mountains.
ClinImmune Labs is accredited by the American Society for Histocompatibility and Immunogenetics
(ASHI), th e College o f American P athologists ( CAP), th e Clinical Laboratory Improvement Act
(CLIA), t he Foundation f or Accreditation of Cellular Therapy ( FACT), and t he AABB ( American
Associations of B lood B anks). A num ber of t he s taff a re bo ard-certified c onsultants in
histocompatibility, diagnostic immunology, allergy and asthma, and pulmonary medicine.
A. Histocompatibility and Immunogenetics Laboratory
Contacts for information or price quotes:
HLA Testing is available for:
• Epitope analysis as part of population studies
• Genetic HLA Disease Association
• Immunotherapy, including vaccine
development
• HPC Transplant
• Pharmacogenetics
Michael Aubrey, MS, CHS
303-724-1313
[email protected]
Linda Cagle, CLDir, CHS
303-724-1315
[email protected]
Brian M. Freed, PhD
Executive Director
[email protected]
Clinically Approved Assays:
• HLA-A, B, Cw, DRB, DQ, DPB1 loci
? Low to high resolution Class I and Class II testing for HLA-A, B, Cw, DRB1,
DRB3/4/5,
DQB1, DPB1
? Low resolution testing for DQA1
? Serological and HLA-A,B testing
• Cylex Immune Function Test, IMMUKNOW®
• HLA Antibody Detection
? Panel Reactive Antibody (PRA)
? Luminex HLA Class I, Class II, and MICA Antibody screen
? Luminex PRA, including HLA Specificity Analysis
? Luminex single antigen beads for allele level Class I, Class II, and MICA antibodies
? Titration/Quantitation studies for transplant immunotherapy protocols
? Flow cross matching for transplant compatibility
? Platelet support panels to assess allo-reactive HLA antibodies and HLA-A,B typing
for selection of matched platelets
Services Provided:
• Initial consultations provided for test selection, cost effectiveness, sample and turn-around
time requirements
• Customized requisitions and clear, concise reports; electronic data transfer
• Additional test interpretation consults upon request
• Analysis of HLA allele frequency
B. University of Colorado Cord Blood Bank
Contact for information or price quotes:
Sabine Stockinger
303-724-1247
[email protected]
The University of Colorado Cord Blood Bank (UCCBB), a major component of ClinImmune Labs,
has a t en year hi story of collecting, processing, banking and distributing umbilical cord bl ood f or
human t ransplantation. UCCBB has c onsented ove r 10,700 w omen a nd ba nked ove r 6,700 c ord
blood units, of which over 500 have been transplanted at 95 different transplant centers in the United
States and abroad. UCCBB is a major provider of Hispanic cord blood units to patients in the United
States, Mexico, Central and South America. UCCBB is a member of t he National Marrow Donor
Program and i s accr edited b y AABB. HRSA awarded UCCBB one o f s ix c ord bl ood c ollection
contracts i n 2006. UCCBB also pr ovides c ord b lood t o s tem c ell i nvestigators i n Michigan, New
York, Tennessee, Washington and Colorado.
Histocompatibility and Umbilical Cord Blood Bank: ClinImmune Labs
and the University of Colorado Cord Blood Bank
Executive Director: Brian M. Freed, Ph.D.
a)
ClinImmune Labs i s a ccredited by t he American Society f or Histocompatibility a nd I mmunogenetics
(ASHI), the College of American Pathologists (CAP), the Clinical Laboratory Improvement Act (CLIA),
the AABB ( American Associations of Blood Banks), and the Foundation for Accreditation of Cellular
Therapy (FACT). All of t hese a ccreditation or ganizations ha ve s trict g uidelines that g overn qu ality
control. ClinImmune Labs requires that each of its programs undergo both internal and external audits on
a regular schedule, including the validation that all reagents and equipment meet strict IQ, OQ and PQ
requirements prior to their use. Testing methodologies and staff are proficiency tested under CAP, SCT,
UCLA an d ASHI. All l aboratory st aff retains cu rrent co mpetency an d cer tifications with o n-going
continuing education.
How is the quality of your measurements evaluated – quality control:
b)
ClinImmune Labs prides itself on c lient satisfaction and meeting t he needs of University of Colorado
clients as well as clients from area wide hospitals, hospitals outside of Colorado, and private industry.
Our turn-a-round times range from 3 to 14 days, depending on the services requested, and are mutually
agreed upon with the clients in our service agreements. Flexible pricing exists for research projects that
are not urgent.
What is the turn-a-round time for the service you provide?
c)
As per our detailed SOPs and depending on the laboratory service required, our medical and laboratory
directors, laboratory supervisors and managers, and quality assurance staff review specific types of data
and at least two reviews are required for sign-off prior to reporting.
Who documents the data provided and signs off on the data?
d)
ClinImmune Labs has a n umber of r esearcher clients f rom i ndustry who r eceive l aboratory ser vices,
cord blood products and electronically transmitted data from us.
Have you had experience providing data for industry?
e)
ClinImmune maintains a detailed quality management pl an and SOP manuals t hat outline GLP, GTP,
and GMP under FDA /CLIA regulatory compliance.
Do you have a standard operating procedure manual?
f)
ClinImmune Labs has a billing staff that tracks the billing of all tests, customizes billing templates, and
develops electronic reports for clients as mutually agreed upon in the service agreement.
How will you track billing and financial aspects of your core?
Histology Core
Contact:
Roberto Gianani, MD
Histology Core Director
Diabetes & Endocrinology Research Center
at the Barbara Davis Center for Childhood Diabetes
303-724-6824
[email protected]
http://www.uchsc.edu/misc/diabetes/DERC/histology.htm
Histology Core
Routine histological services in tissue fixation, processing, sectioning, and staining with
histochemical dyes and immunochemical reagents. Provision of slide and tissue banks of
commonly used tissues or animal models e.g. developmental or NOD disease progression.
Epifluorescence microscopy for acquisition of images and performance of morphometric
analyses.
Confocal microscopy for use by investigators interested in high-resolution fluorescence
microscopy and live cell imaging requiring the use of FRAP and FRET analyses.
In-situ hybridization analyses that include all elements from acquisition and amplification of the
gene of interest, probe synthesis, optimization of hybridization conditions, and performance of
multigene analyses on a moderate scale.
Higher-level microscopy including access to instrumentation and services in Laser Capture
Microscopy, 2-photon confocal microscopy, spinning disk confocal microscopy, Total Internal
Reflectance microscopy, conventional, and immunoelectron microscopy.
Training of fellows and students in morphological and morphometric techniques and
consultation in specific areas including microdissection and single cell microinjection, low-level
computer programming.
Core Personnel
Roberto Gianani, MD (Director) is Assistant Professor, Department of Pathology. Dr. Gianani
is Investigator at the Barbara Davis Center for Childhood Diabetes, UCHSC.
Informatics Core University of Colorado Cancer Center
Contacts:
Jessica Bondy, MHA
Director
303-724-4353
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/informatics/index.aspx
Mission
To increase the efficiency of conducting clinical/ translational trials by insuring the accessibility,
integrity, and security of research databases.
The University of Colorado Cancer Center Informatics Core, located on the 6th Floor of
Building 500 on the Anschutz Medical Campus in Aurora, was established to work with
researchers and clinicians to design, implement and maintain information technology
applications that support the Cancer Center research enterprise.
• We build databases and integrate them with dynamic websites or client/server front ends
• We provide workstation support and network and server administration
We have developed applications in the areas of clinical trials registration, specimen tracking,
clinical trials pathology and prevention and control. In addition, we have developed databases
containing clinical data (prognostic clinical factors, therapies, toxicities, response to treatment
and outcomes) for the Lung SPORE and for breast cancer.
Informatics Core Services
Researchers who have informatics projects have a choice of funding part of an FTE or
purchasing services on an hourly basis. When the informatics project is substantial and planned,
funding part of an FTE is the preferred approach, since projects funded under FTEs will be given
higher priority. When the project is small or unanticipated, the hourly charge back is appropriate.
We offer members discounted hourly rates.
We offer the following services
1. Network administration / workstation support: web-, database-, file- and print server
administration, including backups, access, and security. Workstation configuration and
maintenance.
2. Website development: analysis and development of dynamic or static websites
3. Database design and development: analysis and development of table structures for
appropriate security and performance.
4. Data quality assurance: loading and querying databases to ensure timely and proper data
collection.
5. Report development: analysis and development of static or parameterized reports.
How to order services
To order services, you will need to consult with either the Core Director or Core Manager by
telephone or email. See the contact panel on the right for phone and email information.
Prices
The cost for core services is based time spent, either as part of an FTE or as an hourly fee. For an
estimate of the time your project is likely to require, contact the Core Manager (See the contact
panel on the right for phone and email information).
Service Member
Non-
Member
Application Development & Support $84 $97
Network Administration & Workstation Support:
Complete administration of file and print servers
(backups, access, security). Ensures that workstations
are configured for user's needs.
$67 $78
Prices valid July 1, 2008-June 30, 2009
Informatics Core (UCCC)
From: Bondy, J essica
Sent: Thursday, October 01, 2009 5:09 PM
a) How is the quality of your measurements evaluated – quality control?
N/A
b) What is the turn-a-round time for the service you provide?
N/A
c) Who documents the data provided and signs off on the data?
N/A
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
We write SOPs for the applications we develop.
We don’t really have an SOP for our own work.
f) How will you track billing and financial aspects of your core?
Much of our work is done on an FTE basis. Only about 7% of our budget
comes through our service center. This work is billed hourly. We use a time
tracking system that was developed by the CSPH’s DISC (Development
Informatics Service Center) for the CBC (Colorado Biostats Consortium).
Website (includes services):http://www.uccc.info/for-healthcare-
professional/cancer-center/cores/informatics/index.aspx
Fees:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/informatics/prices.aspx
Institutional Animal Care and Use Committee
(IACUC)
Contacts:
Mark Douse, PhD
303-724-1057
[email protected]
Website:http://www.uchsc.edu/animal/iacuc_index.htm
IACUC
The Institutional Animal Care and Use Committee (IACUC), mandated
by the Health Research Extension Act (HREA) of 1985 and the Animal
Welfare Act (AWA), is responsible for the oversight and evaluation of
the Institution's animal care and use program, procedures and facilities,
ensuring that they are consistent with the recommendations in the
Guide for the Care and Use of Laboratory Animals, Animal Welfare
Regulations and PHS Policy.
The IACUC is an Institutional level committee, the direct representative
of the Chancellor of the University of Colorado Denver and comprises
veterinarian, scientist and non-scientist members, as well as at least
one member who represents the general community interests in the
proper care and treatment of animals, and, is not affiliated in any way
with the Institution other than as a member of the Committee.
AAALAC Accreditation File Number:
00235 (re-approved 10/26/2006)
PHS Animal Assurance of Compliance
#A 3269-01 (expires 07/31/2011)
USDA License:
#84-R-0059 (expires 11/07/2010)
IACUC
From: Douse, Mark
Sent: Monday, November 02, 2009 4:35 PM
Questions:
a) How is the quality of your measurements evaluated – quality control?
Response: The UC Denver Institutional Animal Care and Use Committee
(IACUC) adheres to all federal laws, regulations, and guidelines established by
government and professional groups to protect research animals. The federal law
(Animal Welfare Act) is enforced by the USDA, who performs unannounced site
visits of our Animal Program once or twice a year. We are also voluntarily
accredited by the Association for the Assessment and Accreditation of Laboratory
Animal Care, International. This international oversight body provides an
additional review of our entire Animal Program and holds UC Denver to a higher
standard than is required by the rigorous governmental laws and regulations.
AAALAC performs a site visit of our Animal Program once every three years.
This site visit is very extensive and intensive and is performed by four
professionals over a four day time period. Finally, there are a number of
interested Investigators who do not hesitate in providing feedback on quality
control.
b) What is the turn-a-round time for the service you provide?
Response: The IACUC meets once per month for review of new protocols; the
average turnaround time for final IACUC approval is 40 days and includes
IACUC and Investigator response time. An IACUC sub-committee meets once
every two weeks to review amendments to an existing IACUC approved protocol;
the typical turnaround time is 2 to 3 weeks.
c) Who documents the data provided and signs off on the data?
Response: Director, IACUC Office; IACUC Co-Chairs; Vice Chancellor for
Research
d) Have you had experience providing data for industry?
Response: Yes
e) Do you have a standard operating procedure manual?
Response: Yes
f) How will you track billing and financial aspects of your core?
Response: We do not currently bill for our services. Per Diem and all other
charges are billed through the Office for Laboratory Animal Resources (OLAR).
Interdisciplinary Transcranial Magnetic Stimulation (TMS)
Director: Benzi Kluger, MD
Preferred contact: email
[email protected]
Services:
Review of proposals using TMS, assistance with preparation of IRB materials for TMS projects,
training in the use of TMS and stereotactically guided TMS, performance of TMS on human
subjects for research and therapeutic purposes.
Fees:
TMS conducted on human subjects will be $200/hour for internal users and $400/hour for
investigators outside of the University of Colorado. Other services and discounts for collection of
pilot data or junior investigators may be discussed with Dr. Kluger and the steering committee.
Interdisciplinary Trancranial Magnetic Stimulation
From: Kluger, Benzi M
Sent: Monday, November 09, 2009 1:49 PM
a) How is the quality of your measurements evaluated – quality control?
Transcranial magnetic stimulation (TMS) stimulates and modulates cortical activity. This is
most easily measured by examining motor response to motor cortex stimulation with EMG.
Motor thresholds and motor evoked potentials are routinely performed even when the focus
of TMS is a non-motor region to ensure adequate stimulation.
b) What is the turn-a-round time for the service you provide?
For studies or indications with IRB approvals TMS can be provided within a few weeks.
EMG data for motor studies can be provided within a week of TMS sessions.
c) Who documents the data provided and signs off on the data?
Dr. Benzi Kluger, Director of the Interdisciplinary TMS Laboratory, will review all
protocols prior to TMS, as well as data collection procedures with the PI of the study and
TMS technician. TMS technicians will provide and document data. In cases of inconsistent
data, Dr. Kluger will review the results and records of TMS sessions.
d) Have you had experience providing data for industry?
No, but we are willing to provide TMS services to industry including measures of cortical
excitability, Trancranial direct current stimulation (tDCS) and repetitive TMS treatments.
e) Do you have a standard operating procedure manual?
Yes, but only for depression treatments and current TMS studies. Operating procedures
will be written up on an as needed basis for other protocols.
f) How will you track billing and financial aspects of your core?
The TMS laboratory has its own cost center in the Department of Neurology which can
track billing and sources of funding.
Laboratory Science Core
Contacts:
Elizabeth Connick, M.D.
Director
[email protected]
303-724-4930
Website:http://www.uchsc.edu/ccfar/cores/immunology.htm
The mission of the Colorado CFAR Laboratory Science Core is to provide state-of-the-art tools,
technical support, and training in laboratory-based techniques as well as to identify unmet needs and
fill gaps in laboratory services for D-CFAR members and other investigators to support and promote
research on pathogenesis, treatment, and prevention of HIV-1 infection and its complications.
More information on the Flow Cytometry Unit and an Immunohistopatholgy Unit
can be found by clicking on the links.
Laser Capture Shared Core Service
Contacts:
Wilbur Franklin, MD, PhD
Director
[email protected]
303-724-3080
Jennifer Richer, PhD
Co-Director
[email protected]
303-724-3735
M. Scott Lucia, MD
Co-Director
[email protected]
303-724-3470
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/pathology/laser-
capture/index.aspx
What is Laser Capture Microdissection (LCM)?
Laser capture microdissection (LCM) is technique for obtaining pure cells from specific tissue
sections. A machine uses a laser beam to activate a special transfer film. The film bonds to cells
that have been identified and targeted by microscopy.
Laser capture microdissection (LCM) is a technique that allows pathologists to lift specifically
targeted cells from a section of cell tissue, leaving behind unwanted cells that could contaminate
the molecular purity of subsequent analysis. This technology, which was developed in the late
1990s at NIH in collaboration with bioengineering and cancer pathology groups, is precise,
accurate and automated.
LCM uses a special laser and film, which absorbs the laser energy and leaves the
macromolecules undamaged. Starting tissue can be fixed, embedded in paraffin or frozen.
Why Use LCM in Gene Expression Studies?
To reveal accurate, cell-type specific expression profiles that otherwise might be obscured in
mixed cell samples.
Technology isolates homogeneous populations of cells from tissue sections
• Cells can be collected based on morphologic or immunohistologic features
• Machine can recognize color (stains) or fluorescence
• Cells are harvested for DNA, RNA or Protein analysis
AutoPix LCM Machine
The AutoPix allows you to select all cells or areas to be captured automatically, instead of
manual firing.
• You can train the machine to recognize cells based on morphology or
immunohistochemical or fluorescent staining. We can also store customized recognition
programs.
• The machine's optical upgrade provides improved visualization of non-cover-slipped
tissue sections, allowing for better cell-type recognition.
• You can focus the laser to capture single cells, or use a broader area to capture cell
clusters.
• We provide technical assistance and reagents for dealing with LCM-captured material for
subsequent molecular analysis.
Laser Capture Prices
The Laser Capture Core offers discounted prices to University of Colorado Cancer Center
Members. Non-members can also use the facilities.
Pricing Structure for Cancer Center Members
Member
Price
Non-Member
Price
Service Description
1 Initial Introduction/consultation ($0) $294
2
LCM initial training session on slides of investigator
(feasibility/pilot experiments)
$222 $394
3 Machine Usage LCM $107 $228
4 H & E Staining Frozen $19 $54
4a H & E Staining FFPE $28 $62
5 RNA Isolation $7 $77
6 RNA Amplification Real Time PCR $159 $896
7 Burn CD $1 $1
8 Paraffin Embedded - Amplification $287 $1,025
9 Paraffin Embedded - QC $72 $177
10 Nanochip $21 $56
11 Picochip $23 $57
12 Turbo Labeling $69 $208
13 Paradise WT $51 $329
14 Paradise qrt PCR $205 $735
Prices effective 7/1/08 thru 6/30/09
Laser Capture Shared Core Service
From: Franklin, Wilbur
Sent: Friday, November 20, 2009 6:41 AM
a) How is the quality of your measurements evaluated - quality control?
The answer to this question depends on what is being evaluated. The Pathology Core is
responsible for processing tissues and the endpoint of this tissue processing is frequently
an excellent histologic preparation. Every sample that is prepared by the laboratory for
clinical work and most of the samples that are used for research are evaluated by a
certified pathologist, and the quality of the preparation is commented upon. These
records are open for inspection by CAP inspectors, who regularly recertify the laboratory.
b) What is the turn-a-round time for the service you provide?
This again depends on which service is involved. The animal tissues that we process
generally are not an emergency and so those are queued, and depending on the workload
in the Pathology Core, the queue may be a few days to a few weeks. Also, tissue
microarrays depending on the number of tissues being evaluated may require 2 or 3
weeks. On the other hand, we operate a molecular service that can generate mutational
results with a turn-around-time of 48-72 hours, and as part of the lab, a CALGB protocol
requires predictive testing for KRAS to be completed within 72 hours of receipt of the
specimen.
c) Who documents the data provided and signs off on the data?
For CLIA certified testing, all reports are signed by the Director. For research in the
Core Laboratory, tissues are returned to the investigator, and investigators are responsible
for interpreting their own histologic data.
d) Have you had experience providing data for industry?
The laboratory is responsible for validating methods and biomarkers for the FDA, and is
submitting data as part of a corporate initiative to obtain FDA approval for certain tests.
The answer to this question is yes.
e) Do you have a standard operating procedure manual?
We have standard operating procedures for all components of the core laboratories and
these are available on request. In fact, the Principal Investigator was responsible for the
preparation of a National Manual of Operations for the NCI Cooperative Group Banking
Committee. This document is also available in the Core.
f) How will you track billing and financial aspects of your core?
This depends on which part of the core is being queried. For the Cancer Center
Pathology Core, the PRA responsible for histology in that core tracks services and
expenses. For the SPORE, services are covered in the grant and again, the annual
progress reports document the output of the laboratory as well as more detailed
accounting through our finance administrators. Finally, the Southwest Oncology Group
Solid Tumor Bank is tracked in real time on a web site that maintains an inventory of
specimens accessioned into the core. We also track usage of the specimens and scientific
productivity through an inventory of published reports.
Light Microscopy
Contacts:
Steven Fadul
PRA
303-724-4508
[email protected]
Website:http://www.uchsc.edu/lightmicroscopy/
Bill Betz
Director
303-724-4502
[email protected]
General: Researchers are trained to use the microscopes
and image acquisition software themselves, with staff
assistance when necessary to ensure collection of high
quality images. Data can then be processed off-line for
export into the required format.
New Users: You will need to be trained to use the
microscope(s) and related instruments. You also must
create an account for charges. Contact Steve Fadul at the
facility to make arrangements.
Voice: (303) 724-4508. Email: [email protected]
Trained Users: Use the on-line Booking Page to sign up.
Special Needs
? Need a hefty block of time for your project?
We can help, especially after NIH grant deadlines
(March, July, and November are best).
? Need speci al equipment, like patch clamp,
bath perfusion, stage warmer? We can help with
these things, too.
Please acknowledge the facility appropriately in
publications, and notify us. When we apply for
equipment grants, we need to demonstrate the
usefulness of the facility.
General: We offer different kinds of pricing
(contact us for details). The simplest is by-the-
hour billing. We are especially interested in
working with grant applicants to have support
funds requested on grant applications for projects
that will involve this facility.
Our aim is to train users to be as independent as
possible in using the instruments.
Cancellation policy: Reservations cancelled less
than 24 hours in advance will be billed unless
someone else signs up.
The facility is open to researchers outside UCD
by special arrangement.
Introductory
Rates
? Zeiss 510 NLO confocal microscope: $35/hr
? Other microscopes: $25/hr
? Fuji Pictography prints: see the Manager for
assistance
? These rates are subj ect to change
Light Microscopy
From: Betz, Bill
Sent: Monday, November 02, 2009 10:55 AM
a) How is the quality of your measurements evaluated – quality control?
Feedback from users, regular meetings between director and staff
b) What is the turn-a-round time for the service you provide?
Usually immediate access to microscopes
c) Who documents the data provided and signs off on the data
Not sure what you mean- the users are trained to use the microscopes, and take their data
with them.
d) Have you had experience providing data for industry?
Very little
e) Do you have a standard operating procedure manual?
Web site
f) How will you track billing and financial aspects of your core?
The staff provides regular updates on all billing, machine use, etc.
Machi ne Shop
Contacts:
Ulli Bayer, PhD
Director
303-724-3610
[email protected]
Michael Hall, PhD
303-724-1335
[email protected]http://www.uchsc.edu/neuroscience/Program/cores.htm
The Neuroscience core machine shop is located in room NG003 on the ground floor of Building
500 (northwest corner) at the Fitzsimons campus of UCD/HSC. The shop's equipment and staff
are there to meet the custom machining needs of the faculty, staff and students of the
Neuroscience program and the university research community.
The shop machinery includes:
• 2 manual milling machines with 9" x 42" tables
(1 with digital readout)
• 1 CNC milling machine (full 3-axis automation)
• 2 precision lathes
• 1 surface grinder
• 1 wood/metal-cutting band saw
• 1 table saw
• 1 chop saw
• 2 grinding machines
• 1 drill press
• 1 6" belt sander
• 1 52" shear
• extensive tooling & precision measuring devices
The shop stocks a modest amount of material (acrylic and other
plastics, aluminum, brass, hardware) so most projects can be
completed using material on-hand.
The shop is staffed by one machinist 24 hours/week although
there are currently no routine hours of operation. Contact
Michael Hall at 303-724-1335 or, preferably, by e-mail at
[email protected] to discuss a project, to arrange a
meeting or with questions
Billing is based upon an hourly shop rate plus material cost and charges are levied against a
university speed-type account. At present there is no mechanism for billing outside of the
university system.
Shop services: custom design and production of equipment for scientific experimentation. The
shop is equipped with machining equipment to produce equipment made from plastics,
aluminum, steel or stainless steel.
Fees: The shop rate is $75.09/hour for design and machining services. Material costs are
additional.
Machine Shop
Ulli Bayer, PhD
From: Hall, Michael
Sent: Thursday, October 08, 2009 9: 16 AM
a) How is the quality of your measurements evaluated – quality control?
The machine shop produces products that adhere to the specifications of the design that is
dictated by the end-user/investigator. The requirements may be very exacting (0.0005”)
or less strict. Products are made to the users’ requirements, if known, or they may be
determined as the design is created in conjunction with shop staff. The end-user of the
product must be satisfied with the product they receive or it will be modified or made
again.
b) What is the turn-a-round time for the service you provide?
Turn-around-time is dictated by the complexity of the project requested and the current
work load in the shop. Work is generally dealt with on a first-come-first served basis,
however, the shop staff does strive to meet the requirements of the person requesting the
work and occasionally is able to accelerate the completion of a particular project. Please
provide as much advanced notice of your needed-by date as possible.
c) Who documents the data provided and signs off on the data?
The shop machinist sees that all requirements for product precision are met.
d) Have you had experience providing data for industry?
Not to date, all projects have been at the request of University investigators.
e) Do you have a standard operating procedure manual?
No. The use of shop machinery is restricted to individuals trained in their use.
f) How will you track billing and financial aspects of your core?
Billing is based upon an hourly shop rate plus material cost. This is recorded by the
machinist and charges are levied against a university speed-type number. At present there
is no mechanism for billing outside of the university system.
Shop services: custom design and production of equipment for scientific experimentation.
The shop is equipped with machining equipment to produce equipment made from
plastics, aluminum, steel or stainless steel. Please see the website for a listing of shop
machinery.
Fees: The shop rate is $75.09/hour for design and machining services. Material costs are
additional.
URL:http://www.uchsc.edu/neuroscience/Program/cores.htm - core D is the machine core.
[Department of Anesthesiology Clinical Research and Development]
Contacts:
Uwe Christians
University of Colorado Denver
Bioscience East, Suite 100
1999 North Fitzsimons Parkway
Aurora, Colorado 80045-7503
Phone: 720 961 4489 (direct)
303 724 5670 (office)
Fax: 303 724 5662
[email protected]
Website:http://www.uchsc.edu/bioanalytics/
The CNRU Mass Spectrometry Core is not an institutional core, but is jointly managed by the Clinical
Nutrition Research Unit (Director: Dr. J.O. Hill) and the Department of Anesthesiology, Clinical Research
& Development. The CNRU Mass Spectrometry Core’s mission is to provide a state-of-the-art laboratory
facility, expertise in mass spectrometry technologies and assays as well as to provide education, training
and consulting to investigators with projects relevant to the field of nutrition. As exemplified over the last
years, the Core has continued to develop diagnostic tools to predict disease and monitor the progress and
treatment of disease. In addition, we have provided comprehensive instruction for interested CNRU
investigators in order to increase their proficiency in our highly complex technologies and
instrumentation.
The Core has been, is and will be specifically involved in:
A. measuring enrichments in biomolecules used to follow metabolism and to determine substrate
turnover rates
B. gas isotope ratio determinations for total energy expenditure (TEE) and total body water (TBW)
C. gas isotope ratio determinations for substrate oxidation
D. biochemical profiling (metabolomics) using magnetic resonance spectroscopy and mass
spectrometry
E. proteomic profiling (proteomics) and mass spectrometry-based quantification of proteins
F. quantitative mass spectrometry of small molecules (drugs and endogenous compounds) and
hormones
G. drug metabolism studies
H. pharmacokinetics
In addition to the quantification of small molecule drugs, the CNRU Mass Spectrometry Core offers a
range of assays for targeted and non-targeted analysis of molecular markers and drug metabolism
services. The available assays and strategies are listed in Appendices I (endogenous compounds and
molecular markers) and II (drug metabolism).
The CNRU Mass Spectrometry Core has the track record, experience and infrastructure to assist basic
science departments to bring drug candidates into clinical development and to serve as a resource for
patient research in clinical departments, to serve as a resource for the pharmaceutical industry and to
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Mass Spectrometry Core (CNRU)
function as a interface between the University of Colorado Denver and Colorado biotech industry. The
CNRU Mass Spectrometry Core has experience with all stages of drug development including direct FDA
interactions. This core is a unique facility since it combines quantitative mass spectrometry (drugs, drug
metabolites, other small molecules and large molecules, endogenous compounds), metabolic and protein
profiling technologies under one roof and thus is capable of complex projects ranging from
pharmacokinetics to the development and qualification of molecular markers and novel diagnostic tools.
Core structure:
Regulatory Compliance
The Mass Spectrometry Core is 21 CFR part 58 compliant (FDA good laboratory practice) and is audited
on a regular basis by industry sponsors. The Principal Investigator’s laboratory is also accredited by the
College of American Pathologists (CAP, LAP#7176093, AU-ID: 1374604, last audit November 2008).
Dr. J elena Klawitter (Quality Assurance Officer) assists the Core Director in achieving and maintaining
GLP compliance and CAP accreditation. Drs. Klawitter and Christians were also awarded a Master in
Research Quality Assurance by the British Association of Research Quality Assurance.
Instrumentation
The following resources are currently available:
- 1 GC/MS (Agilent 5973N MS and 6890 GC) equipped with an 7683 autosampler
Uwe Christians, MD, PhD, MRQA
Core Director
Karen J onscher, PhD
Associate Director
CNRU Executive Committee
J essica Collins
Research Manager
Mary O’Connell
Grants and Account Manager
J aimie Henthorn
Laboratory Operations Assistant
Quantitative Mass Spectrometry
Drug metabolism
Keith Hoffman, B.Sc.
Biochemical Profiling
Metabolomics, GC-MS
Touraj Shokati, PhD
Isotope Ratio MS
Kent Hansen, PhD
Proteomics
Karen J onscher, PhD
Biostatistics
Zung Vu Tran, PhD
J eff Consoer, M.Sc.
Quality Assurance Unit
J elena Klawitter, PhD, MRQA
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- 1 preparative HPLC (Agilent series 1100 with diode array detector)
- 1 LC/LC-MS system (Agilent series 1100 Agilent modules with mass selective detector including
the capability of MS-guided fraction collection)
- 1 LC/LC-MS-iontrap (Agilent series 1100 HPLC modules, Agilent MSD-Trap ion trap mass
spectrometer)
- 1 Nano-LC-MS/ion trap, Agilent 1100 series LC/MSD Ultra ion trap mass spectrometer, includes
Agilent 1100 series nanoflow LC and nanospray ion source and software
- 1 HPLC Chip/AP-MALDI MS, Agilent 1100 LC/MSD Ultra ion trap mass spectrometer, includes
HPLC Chip and AP-MALDI ion source and software
- Spectrum Mill software for protein identification
- 1 Electrospray-time-of-flight (TOF) (Agilent) including Agilent 1100 series LC system, dual
spray electrospray source for reference mass correction and TOF-centric software, Chip interface,
GeneSpring MS software and Metlin database
- 1 UPLC-MS system (Micromass)
- 1 LC-MS/MS system (Thermo Quattro Ultra)
- 3 LC/LC-MS/MS system (Agilent series 1100 HPLC components and Sciex API4000 triple and
API 5000 quadrupole mass spectrometer)
- Complete two-dimensional gel electrophoresis system including IPGPhor, EttanDalt6, and all
accessories for large format gels (Amersham /GE Healthcare), and BioRad Criterion system for
small format gels and western blotting, Typhoon laser scanner, and DeCyder and Imagemaster
2D software.
- Thermo Fischer Exactive orbitrap
- Thermo Electron DELTA V advantage mass spectrometer with autosampler, an HD collector,
dual inlet system, and an H/device for reduction of H
2
O to H
2
Facility Users
The experience of the faculty and staff in quantitative mass spectrometry, labeled tracer studies, biochemical
(metabolomics) and protein profiling (proteomics) is not only a resource for analytical services but also for
new technology development, training, education, strategic research planning and support in grant writing
and publication. Although CNRU investigators are given priority, the CNRU Mass Spectrometry Core is
open to all investigators. In fact, the Core receives samples from all over the United States and has
numerous global collaboration partners.
Scheduling
When possible, the Core Director will accommodate users’ requests for specific time slots. Priority will
be given to NIH-supported CNRU investigators engaged in biomedical research, CNRU seed grant
awardees and CNRU investigators generating preliminary data for NIH grant applications. Lowest
priority will be given to industry-sponsored projects. Any minor scheduling conflicts will be handled by
the Core Director in close collaboration with the affected users. Larger issues will be discussed with the
Core Director in collaboration with the CNRU Director and CNRU Executive Committee to ensure a
balanced decision.
Policies and Access
Since July 2005, the CNRU Mass Spectrometry Core is organized as a Service Center. Service Centers are
“at cost” and must adhere to strict regulations that determine how funds are used and how user fees are
determined. User fees are based on 12-month cost studies conducted and reviewed by University of
Colorado. Service Center fees and spending are audited on a 12-month basis.
Users primarily contact the CNRU Mass Spectrometry Core Director. The reasons for contact can be, but
are not limited to, the following:
- to initiate a collaboration involving the use of the CNRU Mass Spectrometry Core for a research
project.
- to request time on instruments
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- to request assistance in study design; often prior to grant submissions
- to be trained on instrument(s) and in technologies available through the CNRU Mass
Spectrometry Core
- to solve logistic, technical, post-processing or data management issues
Rates
Please refer to the CNRU Mass Spectrometry Core Pricing Structure in Appendix III.
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Appendix I
Available Assays for Endogenous Compounds and Molecular Markers
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CNRU MASS SPECTROMETRY
CORE
Summary of Molecular Marker
Assays and Resources
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Page 2
Table of Contents
Assays and Analytical Strategies
3
1. LC-MS/MS Quantification of Endogenous Compounds 4
2. Amino Acids 5
3. High-Energy Phosphates (LC-MS) 7
4. Fatty Acid Profiling (GC-MS) 8
5. Metabolic Profiling (GC-MS and LC-MS) 9
6. Metabolic Profiling (
1
H-NMR) 10
7. High-Energy Phosphates (
31
P-NMR) 12
8. Lipid Patterns (
1
H-NMR) 13
9.
13
C-Labeled Tracers (
13
C-NMR) 14
10. Isotope Ratio Mass Spectrometry and Measurement of Isotope
Enrichment using GC-MS
15
11. Non-targeted Proteomics 16
12. Targeted Quantification of Proteins 17
page
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Page 3
Assays and Analytical Strategies
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Page 4
1. LC-MS/MS Quantification of Endogenous Compounds
Free Isoprostanes
Method: LC/LC-MS/MS
Status: fully validated
Matrices: human plasma, human urine, rat plasma and urine, tissue (partially validated)
Reference: Haschke M, Zhang YL, Kahle C, Klawitter J , Korecka M, Shaw LM, Christians U.
Quantification of 15-F2t-isoprostane in human urine and plasma using high-
performance liquid chromatography – atmospheric pressure chemical ionization-
tandem mass spectrometry. Clin Chem 2007; 53:489-497.
Total Isoprostanes
Method: LC/LC-MS/MS
Status: partially validated
Matrices: human plasma, human urine, rat plasma and urine
Reference: N/A. Modification of the free isoprostane assay including release of bound
isoprostanes using KOH and extraction with affinity columns.
Vitamin D Profiling
VitD2, VitD3, 25(OH)VitD2, 25(OH)VitD3, 1(OH)VitD3, 1,25(OH)
2
VitD2 and 1, 25(OH)
2
VitD3
Method: LC/LC-MS/MS
Status: partially validated
Matrices: human plasma
Reference: ASMS presentation, publication in preparation
Steroid Hormones
Testosterone (total and free), estrogen (total)
Method: LC/LC-MS/MS
Status: partially validated
Matrices: human plasma
Reference: publication in preparation
In preparation:
Endothelin, angiotensin, aldosterone, ADMA
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Page 5
2. Amino Acids
Method: LC-time-of-flight MS
Status: fully validated
Matrices: human plasma
Reference: Armstrong M, J onscher K, Reisdorph NA. Analysis of 25 underivatized amino
acids in human plasma using ion-pairing reversed-phase liquid
chromatography/time-of-flight mass spectrometry. Rapid Commun Mass
Spectrom. 2007;21(16):2717-26.
Analytes:
Compound
Molecular
formula
Exact
mass
[M+H]
Extracted
ion
window
Low cal
std
(nM/mL)
High
cal std
(nM/mL)
S/N ratio
(pM
injected) IS used for quantitation
Taurine C2H7NO3S 126.0224 126.00-
126.04
1.56 400 851
(125)
Glutamine-d5
Aspartic acid C4H7NO4 134.0453 134.01-
134.05
1.56 400 52.5
(125)
Glutamic acid-d3
Hydroxyproline C5H9NO3 132.0660 132.03-
132.07
1.56 400 1750
(125)
Glutamine-d5
Serine C3H7NO3 106.0504 106.02-
106.06
1.56 400 267
(125)
Glutamic acid-d3
Glycine C2H5NO2 76.0398 76.01-
76.05
25 3200 22.3
(3125)
Glutamic acid-d3
Glutamine-d5
*
C5H5D5N2O3 152.1000 152.05-
152.15
NA NA 637
(1000)
NA
Glutamine C5H10N2O3 146.0769 147.04-
147.08
25 3200 1450
(3125)
Glutamine-d5
Asparagine C4H8N2O3 133.0613 133.03-
133.07
1.56 400 94.9
(125)
Glutamine-d5
Threonine C4H9NO3 120.0660 120.03-
120.07
1.56 400 315
(125)
Glutamic acid-d3
Glutamic acid-
d3
*
C5H6D3NO4 151.1000 151.05-
151.15
NA NA 15.2
(1000)
NA
Glutamic acid C5H9NO4 148.0609 148.03-
148.07
12.5 1600 714
(1562)
Glutamic acid-d3
Alanine C3H7N02 90.0555 90.02-
90.06
12.5 1600 345
(125)
Leucine-d10
(Cysteine)2 C6H12N2O4S2 241.0316 241.01-
241.05
1.56 400 1160
(125)
Methionine-d3
Citrulline C6H13N3O3 176.1035 176.01-
176.05
1.56 400 383
(125)
Glutamine-d5
Proline C5H9NO2 116.0711 116.04-
116.08
1.56 400 355
(125)
Glutamine-d5
Gly-Gln
*
C7H13N3O4 204.2000 204.10-
204.30
NA NA 2560
(1000)
NA
Ala-Gln C8H15N3O4 218.1140 218.08-
218.12
1.56 400 508
(125)
Gly-Gln
Valine C5H11NO2 118.0868 118.05-
118.09
1.56 400 163
(125)
Leucine-d10
Methionine-d3
*
C5H8D3NO2S 153.1000 153.05-
153.15
NA NA 1810
(1000)
NA
Methionine C5H11NO2S 150.0588 150.03-
150.07
1.56 400 737
(125)
Methionine-d3
Tyrosine C9H11NO3 182.0817 182.05- 1.56 400 722 Leucine-d10
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Page 6
182.09 (125)
Isoleucine C6H13NO2 132.1024 132.08-
132.12
1.56 400 340
(125)
Leucine-d10
Leucine-d10
*
C6H3D10NO2 142.2000 142.00-
142.30
NA NA 1450
(1000)
NA
Leucine C6H13NO2 132.1024 132.08-
132.12
1.56 400 228
(125)
Leucine-d10
Phenylalanine C9H11NO2 166.0868 166.06-
166.10
1.56 400 1010
(125)
Leucine-d10
Histidine C6H9N3O2 156.0773 156.05-
156.08
1.56 400 1090
(125)
Tryptophan-d5
Tryptophan C11H12N2O2 205.0977 205.08-
205.12
1.56 400 383
(125)
Tryptophan-d5
Tryptophan-
d5
*
C11H7D5N2O2 210.1000 210.00-
210.30
NA NA 1110
(1000)
NA
Arginine C6H14N4O2 175.1195 175.09-
175.13
1.56 400 1700
(125)
Tryptophan-d5
Ornithine C5H12N2O2 133.0977 133.08-
133.12
1.56 400 544
(125)
Tryptophan-d5
Lysine C6H14N2O2 147.1133 147.09-
147.13
1.56 400 448
(125)
Tryptophan-d5
*
Internal standard.
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3. High Energy Phosphates (LC-MS)
Method: LC-MS
Status: fully validated
Matrices: Tissues
Reference: Klawitter J , Schmitz V, Klawitter J , Leibfritz D, Christians U. Development and
validation of an assay for the quantification of 11 nucleotides using LC/LC-
electrospray ionization-MS. Anal Biochem. 2007 J un 15;365(2):230-9.
Analytes:
AMP (m/z=346)
ADP (m/z=426)
ATP (m/z=506)
GDP (m/z=442)
GTP (m/z=522)
UDP (m/z=403)
UTP (m/z=483)
CDP (m/z=402)
CTP (m/z=482)
NAD
+
(m/z=662)
FAD (m/z=784)
internal standard 6-aminohexyl-ADP (m/z=525).
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Page 8
4. Fatty Acid Profiling (GC-MS)
Method: GC-MS
Status: partially validated
Matrices: human and rat plasma and tissues
Reference: N/A
Analytes:
C12
C14
C16
C18
C20
C22
C24
C14:1
C16:1
C18:1
C22:1
C18:2
C18:3
C20:4
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Page 9
5. Metabolic Profiling (GC-MS and LC-MS)
Method: GC-MS
Status: partially validated
Matrices: human and rat plasma, urine and tissues
Reference: N/A
Analytes:
3OH-butyrate
Acetic acid
Alanine
Aminomalonate
Creatinine
Galactonic acid
Glucitol
Glucoronic acid
Glutamine
Glycine
Hippurate
Histidine
Indolacetate
Isocitrate
Isovalerate
Lactic acid
Oxalate
Proline
Pseudouridine
Pyruvic acid
Ribose
Serine
Succinate
Threonine
Tyrosine
Uric acid
Valine
Xylitol
Please note that only the major metabolites are listed. Typically, more than 100 metabolites can be
detected within one GC-MS run, allowing either for quantitation or emi-quantitative comparison.
In addition, LC-TOF and LC-MS-TOF assays are set up and available. Metabolites can be identified
using the METLIN database. However, it must be noted that due to the inherent problem of ion
suppression in the electrospray source use of this data for semi-quantitative comparison may be
limited.
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Page 10
6. Metabolic Profiling (
1
H NMR)
Method: proton nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: human and rat plasma, urine and tissues
Reference: N/A
Analytes:
No. metabolite 1H
[ppm]
13C
[ppm]
blood urine
1 leucine 0.94 22 ? ?
2 leucine 0.96 23 ? ?
3 valine 0.97 18 ?
4 isoleucine 1.00 16 ? ?
5 valine 1.03 19 ?
6 (isobutyrate / 3oxo-isovalerate) 1.13 23.1 (?)
7 3-hydroxybutyrate 1.19 23 ?
8 threonine 1.29 20.5 ?
9 lactate 1.32 21.3 ? ?
10 lysine 1.43 + 1.47 22.8 ?
11 alanine 1.46 17.5 ? ?
12 arginine 1.67 25.3 ?
13 leucine 1.68 25.0 ? ?
14 leucine 1.69 41.0 ?
15 leucine 1.69 40.2 ?
16 lysine 1.70 27.6 ?
17 2-hydroxyglutarate 1.83 31.9 ?
18 lysine 1.87 31.5 ?
19 arginine 1.87 29.3 ?
20 2-hydroxyglutarate 1.98 31.5 ?
21 acetate 2.02 23.4 ? ?
22 glutamate 2.08 28.3 ?
23 glutamine 2.12 28 ?
24 hydroxyglutarate 2.26 34.3 ?
25 glutamate 2.32 34.7 ?
26 succinate 2.43 34 ?
27 glutamine 2.44 32.1 ?
28 2-oxoglutarate 2.45 31.5 ?
29 glutathione (Glu) both froms 2.49 32.7 ?
30 citrate 2.56 46.2 ?
31 dimethylamine 2.70 35.7 ?
32 citrate 2.71 46.2 ?
33 trimethylamine 2.87 45.7 ?
34 GSSG (Cys) oxidized 2.95 39.9 ?
35 2-oxoglutarate 2.97 36.8 ?
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Page 11
No. metabolite 1H
[ppm]
13C
[ppm]
blood urine
36 lysine 3.01 40.3 ?
37 creatine 3.02 38.3 ? ?
38 creatinine 3.04 31.4 ? ?
39 R-N
+
-(CH
3
)
3 several signals
3.18 - 3.27 53.1 - 55.5 ? (?)
40 taurine 3.20 49.9 ? ?
41 ?-glucose C2 3.23 75.3 ? ?
42 arginine 3.23 41.7 ?
43 trimethylamine N-oxide 3.25 60.8 ? ? 3.3
ppm
44 phenylalanine 3.28 36.9 ?
45 GSSG (Cys) oxidized 3.30 39.8 ?
46 taurine 3.32 36.8 ? ?
47 ?, ?-glucose C4 3.40 70.8 ? ?
48 ?-glucose C3/C5 3.48 77.1 ? ?
49 ? -glucose C2 3.52 72.6 ? ?
50 glycine 3.54 42.8 ? ?
51 glutathione+Gln+Glu 3.69 55.7 ?
52 ?-glucose C3 3.69 73.9 ? ?
53 ?, ?-glucose C6 3.72 61.9 ? ?
54 glutathione (Gly) both froms 3.75 44.7 ?
55 alanine 3.75 51.7 ? ?
56 ?-glucose C5 3.82 72.6 ? ?
57 ?, ?-glucose C6 3.87 61.9 ? ?
58 creatine 3.91 55.0 ? ?
59 hippurate 3.94 45.1 ?
60 creatinine 4.09 56.9 ?
61 lactate 4.09 69.7 ? ?
62 ?-glucose C1 4.64 97.1 ? ?
63 ?-glucose C1 5.21 93.3 ? ?
64 urea 5.80 -------- ?
65 phenylalanine 7.31 130.5 ?
66 phenylalanine 7.34 128.0 ?
67 phenylalanine 7.41 129.9 ?
68 hippurate 7.50 129.9 ?
69 hippurate 7.59 133.2 ?
70 hippurate 7.79 128.2 ?
71 fumarate 8.46 147.9 ?
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Page 12
7. High Energy Phosphates (
31
P NMR)
Method: phosphorous nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: Tissues
Reference: N/A
Analytes:
phosphomonoesthers (PME)
phosphodiesters (PDE) (both precursors for membrane phospholipid metabolism)
sugar phosphates (UDPG)
phosphocreatine (PCr)
NAD
+
,
NMP
NDP
NTP.
Anorganic phosphate (can be used for monitoring in vivo pH changes in perfused organs and
cells)
NMP, NDP and NTP: nucleotide mono, di and tri phosphates such as AMP, ADP, ATP etc.
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Page 13
8. Lipid Patterns (
1
H NMR)
Method: proton nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: human and rat blood, plasma and tissues
Reference: N/A
Analytes:
poly- and mono-unsaturated fatty acids (PUFA and MUFA)
total fatty acids
triacylglycerols
glycerophosphates
phosphatidylcholine
phosphatidylethanolamine
cholesterol.
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Page 14
9.
13
C-Labeled Tracers (
13
C NMR)
Method:
13
C nuclear magnetic resonance spectroscopy
Status: partially validated
Matrices: tissues, ex vivo perfused organs, perfused and extracted cell cultures
Reference: N/A
Analytes:
Depending on
13
C labeled tracer used. For example in the case of 1-
13
C-glucose:
Metabolic fate of
13
C-label from [1?
13
C]glucose. Label distribution in glycolytic and tricarboxylic acid
(TCA) cycle intermediates during metabolism of [1?
13
C]glucose
3 2
1
O
5
4
OH
H
OH
H
OH
H
CH
2
OH
6
H
OH
OOC
CH
2
O PO
3
COO
CH
3
O H H
COO
CH
3
O
COO
CH
3
H H
3
N
SCoA
CH
3
O
COO
CH
2
COO
H O H
COO
CH
2
COO
O
CH
2
CH
2
COO
COO
COO
O H
COO
CH
2
COO
H H
3
N
CH
2
CH
2
COO
COO
O
CH
2
CH
2
COO
COO
CH
CH
COO
COO
COO
CH
2
CH
2
COO
H
3
N H
(CONH
2
)
2-
oxalacetate
malate
citric acid
aspartate
acetyl-CoA
1-13C-glucose
pyruvate
lactate
alanine
phosphoenol-
pyruvate
succinate
2-oxoglutarate
fumarate
glycolysis
PK
LDH
PDH
PC
ME
PEPCK
Krebs-cycle
+
-
-
PDH:
glutamate
PC:
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Page 15
10. Isotope Ratio Mass Spectrometry and Measurement of Isotope Enrichment
Using GC-MS
Carbon Dioxide Enrichment
Method: Automated carousel and reference gas system in combination with a double-
focusing sector field mass spectrometer
Status: partially validated
Matrices: breath and blood
Reference: N/A
Singly Labeled Water for Determination of Total Body Water and Doubly Labeled Water
Enrichment for the Measurement of Total Energy Expenditure
Method: double-focusing sector field mass spectrometer with autosampler, an HD
collector, dual inlet system, and an H/device for reduction of H
2
O to H
2
Status: partially validated
Matrices: human and rat plasma
Reference: N/A
Labeled Glucose and Glycerol in Plasma
Method: GC-MS
Status: fully validated
Matrices: human and rat plasma
Reference: N/A
The assay was developed and validated using 6,6-d
2
-glucose and d
5
glycerol. This method can be
easily adapted to glucose and glycerol with other
13
C and deuterium labeled analogues.
Labeled Essential and Non-Essential Amino Acids
Method: GC-MS
Status: fully validated
Matrices: human and rat plasma
Reference: N/A
The assay is established and validated for the measurement of stable isotope enrichment such as
methionine-d
3
, phenylalanine-1-
13
C, lysine-1-
13
C, tryptophan-d
5
and leucine-1-
13
C.
1-
13
C-labeled Fatty Acids
Method: GC-MS
Status: fully validated
Matrices: human and rat plasma
Reference: N/A
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Page 16
11. Non-Targeted Proteomics
Extraction, Separation and Analytical Technologies:
- 1D and 2D-gel eledctrophoresis
- Spot cutting, trypsination
- Immunoprecipitation
- Fractionation by semi-preparative HPLC
- 1D- and 2D HPLC, nano-LC, chromatography chip
- MALDI
- Protein identification: iontrap-MS, electron transfer dissociation iontrap MS, time-of-flight
mass spectrometry, quadrupole-time-of-flight mass spectrometry, triple stage quadrupole
mass spectrometry, triple stage quadrupole- linear ion trap mass spectrometry in
combination with database searches
Labeling Technologies:
- SILAC (in combination with cell culture facility)
- iTRAQ
Qualification of Database Hits:
- Western blot
- PCR
- gene knock down (in combination with cell culture facility)
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Page 17
12. Targeted Quantification of Proteins
General strategic approach:
Plasma
Sample
Extraction
- protein precipitation
- gel chromatography
- immuno capture
- immuno depletion
Digestion
LC-MS/MS
of peptides
Derivatization
Labeled internal
standard
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Appendix II
Available strategies to assess drug metabolism
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Questions:
-Metabolite pattern?
-Phase I/ II metabolism?
-Which enzymes are involved?
-Drug-drug interactions?
-Enzyme induction?
-Structures of metabolites?
-Permeability trough blood-brain
And intestinal barriers ?
Study drug
Analytical assay (LC-MS/ LC-MS/ iontrap)
MS fragmentation
Extraction
Basic validation (linearity, recovery, stability)
Initial metabolism screen
- Pooled human liver microsomes, human hepatocytes, cytosol, mitochondria
?Metabolite patterns, preliminary structural information, phase I/II
Choice of appropriate in vitro models and analytics
Phase I Phase II Phase I +II
Human microsomes
?Cytochrome P450
e.g. Human microsomes
?UGT glucuronidation
Hepatic cytosol
?Sulfate conjugation
Human hepatocytes
and/or liver slices
Establish time-, drug-, and protein concentration dependency
Evaluate dependency on species and gender
Determine K
m
, V
max
and CL
int
(corrected for protein binding, several
species)
Identification of specific enzymes involved using:
- Isolated enzymes
- Specific chemical inhibitors
- Specific antibodies
Drug-drug interactions (inhibition, inhibitors will be selected on the basis of results above):
-Effect of study drugs on metabolism of other drugs
-Effect of other drugs on metabolism of study drug
-Mechanism-based inhibition by study drug
Drug-drug interactions (induction):
?Western blotting, metabolism of specific CYP probes, gene expression ?gene arrays (if necessary)
- Human hepatocytes
- After treatment of rats and isolation of liver microsomes
Structural identification of metabolites:
-If necessary: upscale production of metabolites (microsomes, animals, bacterial culture and preparative HPLC)
-Establish quantity and purity of metabolites (mass spectrometry, HPLC/UV)
-Mass spectrometry (MS/MS, MS/ion trap, MS/time-of-flight, validate fragment structures?HR/MS, H/D exchange)
-Mono- and heteronuclear, one- and two-dimensional high-resolution NMR, LC/NMR
Develop and validate LC/MS/MS or GC/MS assays of parent and metabolites
-High-throughput assays for animal studies and samples from other experimental sources
(required for enzyme kinetics, drug-drug interaction and permeability studies)
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Appendix III
Pricing Structure
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CNRU Mass Spectrometry Core Pricing Structure 2008/2009
Proteomics First Sample Additional samples *
1D gel per sample $63.00 $29.25
11 cm 2D gel per sample $119.25 $94.50
24cm 2D gel per sample $221.25 $191.00
Gel Imaging small gel $24.00 $7.00
large gel $38.00 $24.25
2D Spot Analysis per hour $51.00 N/A
Spot Cutting per hour $51.00 N/A
Sample Preparation
Desalting column up to 6 samples $42.50 $7.75
Bradford up to 6 samples $46.75 $2.20
BCA p to 40 samples in du $57.25 N/A
2D Quant kit up to 6 samples $39.50 $0.50
2D clean up kit up to 6 samples $40.50 $5.50
Concentrator Tubes up to 6 samples $42.25 $7.25
HPLC Immunodepletion sample(triplicate) $243.00
single sample $75.50
Stains (small gel)
Coomassie per gel NC
Silver stain per gel $22.50
Sypro stain per gel $30.39
Phospho stain per gel $43.00
Stains (large gel)
Coomassie per gel NC
Silver stain per gel $92.50
Sypro stain per gel $146.50
Phospho stain per gel $400.00
Protein Identification (Mass Spectrometry) First sample Additional samples *
In Solution Protein Digest per sample $47.15 $7.00
In Gel Protein Digest per sample $76.70 $11.70
Nano-LC Trap per sample $90.80 $79.10
Chip-LC trap per sample $75.50 $67.50
ESI-TOF per hour $100.00 $100.00
Database Searching per sample $12.75
Data Analysis per hour $51.00
GC/MS and Metabolomics First sample Additional sample10-100 Samples
Single Amino Acid per sample $131.30 $39.00 $27.50
Amino Acid Panel per sample $150.00 $100.00
fatty acid per sample $111.80 $31.50 $12.60
Glucose/Glycerol per sample $112.00 $31.75 $21.80
Lactate (same as glucose) per sample $112.00 $31.75 $21.80
Breath CO2 $21.35
Body CO2 $26.00
DLW $404.50
Exact Mass Determination per hour $100.00
Instrument Rental
Triple Quadrupole per hour $60.00
GCMS per hour $50.00
Quadrupole Ion Trap per hour $50.00
Consulting per hour $51.00
Assistance per hour $35.00
*Additional samples are those in the same order up to a maximum of 12 gels for proteomics and 100 samples for GC/MS
Revision Date: 10/21/08
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Version 05/26/2009
Page 26 of 26
Mass Spectrometry Facility Structure
(National Jewish Hospital)
Contact:
Nichole Reisdorph, PhD
Assistant Professor, Immunology
Director, Mass Spectrometry Facility
National Jewish Health
303-398-1964
www.proteomicstraining.org
www.reisdorphlab.org
Services
A. Sample preparation, fractionation, and simplification/purification
a. Column chromatography (HPLC with fraction collector)
b. Sample cleanup, protein precipitation, dialysis, purification
c. Protein digestion
d. 1D gel electrophoresis
e. Small format 2D gels
f. Isoelectric focusing (Off-gel electrophoresis)
B. Protein identification and characterization
a. Identification of proteins from simple and complex mixtures
b. Post-translational modification analysis
c. Protein sequence determination
C. Quantitative
a. Proteomics
i. Labeling and non-labeling MS-based methods for differential protein
expression analyses
ii. Note: there are no large-scale 2D gel experiments at NJ, gels can be run
at UC Denver and analyzed at NJMRC
b. Small molecule analysis
i. Targeted
1. Leukotriene B4, C4, D4, and E4
2. PGE2
3. Steroid hormones (eg testosterone)
4. Vitamin D2 and D3
5. Amino acid panel
ii. Discovery-based Metabolic Profiling
c. Accurate mass and percent purity determination (for synthesized molecules)
D. Assay development
a. Basic science
b. Clinical diagnostics
E. Genomics
a. RNA quality assessment (Bioanalyzer)
b. Microarray applications
i. expression analysis
ii. comparative genomic hybridization
iii. methylation analysis
iv. splice variant analysis
v. microRNA analysis
F. Informatics
a. Protein database searching
b. Quantitative omics programs (Genespring, Mass Profiler)
c. Biostatistics
G. Training and education
a. International hands-on and web-based proteomics, metabolomics, genomics,
and informatics training program
b. Training of investigators, students, and technicians through collaborations, co-
investigator projects, and training program.
Mass Spectrometry Facility Structure
(National Jewish Health)
From: Reisdorph, Nichole [mailto:[email protected]]
Sent: Tuesday, November 17, 2009 4:44 PM
www.proteomicstraining.org
www.reisdorphlab.org
a) How is the quality of your measurements evaluated – quality control?
For protein identification and characterization experiments utilizing liquid
chromatography mass spectrometry (LC/MS), standards are analyzed at the beginning
and end of each set of samples. An aliquot of digested bovine serum albumin is analyzed
by LC/MS. Total ion chromatograms are reviewed to ascertain good resolution of peaks,
signal between 10
7
and 10
9
, background under 10
4
, and quality of MS and MS/MS data is
assessed. Data is searched against a protein sequence database, Spectrum Mill and a
minimum of 45% coverage is expected. A moderately complex mix of proteins is used
for QC when more complex samples (> 50 proteins) are analyzed.
For absolute quantization of small molecules (eg. Leukotrienes, Vitamin D, steroid
hormones, amino acids) an external calibration curve is generated daily, high/low
samples are analyzed throughout the runs, and labeled internal standards are spiked in to
each sample. Each of these assays has been extensively validated.
b) What is the turn-a-round time for the service you provide?
Analysis of samples using validated methods is generally conducted within 1 week.
Large batches (>500 samples) may take up to one month. Studies involving method
development can take anywhere from 2 weeks to 1 year.
c) Who documents the data provided and signs off on the data?
Individual technicians document the data which is stored on dedicated servers and backed
up on a weekly/monthly basis. The Core Director or Associate Director approves data
reports.
d) Have you had experience providing data for industry?
Yes although we do not have a formal reporting procedure/materials.
e) Do you have a standard operating procedure manual?
We have SOPs for individual assays and have begun the process of developing a
comprehensive manual.
f) How will you track billing and financial aspects of your core?
Financials are organized with the assistance of the Office for Academic Affairs. Core
personnel record analysis information in a master log. This includes the date of service,
customer and technician names, type and number of analyses provided, discount or
special pricing information, and miscellaneous information. At the end of each month
this information is used to create invoices which are emailed/mailed to individual
investigators. The Core accepts POs, checks, credit cards, and direct transfers within
NJH.
Medicinal Chemistry Core Facility
Michael F. Wempe, PhD
Associate Research Professor and Director, Medicinal Chemistry Core Facility
Department of Pharmaceutical Sciences, School of Pharmacy
University of Colorado Denver
C238-P15 Research 2, Room P15-4003,
12700 East 19th Avenue, Aurora, CO 80045.
“Medicinal or Pharmaceutical Chemistry is a discipline at the intersection of chemistry
and pharmacology involved with designing, synthesizing and developing pharmaceutical
drugs. Medicinal chemistry involves the identification, synthesis and development of new
chemical entities suitable for therapeutic use. It also includes the study of existing drugs,
their biological properties, and their quantitative structure-activity relationships (QSAR).
Pharmaceutical chemistry is focused on quality aspects of medicines and aims t o assure
fitness for the purpose of medicinal products.” (Wikipedia).
A medicinal chemistry c ore f acility at UC Denver – housed within t he Department of
Pharmaceutical Sciences (DOPS) – has been initiated. The facility has been established to
offer researchers with small molecule synthesis and drug metabolism expertise (i.e. pre-
clinical evaluation capabilities). The main goal of the core will be to help facilitate and
stimulate fundamental and collaborative research at the university; a chemical synthesis
core geared t o provide c ompounds t o help r esearches validate pr oof-of-principle t arget
discovery studies and/or assist in pre-clinical evaluation.
Services:
- Synthesis of known, but not commercially available compounds
- Design and custom synthesis of bio-active molecules
- Assistance in the identification and optimization of lead compounds
- Structure-Activity Relationship (SAR) elucidation
- In vitro Metabolic stability screening (mouse, rat, dog, monkey, human)
- Metabolite identification
- In vitro Permeability assessment, protein binding, plasma stability
- In vitro drug-drug interaction studies
- In vitro drug transporter studies
- Bio-Analytical Pharmacokinetic (BAPK) method development
- Determination o f d rug c andidate a nd me tabolite(s) in b iological ma trix
(i.e. plasma, liver, brain, kidney, heart, fat and muscle)
- Formulation development
* For consultation, research proposals, current facility and labor charges, contact:
[email protected] (Tel) 303-724-8982
Medicinal Chemistry Core Facility
Michael F. Wempe, PhD
a) How is the quality of your measurements evaluated – quality control?
Good Labororatory Practices (GLP) are used in the Medicinal Chemistry Core regarding non-
clinical studies conducted for the assessment of the safety of chemicals to man, animals and
the e nvironment. Therefore, our G LP m ethods (i.e. internal s tandards, qua lity c ontrols
samples, et c) provide a f ramework w ere l aboratory st udies a re p lanned, p erformed,
monitored, recorded, reported and archived.
b) What is the turn-a-round time for the service you provide?
Because the scope of the poject can significantly vary (i.e. synthesis, vs. in vitro, vs. in vivo
pre-clinical evaluations), the turn-a-round time is project specific.
c) Who documents the data provided and signs off on the data?
The Director of the Medicinal Chemistry Core signs off on data.
d) Have you had experience providing data for industry?
Yes, we have hands-on experience providing data to industry.
e) Do you have a standard operating procedure manual?
We are actively preparing SOP’s for various preclinical evaluations.
f) How will you track billing and financial aspects of your core?
Billing and financial aspects related to the core will be tracked using a ‘Service Center Cost
Study Summary’ template.
University of Colorado Cancer Center
Metabolomics Core
Contact:
Natalie Serkova, PhD, Director
Associate Professor, Dept. of Anesthesiology and Radiology
303-266-2910 pager
[email protected]
303-724-1086 phone
303-359-6574 cell
Manager: Andrea Merz (pager 303 266 7514)
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/metabolomics/index.aspx
Dr. Natalie Serkova
Metabolomics, one of the “omic” sciences in systems biology, is the global assessment and
validation of endogenous small-molecule biochemicals (metabolites) within a biologic system.
Metabolite detection and quantification is usually carried out by nuclear magnetic resonance
(NMR) spectroscopy while mass spectrometry (MS) provides another highly sensitive
metabolomics technology. The UCCC Metabolomics Core provides all NMR-related
metabolomics services on human and animal cells, bipsies, and body fluids. Various metabolic
biomarkers, related to glycolysis, mitochondrial citric cycle acid, choline, phospholipids and
fatty acid metabolism, were recently reported to play important roles in cancer development and
responsiveness to anti-cancer treatment using NMR-based metabolic profiling.
The Metabolomics Core consists of the high-resolution NMR facility, which is located at the
Anschutz Medical Campus, Research Complex-2 (Suite P15-1109).
The facility is fully equipped for all aspects of nuclear magnetic resonance spectroscopy (1H-,
13C-, and 31P-NMR and two-dimensional NMR). We performed expanded quantitative
metabolic analysis:
• on cells
• cell extracts
• human and animal tissues and biopsy extracts
• body fluids (including blood, plasma, urine, cerebral and prostatic fluids etc).
Our Services
• Project design and consultation: recommendations and advice on end points to be
monitored, budget, suggestions for data analysis.
• Sample Handling and Extraction for Metabolic NMR: Facilities for tissue, body fluids,
and cell extraction, sample lyophilization, and sample preparation for NMR. Sample
storage is also available.
• NMR based metabolic protocols: Structure determination based on two-dimensional
NMR is used for metabolite identification, specially designed 1D-NMR program is used
for precise metabolite quantification, various statistical packages are available to perform
principle component analysis (PCA), linear regression etc. analysis on metabolic data
sets.
• Data set collection is available.
• Access to computational facilities.
• Data analysis and publication and grants preparation/ assistance.
• Training in MR safety (for all users).
• Training in MR operation (for advanced users only)
• Data handling and storage
Metabolics Core Pricing for FY2008/2009
Full Service Self Service
Service Description
Member
Rate
Non Member
Rate
Member
Rate
Non Member
Rate
Biopsy $116 $144 $69 $70
Blood $59 $80 $23 $23
Cell Culture $324 $405 $188 $193
Quality Control (HSQC) $185 $190 $185 $190
Other - Minimum
Processing
$43 $54 $24 $24
• Prices effective 7/1/08 thru 6/30/09
Metabolics Core Pricing for FY2009/2010
2009/ 2010 Full Service Self Service
Service Description
Member
Rate
Non
Member
Rate Commercial
Member
Rate
Non
Member
Rate Commercial
Biopsy $121 $149 $69 $70
Blood $63 $84 $23 $23
Cell Culture $341 $422 $188 $192
Quality Control (HSQC) $185 $190 $185 $190
Other - Minimum Processing $45 $56 $24 $24
* only experienced NMR/ Radiologist scientists after on-site training by Dr. Serkova
NMR Metabolomics
From: Serkova, Natalie
Sent: Thursday, October 01, 2009 2:26 PM
a) How is the quality of your measurements evaluated – quality control?
For NMR Metabolomics: External s tandards f or NMR c hemical s hifts a nd me tabolite
quantification are re-evaluated every 3 months.
b) What is the turn-a-round time for the service you provide?
For NMR Metabolomics: 20 m in – 24 h rs pe r s ample. For a s ingle s tudy, t he pr oject
period can be up to 3 months.
c) Who documents the data provided and signs off on the data?
Metabolomics and Animal Imaging: The Core staff: NMR f acility manager and animal
facility manager. The Core Director provides monthly reports to the Cancer Center based
on the data from the staff.
d) Have you had experience providing data for industry?
Yes, we run 5-10 industry sponsored studies per year.
e) Do you have a standard operating procedure manual?
NMR Metabolomics (published, books) and for animal imaging (per requested, approved
by the IACUC).
f) How will you track billing and financial aspects of your core?
We do it already for the past 3 years: Cancer Center provides us with our cost study every
fiscal year. It is posted on our website
METABOLIC CORE LABORATORY
Services 2007
Contact:
Jacob E. (Jed) Friedman, Ph.D.
Director
(303) 724-3983
[email protected]
For body composition/calorimetry and assays of LPL and HSL, contact:
Robert Eckel, MD
Professor
(303) 724-3969
[email protected]
Pricing contact:
Rachel Janssen
303-724-3979
[email protected]
Website:http://www.uchsc.edu/nutrition/Friedman/MetabolicCoreLab.htm
I. Description:
The main services of the Metabolic Core are gene expression analysis using real-time
quantitative PCR and tissue procurement/preparation and processing for analysis of
phosphorylation and expression of key post-receptor insulin signaling proteins that regulate
insulin sensitivity and lipid metabolism at the cellular level. The Core also provides selected
assays for specific hormones and metabolites. This Core provides an array of assays over a
broad range of species (rat, mouse, human, sheep) and tissue types (fat, muscle, liver), for
multiple investigators studying the clinical consequences of nutrition-related disorders. The
Metabolic Core lab also provides members of the Center with reagents, access to
equipment, and exposure to new techniques (insulin clamping, insulin signaling, real-time
PCR) that have helped to expand the quantity and quality of nutrition research in the CNRU.
The services of the Metabolic Core Laboratory have been used by many investigators to
extend their research beyond the specific hypotheses proposed in their RO1 grants. For
example, many investigators who did not previously assess insulin action in their own
studies have taken advantage of this core laboratory to obtain these measures using the
insulin signaling assays. Thus, the Metabolic Core of the Nutrition Center achieves an
overall cost-savings and provides more important investigator time in their own laboratories
for their own experiments.
II. Organization and Description of Services:
The Core services the needs of the CNRU on a reduced fee-for service basis including:
• RNA isolation, analysis, quantitation, real-time quantitative RT-PCR. TaqMan probes
available from the Core range from genes involved in gluconeogenesis and
lipogenesis to neuropeptides and transcription factors, as well as reference genes
for normalization of gene expression.
• Western blot analysis of insulin receptor signaling cascade including (but not limited
to) IRS-1, PI 3-kinase, Akt, GSK3, JNK, TNFalpha, and GLUT4 protein levels in
muscle, fat, and liver from human, rodent, and sheep. The Core measures activity
and phosphorylation state (tyrosine and/or serine) where appropriate. Analysis of
insulin/IGF-1 cell signaling via mTOR, p70S6 kinase and E1F2alpha and 4E-BP1 as
cellular markers for protein synthesis, including site-specific activation in tissues and
cells.
• Radioimmunoassay of hormones including insulin, leptin, adiponectin and resistin.
• Substrate determination of glucose, triglycerides and free fatty acids.
• Consult for tissue and plasma assays for plasma lipoprotein lipase (LPL) and
hormone sensitive lipase (HSL).
• Consult for hyperinsulinemic-euglycemic clamp procedures in mice and rats.
New investigators, particularly CNRU pilot awardees, are encouraged to consult with Dr.
Friedman in advance to help plan experiments involving the services listed above.
The Metabolic Core lab is also a resource for providing expertise and technology for
analysis of genetically defined mouse and rat models relevant to nutrition research. We
provide experimental support and technical advice regarding measurement of insulin
sensitivity in vivo (insulin clamps) and end organ-based metabolism (e.g. glucose and fatty
acid uptake, oxidation, and synthesis) and metabolic biochemistry (cytokines, receptor
proteins) and gene expression (RNA analysis) These services promote interaction between
investigators and foster multidisciplinary research training in clinical nutrition and obesity
across the UCD campus.
Facilities: The Metabolic Core Laboratory is located in the Center for Human Nutrition within
basic science Division of Adult Endocrinology in Dr. Friedman’s laboratory (Research
Complex 1, 7 th floor at Anschutz Medical Campus). The laboratory is 1150 sq. ft. and
includes all of the major equipment needed for research in molecular nutrition (listed below).
The lab is adjacent to a satellite animal facility set up for performing chronic animal
surgeries, energy balance, and hormone infusion studies in mice. This section of the lab
includes a general work area, surgery set-up, lamps, Harvard infusion pumps and metabolic
chamber. Within the PI’s laboratory is a designated area with water bath for performing
glucose transport studies. Across the hallway is a 150 sq. ft. tissue culture facility used for
growing human and non-human mammalian cells, including tissue culture supplies, light
microscope, CO 2 incubators, liquid nitrogen storage tank, sink, and two laminar flow
hoods. The following major items of equipment are within the PI’s lab: real-time PCR
detection system, automated RNA and protein analysis system, two PCR thermal cyclers,
high-speed refrigerated centrifuge, microfuges, horizontal and vertical gel electrophoresis
systems and power supplies, gel documentation camera equipment and computer software
for image quantification, UV spectrophotometer, walk-in cold room, three -20C freezers, and
two ultra-cold -80C freezers for storing biological samples. The following major pieces of
shared equipment are located on the floor of the PI’s laboratory: Several refrigerated
ultracentrifuges and high-speed rotors, Beckman liquid scintillation counter, autoclaves, film
developer, fluorometer, luminometer, and distilled water purification system. The PI shares
the maintenance contract on these items with other members of the department and has full
access to this equipment.
III. Management of Core Operation – Cost Effectiveness/Quality Control:
The extent of resource support requested by the investigator is discussed with the PI during
the planning stages of the project and reviewed at a meeting with the PI prior to initiation of
the project. The extent of support provided by core staff will depend largely on the type of
extramural support available for the project, with priority given to those projects for which
funds for personnel expenses are limited (pilot/exploratory studies, career development
awards, etc). Detailed plans for prioritizing samples are based on the source of funding and
the type of award, as follows:
1. Pilot project recipients and members of the research base with NIH career
development awards (K Awards)
2. Members of the research base with federal funding. The source of funding plays a
role in the prioritization as follows: 1 = federal (NIH, NSF, USDA, VAMC, AHA, ADA
etc), 2 = foundation (Aging, Liver foundation, etc), 3 = industry, investigator-initiated,
4 = industry, not investigator-initiated.
3. Investigators proposing projects to collect preliminary data for nutrition-related NIH
grant applications.
4. Members of the research base with non-federal funding for nutrition/obesity projects.
5. Members of the research base with non-federal funding for non nutrition/obesity
projects.
6. Unfunded members of the research base.
The mechanisms for monitoring budgetary overlap of current funded projects and the
Metabolic Core lab are handled by Dr. Friedman in consultation with other core directors.
This Core continues to provide services at no cost to new investigators without grant funds
and at subsidized rates for pilot awardees in order to help them compete at the national
level for independent funding. The Core lab thus provides members of the Center with
reagents, access to equipment, and exposure to new techniques that have expanded the
quantity and quality of nutrition research in the CNRU. Because CNRU investigators
continue to submit new grant applications that propose the use of the core facility, we
suggest that core activity be planned in advance whenever possible.
Consultation /Research training: Quality control is part and parcel of the services provided
by this core. Core personnel are actively involved with investigators in providing assistance
with the selection of assessment methods and the design of experimental protocols to
insure the samples we receive are of high quality. Investigators receive assistance in
determining the most appropriate assay for a specific research study. In helping each
investigator to decide on which assay is best to use, the following issues are addressed: 1)
appropriateness of assay to the study, 2) appropriateness of a given assay to the scientific
question, and 3) cost. To insure the samples we receive are treated appropriately, when
assaying insulin sensitivity in human muscle biopsies for example, we routinely send an
assistant with the investigator to ensure the first biopsies are properly dissected, frozen
immediately, or placed in RNAlater for future use. For animal studies, we make sure the
time of fasting is controlled for, and that to the extent possible, hormone treatments are
carried out in conjunction with assay of proteins to examine phosphorylation patterns. In
terms of assay quality control, for hormones we assay known standards to ensure our inter-
assay and intra-assay variability is within 5%. For Western blotting, we use internal controls
(either manufacturer’s standard or excess sample from the study) on every blot to account
for inter-blot variability, and use GAPDH as a loading control to control pipeting error and/or
transfer of protein. For gene expression analyses, we run all quantitative real-time PCR
reactions in duplicate and normalize the data to reference genes.
IV. Personnelhttp://www.uchsc.edu/nutrition/Friedman/MetabolicCoreLabPersonnel.htm
List of Reagents:
Please see Website
Metabolic Cost Service Center costs prices revised 2/6/2009
Cost Per Set
Test Name
# of Tests
per Set CNRU Members Non-Pilot Non-CNRU Member
20% discount
RNA Isolation-muscle tissue 10 $182.98 $240.06
RNA isolation-adipose tissue 10 $197.27 $254.35
RNA Analysis and Quantitation 1 $53.32 $62.84
qPCR plate charge 1 $14.09 $14.09
RNA Duplicate (probe) 1 $19.88 $22.73
RNA Duplicate (SYBR) 1 $19.32 $22.18
cDNA Synthesis 10 $43.82 $53.34
DNA Duplicate (probe) 1 $11.83 $14.68
DNA Duplicate (SYBR) 1 $10.52 $13.37
Western Blot (in-stock primary antibody) 10 $347.06 $442.20
Lipid Extraction/TG Assay 10 $121.61 $159.66
FFA Assay 10 $95.78 $110.05
Glycerol Assay 10 $35.86 $45.38
BCA assay 10 $23.51 $33.02
PI3K Assay 10 $491.86 $653.59
ELISAs:
ELISA kit (insulin, adiponectin, resistin, etc) 1 variable variable
consumables for ELISAs 1 $16.06 $16.06
Metabolic Core
From: Friedman, Jed
Sent: Thursday, October 01, 2009 3:59 PM
a) How is the quality of your measurements evaluated – quality control?
Internal standards and regular calibration with known controls provide a means of
evaluating q.c.
b) What is the turn-a-round time for the service you provide?
This depends on the waiting list and how detailed/amounts of service is required.
Generally speaking 1-2 weeks.
c) Who documents the data provided and signs off on the data?
Dr. Friedman, the core director.
d) Have you had experience providing data for industry?
Yes, but not on this campus.
e) Do you have a standard operating procedure manual?
All protocols have been painstakingly tracked for purposes of creating a cost-center.
f) How will you track billing and financial aspects of your core?
Through the Administrative core for the NIH center grant “Nutrition and Obesity
Research Center”
Molecular Discovery (IDDRC)
Directors:
Frank Frerman, PhD
303-724-3807
[email protected]
Elaine Spector, PhD
303-724-3801
[email protected]
Mission:
The objective of the Molecular Discovery Core Unit is to provide advice, training and service to
Colorado IDDRC investigators in molecular IDD research, from hypothesis generation to
characterization of macromolecules. This includes: molecular bioinformatics focused on IDD;
genome transcriptome and proteome analysis; characterization of protein structure, activity and
interactions; and access to shared instrumentation, such as centrifuges and fluorescence imaging.
Staff:
Molecular Structure
• Frank Frerman, PhD
• Robert Hodges, PhD
DNA Sequencing, Comparative Genomic Hybridization
• Elaine Spector, PhD
Vector Construction
• Wallace Chick, PhD
• Kristina Williams, BS
Bioinformatics
• Katheleen Gardiner, PhD
• Xiaolu Sturgeon, PhD
Proteomics
• Kirk Hansen, PhD
• Mark Duncan, PhD
DNA Array
• Bifeng Gao, PhD
• Mark Geraci, MD
Quantitative PCR
• Umarani Pugazhenthi
• Bryan Haugen, MD
Services:
Several of the IDDRC services are provided through cooperative agreements with other units,
such as the University of Colorado Cancer Center.
IDD-focused bioinformatics.
Contact: Katheleen Gardiner, PhD
Website:http://gfuncpathdb.ucdenver.edu/iddrc/iddrc/GeneQuest.php
Goals: To provide Center investigators and the wider scientific community with a database of
comprehensive information on genes, gene products, and signaling pathways relevant to IDD.
The database searches and tools are designed to aid both basic and clinical researchers in
discovery and integration of IDD gene knowledge and in hypothesis generation. The IDD
Bioinformatics facility is being built on “The chromosome 21 gene function and pathway
database” initially developed for studies on Down Syndrome.
Mass spectrometry (MS)/proteomics.
Contact: Kirk Hansen, PhD
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/proteomics/index.aspx
Goals: To provide high-throughput, qualitative and quantitative analysis of proteins from
tissues, cells, and fluids that can change with respect to time, physiology, and pathology. In
addition to proteomic studies, the MS section of the facility also contributes to investigations
involving small molecule analysis.
The Mass Spectrometry/Proteomics core is operated by the Program in Biomolecular Structure
and the Colorado Cancer Center.
Expression Microarray, QPCR.
Contact, DNA Array: Bifeng Gao, PhD
Contact, Quantitative PCR: Umarani Pugazhenthi
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/gene-
expression/index.aspx
Goals: To characterize IDD-related physiological, developmental, and pathological alterations in
gene expression. Access to appropriate technologies is being provided through collaborative
agreements with the Gene Expression Core of the Cancer Center.
Real-time QPCR services to IDDRC investigators are provided through a collaborative
arrangement with the Gene Expression Core of the Cancer Center directed by Bryan Haugen.
IDDRC members are invited to watch a short video on Microarrays.
For additional information, IDDRC members are invited to watch a video on Demystifying
Microarrays.
Comparative genomic hybridization (CGH).
Contact: Elaine Spector, PhD
Websites:http://www.uchsc.edu/pathology/cgl/tests.htm
http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/cytogenics/index.aspx
Goals: To analyze subtle genomic variations, such as CNVs.
Array CGH detects subtle genomic abnormalities, such as unbalanced translocations and, most
importantly, copy number variations (CNV) genome-wide. In contrast to expression arrays,
CGH uses BAC (bacterial artificial chromosome) or, in some cases, oligonucleotide arrays.
IDDRC investigators can access the facilities of the Colorado Genetics Laboratory (CGL) for
BAC-based array assays of clinical samples. This is a well-established facility providing high
quality of service (CLIA- and CAP-certified). All array analyses are performed twice, with the
dyes switched between control and test samples to confirm gains or losses of genomic material.
Array CGH and other molecular cytogenetic techniques are also available through the Cancer
Center Cytogenetics core for research samples (M. Garcia, PhD, Director). E. Spector serves as
the coordinator of these activities for members of the IDDRC.
DNA sequencing.
Contact: Elaine Spector, PhD
Goals: To provide accurate, rapid-turn-around DNA sequencing to fit the needs of the individual
investigators (from small to large scales) with economy of service. E. Spector, who also is
involved in genotyping for the Animal Models Core, in the biobanking section of the
Translational Nexus (see those core descriptions), and in array CGH, is supervising DNA
sequencing for IDDRC members. This arrangement guarantees high quality (CAP and CLIA
certifications), local service with rapid turn-around (typically 24-48 hours), and very favorable
pricing. For high-volume needs (over 96 or multiples of 96 reactions at a time) sequencing is
outsourced to a commercial sequencing laboratory. This will be coordinated by E. Spector’s
laboratory. The laboratory also carries out DNA profiling for authenticating human cell line
identity, which includes access to a large database of in-house determined profiles of common
human cell lines (see Cell Systems and Analysis).
Lipidomics and glycomics.
Contacts: Frank Frerman, PhD; Karl Pfenninger, MD
Goals: To identify and quantify lipids, fatty acids and their derivatives; and to identify
oligosaccharide sequences. This Medical School has unique strengths in these areas. Dr. Robert
C. Murphy (Department of Pharmacology) directs one of the large NIH-funded “Lipid
Metabolites and Pathways Strategy (LIPID MAPS) Centers focusing on the characterization of
lipid compounds. Dr. Brad Bendiak (Department of Cell and Developmental Biology) is a
widely recognized expert in the field of oligosaccharide analysis and sequencing. Should
significant need arise the Center plans to develop cooperative agreements with these laboratories
to make their expertise accessible to IDDRC investigators.
Vector construction.
Contact: Wallace Chick, PhD
Website:http://www.uchsc.edu/neuroscience/Program/cores.htm
Goals: To provide the IDDRC members with state-of-the-art services for the design and
generation of genetically engineered mouse models of IDD. The vector facility constructs
vectors to generate transgenic, knockout and knockin animals and vectors with tissue-specific
promotors. The IDDRC has teamed with the NINDS-funded Vector Core of the RMND Center
to provide these services. In consultation with A. Messing and Q. Chang at the Waisman Center
of the University of Wisconsin, whose core performs the cell and animal work (see Animal
Models Core), W. Chick designs the constructs that are subsequently engineered by K.
Williams. Should the need arise the IDDRC Executive Committee will determine priority for
usage of this core. Criteria for judging priority include, but are not limited to, relevance to the
goals of the IDDRC and scientific merit.
Molecular Structure Analysis.
Contact: Frank Frerman, PhD
Website:http://biomol.uchsc.edu/index.html
Goals: To provide facilities and training in biophysical methods applied for the determination of
molecular structure and interactions. This is accomplished in cooperation with the Biophysics
Laboratories, a user facility operated by the Program in Biomolecular Structure at the University
of Colorado Denver (directed by R. Hodges). Instrumentation is available for the structural
characterization of proteins and nucleic acids by chemical and thermodynamic methods. The
Biophysics Laboratories offer training (group and one-on-one) for a fee. After training,
instrument user fees are assessed. Assistance also is available for peptide synthesis, purification
by HPLC, and composition analysis. More extensive structure analyses may be arranged through
collaborations with x-ray crystallographers and NMR spectroscopists in the Biomolecular
Structure Program.
IDDRC Shared Instrumentation
The major, shared instrumentation that is currently available to Colorado IDDRC members is
listed below. The Center maintains these instruments. The equipment is located on the 4th
floor, RC1 North. For access to equipment and further information, contact Frank Frerman.
Shared Instrumentation of the IDDRC
Shimadzu UV-2401PC UV-VIS recording
spectrophotometer
Shimadzu 5301PC spectrofluorophotometer
Beckman Syetem Gold high performance liquid
chromatograph
Hewlett-Packard 89090A diode array spectrophotometer
General Electric Acta FPLC
Savant lyophilizer
Beckman LS 3801 liquid scintillation counter
Beckman TL-100 ultracentrifuge
Beckman J-21 centrifuge
2 Beckman J-25 (Avanti) centrifuges
Beckman L8-M ultracentrifuge
For fluorescence imaging Colorado IDDRC members have access to a General Electric Typhoon
9410 multi-mode fluorescence laser scanner/phosphorimager. This instrument, equipped with
three lasers and capable of scanning gels, blots, storage phosphor screens, tissue sections, and
multi-well plates is located in the area occupied by the Biomolecular Structure Program and
easily accessible to Center members.
User Fees:
Services Fee for IDDRC
Member
Fee for Non-Member Contact
DNA Sequencing
Small Scale
$5.25/reaction $7.00/reaction Elaine Spector,
PhD
DNA Sequencing
Large Scale
$2.20/reaction for
multiples of ³ 96 PCR
reactions
Please inquire Elaine Spector,
PhD
IDD Bioinformatics No charge No charge Katheleen
Gardiner, PhD
Mass Spectrometry/
Proteomics
Instrument time charge
only
$1300 prep fees + $65-$100
instrument time per sample
Kirk Hansen,
PhD
Expression
Microarray
20% discount of
standard rate
$1000/sample (covers RNA
prep, RNA quality control,
analysis)
Bifeng Gao,
PhD
Quantitative PCR 30% discount of
standard rate
Please inquire Umarani
Pugazhenthi
Comparative
Genomic
Hybridization
Please inquire Elaine Spector,
PhD
Vector Construction $1500/vector Please inquire Wallace Chick,
Morphology and Phenotyping Core
Contacts:
Maranke Koster, PhD
Director
303-724-1640
[email protected]
Laura Hoaglin
Histology Technician
303-724-0528
[email protected]
Website:http://www.uchsc.edu/stemcell/resources/histo.htm
Although the Morphology and Phenotyping Core specializes in
processing and analyzing skin samples, it has expertise in the
processing of all types of tissues
Although all tissue samples can be processed by the Core, the Core particularly specializes in
skin samples. For instructions on preparing skin samples for histological processing, please see
below:
Harvesting skin samples for histological analysis
1. Samples for paraffin embedding
General:
Make sure that the volume of formalin used for fixing the tissue equals >10x the volume of the
sample. Fix your s amples i n 10% neutral buf fered f ormalin (NBF) O/N at 4°C. The next day,
replace the formalin with 70% EtOH and keep the sample at 4°C.
Fill o ut th e requisition f orm a nd email it to Laura Hoaglin ( [email protected]).
Leave your s amples i n Maranke Koster’s f ridge i n t he hallway ( RC-1N 8th floor, across from
P18-8403E). Make sure your samples are clearly labeled with your initials, the date, and sample
ID.
Back skin (E17.5-adult mice):
Within the same experiment, skin samples should be harvested from the same area of the body.
Often, t he ba ck of t he mouse i s c hosen f or t his pur pose. If you a re us ing ba ck s kin, t ake t he
biopsy f rom t he middle of t he b ack ( on t op of t he s pine) midway b etween t he h ead a nd t ail.
Using a r azor bl ade or s calpel, t rim t he bi opsy i nto a r ectangle, s uch t hat t he long axis of t he
rectangle corresponds to the A-P axis of the mouse. Unless otherwise indicated, the biopsy will
be sectioned along the long axis of the rectangle. If sectioned this way, your sections will provide
a good view of the interfollicular epidermis as well as the hair follicles. If you prefer sectioning
along a different axis, please indicate this clearly on the requisition form.
Place your rectangular piece of skin flat on a piece of Whatman filter paper or unlined index card
(dermis side down). This will ensure that the skin sample will remain flat while it is fixing. Then
place the paper with the skin in 10% neutral buffered formalin and proceed as above.
Embryonic skin (up to E16.5):
For e mbryos up t o E 16.5, f ix the e ntire e mbryo r ather than a ttempting t o r emove t he s kin.
Carefully dissect the embryo free from extraembryonic tissues, place it in 10% NBF or Bouin’s
fixative, and proceed as above.
Unless otherwise indicated, embryos will be sectioned from the midline along the sagittal axis.
Ear skin:
Remove the entire ear of an adult mouse and trim the biopsy into a rectangle, such that the long
axis of the rectangle is perpendicular to the head of the mouse.
Tumors:
After dissecting out the tumor, trim the tumor to prepare a biopsy with at least one straight edge.
The straight edge will be the cutting edge of the sample. If possible, the cutting edge should be
perpendicular to the skin of the mouse, such that your section will contain the most superficial as
well as the most basal part of the tumor.
1. Samples for OCT embedding
If you ha ve n ever e mbedded s kin i n O CT, pl ease c ontact M aranke K oster
([email protected]) for help with your first sample.
As a general guideline, prepare t he skin sample as above ( i.e. r ectangular pieces of back skin,
etc). Since the sample will be sectioned from the bottom of the cryomold, your sample should be
placed in the cryomold accordingly. For example, rectangular pieces of back skin must be placed
on the bottom of the cryomold on the edge of the long side (see figure [drawn by Irene Choi]).
Slowly fill the cryomold with OCT and place the sample in the middle of the cryomold. Once
you have pos itioned t he bi opsy i n OCT, make s ure t o r emove any bubbles t hat may s urround
your t issue, as t hey can cause pr oblems with cutting. You can r emove t he bubbl es with a t hin
needle. Place the cryomold + OCT + biopsy on dry ice to allow the OCT to freeze (it will turn
white). Once the OCT is frozen, store your samples at -80°C.
Embryos must be pr ocessed t hrough a s ucrose gradient pr ior t o e mbedding i n OCT. P lease
contact Maranke Koster for the protocol.
After embedding your s amples, f ill o ut th e r equisition f orm and e mail it to Laura
([email protected]). Leave the samples in a box labeled with your initials, date and
sample ID on t he t op s helf i n Maranke Koster’s -80°C freezer (RC-1N 8th floor, across from
P18-8212).
1. Further information
For more information on the use of different fixatives and on processing skin tissue:
Seymour R, Ichiki T, Mikaelian I, Boggess D, Silva KA, and Sundberg JP. 2004. Necropsy
Methods. In: Handbook of Experimental Animals: The Laboratory Mouse, Hedrich HJ (ed),
Academic Press, London, pp 495-516.
Core services include assistance with skin harvesting, preparation of paraffin blocks, sectioning
of paraffin and frozen blocks, and standard H&E histology.
For a histology request form, please go to website.
The following services are available:
Paraffin histology Regular price
*SDRC
Member
Processing and embedding (per sample) $12.00 $5.50
One unstained slide (per slide) $3.50 $1.75
H&E staining (per slide) $6.50 $3.25
Frozen section histology Regular price
*SDRC
Member
First unstained slide (per block) $10.00 $5.00
Additional unstained slides (per slide) $2.75 $1.50
H&E or toludine blue staining (per slide) $6.50 $3.25
* Skin Diseases Research Core Center Member Price
Please see the Pathology Shared Core (University of Colorado Cancer Center) for more
general dermal and tissue pathology services.
Morphology and Phenotyping Core
From: Koster, Maranke
Sent: Monday, November 02, 2009 8:43 AM
a) How is the quality of your measurements evaluated – quality control?
To ensure that investigators receive high quality skin sections, each Core user will receive
detailed instructions on harvesting and fixing skin/epithelial samples for histology. In
addition, reagents and equipment used for histological processing will be subject to quality
control. Reagents will be maintained and stored as specified by the manufacturer and
disposed of on expiration. In addition, equipment will be maintained and serviced on a
regular basis by a certified technician. Specifically, the tissue processor will be cleaned
daily, alcohols will be rotated every 100 blocks, all reagents will be changed every 400
blocks, and preventive maintenance will be performed annually. The embedding center will
be cleaned daily, the paraffin will be changed and refilled as needed, and preventive
maintenance will be performed annually. The microtome will be cleaned daily and
preventive maintenance will be performed annually. The paraffin pot will be emptied and
cleaned monthly.
Annual surveys will distributed to Core users to evaluate the quality of the current
services and to inquire about interests in new services.
b) What is the turn-a-round time for the service you provide?
The regular turn-around time is approximately 1-3 weeks (depending on the
workload). We also offer expedite processing, with a guaranteed 72-hour
turnaround time.
c) Who documents the data provided and signs off on the data?
The histology technician. If any questions arise regarding quality or billing, the Core
director will respond to these.
d) Have you had experience providing data for industry?
No
e) Do you have a standard operating procedure manual?
We do not have this at this time. We could certainly make one though.
f) How will you track billing and financial aspects of your core?
We maintain a database in which all service requests (and their costs) are entered.
Each month, we generate a billing statement for each Core user, which includes all
rendered services and their cost. Services are paid for by Interdepartmental
Invoices, and the funds are deposited in our service center account.
Mucosal and Vaccine Research Colorado (MAVRC)
Flow Cytometry Core Facility
Edward N. Janoff, MD
Director
Phone: 303-724-8499
Fax: 303-724-0802
[email protected]
Contact: Melissa Keays
303-399-8020 x3497
[email protected]
http://www.ucdenver.edu/academics/colleges/medicine/research/MAVRC/ResearchResources/S
haredFacilities/Pages/MAVRCCoreFacilities.aspx
The MAVRC/Denver VA Flow Cytometry Core is a user-supported facility purchased by
the VA (VA Eastern Colorado Health Care System) in January 2009. Located in Building
23 at the Denver Veteran's Administration, 1055 Clermont Street, the 3-laser instrument
evaluates from 1-14 colors, size and granularity of cells.
After initial training, the instrument can be operated successfully by laboratory personnel
without a core operator, although assistance is available from the Core Supervisor.
LSR II Flow Cytometer 3-Laser Configuration:
Each lettered circle represents a photomultiplier tube (PMT). The rectangle closest to the PMT is the
"high pass" filter that shows the range of wavelengths passing through the filter (e.g., 780/60 = 750-
810?). The lower rectangle is the "long pass" filter that shows the highest wavelength emitted to the next
alphabetical PMT (e.g, 755 LP). Additional filters: 635 LP; 600LP; 670/14; 610/20; and 585/42.
BILLING:
LSRII VA user $60/hr x ____ hours = $______
Alone: Non-VA user $80/hr x ____ hours = $______
LSRII VA user $75/hr x ____ hours = $______
Assisted: Non-VA user $90/hr x ____ hours = $______
** Charges are applied in 15 minute increments **
** Cancellations less than 24 hours prior will be charged 40% of reservation **
VA/MAVRC user____ Non-VA/MAVRC user____
SAMPLES:
Cell type/source: Human: Other:
Number of tubes:
Concentration:
Volume/tube:
Infected (e.g. HBV, HCV, EBV, HIV, etc.)? Yes ____ No ____
Fixed in at least 1% Paraformaldehyde? (Required) Yes ____
BILLING:
LSRII VA user $60/hour x ____ hours = $______
Alone: Non-VA user $80/hour x ____ hours = $______
LSRII VA user $75/hr x ____ hours = $______
Assisted: Non-VA user $90/hr x ____ hours = $______
Date: Time in: Time out:
User Name:
Billing Address:
User Email:
User Phone:
PI Name:
VA Grant Name or Speedtype:
VA Grant Name ____________ UCD Speedtype ____________
Department/Administrator contact:
Name: Email: Phone:
Eastern Colorado Health Care System, Denver VAMC
Mucosal and Vaccine Research Colorado (MAVRC)
FLOW CYTOMETRY CORE FACILITY
Billing Form
** Charges are applied in 15 minute increments **
** Cancellations less than 24 hours prior will be charged 40% of reservation **
Mucosal & Vaccine Research Ctr.
From: Janoff, Edward
Sent: Tuesday, November 03, 2009 10:43 PM
a) How is the quality of your measurements evaluated – quality control?
We test and record internal validation of the B-D LSR II flow cytometry daily and use
standardized fluorescent beads daily as well to standardize the equipment.
b) What is the turn-a-round time for the service you provide?
Samples can typically be run the same day
c) Who documents the data provided and signs off on the data?
The core supervisor reviews and validates all data run by the core technicians. Most
investigators test their own samples after instruction on the instrument's use.
d) Have you had experience providing data for industry?
Yes.
e) Do you have a standard operating procedure manual?
Not as yet.
f) How will you track billing and financial aspects of your core?
Investigators can be billed on University Speed types.
Pathology Shared Core Service
University of Colorado Cancer Center
Contacts:
Wilbur Franklin, MD, PhD
Director
[email protected]
303-724-3080
Jennifer Richer, PhD
Co-Director
[email protected]
303-724-3735
M. Scott Lucia, MD
Co-Director
[email protected]
303-724-3470
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/pathology/pathology.aspx
The University of Colorado Cancer Center Pathology Core ensures that well-characterized
human tumors and materials derived from human tumors to are provided to Cancer Center and
other funded investigators for research in human cancer. The Pathology Core:
1. Establishes priorities for tissue collection. With the support of the Core, members of the
UCCC have obtained separate funding to support large organ-based repositories
2. Serves as a central planning resource for these separate repositories
3. Interacts with the Biostatistics/informatics and Clinical Investigation Cores to provide an
optimal infrastructure for the conduct of translation research
4. Provides supplemental and backup support for the repositories
5. Offers diagnostic assistance and tissue processing services, including histological and
immunohistochemical services, to Cancer Center investigators who are not supported by
a separate tissue bank
The Core provides central infrastructure for separately funded banks that are increasing in
number and sophistication. In 2007, the Southwest Oncology Group solid tumor banks moved
entirely to Colorado.
Tissue Procurement Shared Core Service
The Tissue Procurement Core provides University of Colorado Cancer Center members and
other funded researchers with well-characterized human tumors and materials derived from
human tumors for research in human cancer. Our organ-based pathology subspecialists
contribute anatomic expertise to organizing collection protocols and verify histopathological
classification of specimens we collect.
We provide investigators with IRB-approved protocols and pathology subspecialist collaborators
with:
• frozen tissue fragments
• tissue sections
• DNA
• RNA
• cells purified by microdissection from tumors, preneoplastic lesions and matched normal
control tissue
Services We Provide
• Tissue grossing
• Tissue processing
• Tissue embedding
• Cutting paraffin and frozen sections
• HE staining
• Cell line fixation, including cell pallet creation
• Tissue array block creation from donor blocks
• Tissue array cutting
• Special cutting and staining sections for microdissection
• Immunohistochemistry staining, including antibody standardizations
• Tunnel assay staining
• Histology special stains #88312 & 88313
• Ventana Benchmark XT for automated immunohistochemistry
Turnaround time depends on the specimen or project. Please contact Betsy Baker for a time
estimate for your project.
Equipment
• Ventana Benchmark XT for automated IHC
• Tissue-Tek Vacuum Infiltration Processor
• Microm Tissue Embedding Unit
• Microm Paraffin Microtome
• Biocare Medical Decloaking Chamber for Antigen Retrieval
• Fisher Tissue Prep Flotation Bath for Paraffin Sections
• Thermo Shandon Slide Heater-Oven
• Fisher Isotemp 205 Water Bath for heating up reagents
• Fisher Isotemp Table Top Oven for Reagent Incuvation
• Forma Liquid Nitrogen Freezer with Inventory Storage System
Tissue Procurement Prices
The Tissue Procurement Core offers discounts to University of Colorado Cancer Center
Members. Other investigators are also welcome to use our services.
Description of Procedures
Cancer Center Member
Price
Non-Cancer Center Member
Price
Grossing $ 1.00 $ 2.00
Processing $ 4.00 $ 6.00
Embedding $ 2.00 $ 4.00
Cutting blanks $ 1.00 $ 4.00
HE stain from slide $ 4.00 $ 5.00
Special Fixation of Cell lines $ 2.00 $ 14.00
Cell Pallet Creation $ 1.00 $ 14.00
Tissue Array Block Creation $ 49.00 $ 554.00
Cut Tissue Array $ 4.00 $ 8.00
Cut 10µm blanks for
Micordissection
$ 1.00 $ 5.00
Stain blanks for Micro-dissection $ 3.00 $ 10.00
Cut 50µm rolls for DNA
extraction
$ 1.00 $ 2.00
Cytospins $ 1.00 $ 3.00
Remove Coverslips $ - $ 2.00
Cut 1st blank - Frozen $ 11.00 $ 24.00
Cut addn blanks - Frozen $ 2.00 $ 7.00
Cut-Stain (HE) - Frozen $ 16.00 $ 34.00
Manual IHC Stain $ 25.00 $ 68.00
Automated IHC Stain $ 24.00 $ 59.00
Tunnel Assay $ 8.00 $ 33.00
Scraping Microdissection $ 38.00 $ 38.00
Laser Microdissection - Manual $ 66.00 $ 66.00
Laser Microdissection -
Automated
$ 59.00 $ 59.00
Tissue Request $ 2.00 $ 28.00
Core Punch from FFPE Block $ 3.00 $ 16.00
DNA Extraction $ 20.00 $ 148.00
Lightcycler HRM Screening $ 18.00 $ 171.00
Direct Sequencing of Mutations $ 23.00 $ 279.00
Prices effective 7/1/08 to 6/30/09
Please see the Morphology and Phenotyping Core for specialty dermal and tissue pathology
services.
Peptide and Protein Chemistry Core
Contacts:
Robert Hodges, PhD
Director
303-724-3268
fax: 303-724-3249
12801 E. 17
th
Avenue, Mail Stop 8101
RC-1 South Tower, Room 9121
[email protected]
Dziuleta Cepeniene,
Operations Specialist
Voice: 303-724-3336
12801 E. 17
th
Avenue, Mail Stop 8101
[email protected]
Website:http://biomol.uchsc.edu/cores/peptidechem/main.html
The Peptide and Protein Chemistry core at the University of Colorado Fitzsimons campus
provides peptide synthesis, purification and peptide/protein composition analysis as well as mass
spectrometry services for academic and industrial clients.
The Peptide and Protein Chemistry core personnel help users choose and design experiments
using appropriate chemistry/instrumentation, to obtain the necessary data, and interpret the
results. The Core also provides instruction for graduate students and postdoctoral fellows for the
use of HPLC and LC/MS approaches.
The core is equipped with state of the art instrumentation and technical support suitable for
diverse applications and samples.
Rates
PEPTIDE SYNTHESIS
• Minimum charge is for 10 residues ($250)
• 0.1 mM scale (50-100 mg crude peptide): $25 per residue
• 0.25 mM scale (100-300 mg crude peptide): $40 per residue
• All peptides are cleaved from the resin, resolubilized in appropriate solvent, and analyzed
by reversed phase HPLC and mass spectrometry
• Preparative HPLC purification of synthetic peptides: $100 per peptide
• Additional modification of peptides:
o phosphorylation: $100 - $150
o acetylation: $15
o C-terminal biotin: $175
o fluorescent label: $200
o N-terminal biotin: $100
o methylation: $175 - $400
AMINO ACID ANALYSIS
• $40 per sample
MASS SPECTROMETRY
• Mass determination of peptides by LC/MS: $15 per sample, $100/hour
• LC/MS/MS analysis: $30 per sample, $100/hour
Pharmacology Core
Contacts:
Daniel L. Gustafson, PhD,
Director
[email protected]
970-297-1278
Ryan J. Hansen, Ph.D.
[email protected]
Brad Samber
[email protected]
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/pharmacology/index.aspx
The University of Colorado Cancer Center Pharmacology Core, located at Colorado State
University in Fort Collins, was established to work with researchers and clinicians in a
collaborative manner to design and implement studies to measure xenobiotics (drugs, toxicants,
natural products, inc.) in biological systems and matrices.
• We are an analytical laboratory focused on drug measurement.
• We help investigators with study design, sample collection, sample analysis and data
interpretation.
The mission of the Pharmacology Core is to assist in the prospective design of studies to assess
drug exposure in biological systems, to measure drug levels using validated analytical assays,
and to analyze, model and interpret the results.
Pharmacology Core Services
We offer services based on our experience with use requests through our years of operation. We
regularly modify the services we offer depending on Cancer Center members' needs and how
they use the Core. We offer members discounted fees for service, which are calculated either per
sample or on an hourly basis.
We offer the following services.
1. Analyte determination and quantitation in matrix (per sample)
2. Assay setup and validation (hourly)
3. Metabolite identification and analysis (hourly)
4. Sample analysis and identification (hourly)
5. Pharmacokinetic modeling (hourly)
6. Animal treatment and sampling (hourly)
How to Order Services
To order services, you will need to consult with either the Core Director or Core Personnel by
telephone or email. See the contact panel on the right for phone and email information.
Prices
The cost for various core services is based on either hourly charges or per sample charges
depending on the requested service. For the quantitation of an analyte in a submitted sample,
prices depend on whether we have a validated assay for that analyte and the number of samples
submitted. Listed below is our current pricing structure:
Service UCCC Member UCCC Non-Member
Analyte Quantitation (per sample)
Batch size 1 - 40 samples $78.35 $126.44
Batch size 41 – 500 samples $45.00 $72.62
500+ samples Contact for Quote
Assay Setup and Validation (per hour)
$144.75 $204.54
Metabolite ID and Analysis (per hour)
$225.36 $333.50
Sample Analysis and ID (per hour)
$225.36 $333.50
Pharmacokinetic Modeling (per hour)
$64.40 $159.89
Animal Treatment and sampling (per hour)
Contact for Quote
*Batch size is determined by the number of samples expected to be analyzed at a given time. For
example, if a study includes a total of 200 samples but are shipped to us and expected to be
analyzed in groups of 20 for data reporting, the batch size is 20.
The Pregnancy Core
Peggy Neville, PhD
303-724-3505
[email protected]
The Pregnancy Core in the Department of Ob/GYN is designed to assist researchers from all
departments at University of Colorado Denver with their research on pregnant women and
eventually their offspring. We offer assistance with recruiting of subjects in a number of venues,
a biological sample repository with facilities for bar coded samples is available at cost, services
on labor and delivery including cord blood and placental samples, a database with about 500
variables collected on all subjects who deliver at University Hospital, information on studies
conducted on the adult CTRC on pregnant women. Use of these facilities is subject to project
review by the OB/GYN Research Review Committee and relevant fees will be charged for most
services. For additional information please contact [email protected].
University of Colorado Cancer Center
Protein Production/MoAB/Tissue Culture
Shared Core Service
Contacts:
Steve Nordeen, PhD
Director
[email protected]
303-724-4301
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/tissue-
culture/index.aspx
The Protein Production/MoAB/Tissue Culture Core, located on the Anschutz Medical Campus,
offers services to UCCC members, other academic investigators and private companies. We have
more than 10 years of experience with protein production in the baculovirus system cell fusion,
as well as developing new monoclonal antibodies and small- to large-scale culture of a wide
range of cell lines.
Services We Offer
Custom Hybridoma Services
• Construction of new hybridomas
• In vitro production of monoclonal antibodies from existing hybridomas
Custom Baculovirus Services
• Construction of recombinant virus
• Amplification and titering of recombinant baculovirus stocks
• Protein production in insect cells
Cell Line Repository
• >150 cancer cell lines, including 51 different lung cancer cell lines and 11 breast cancer
cell lines
On-Site Culture Media/Serum Supply Center
Offered to all UCCC and UC Denver investigators at prices substantially below list
• Liquid cell culture medium from Invitrogen and HyClone
• Supplements
• Serum from HyClone
Tissue Culture & Monoclonal Antibody Core
Prices
Members
Non-
Members
Commercial
Baculovirus
Co-transfection $95 $470 $940
Bacmid Transfection $132 $208 $417
Titer a virus $18 $66 $133
Plaque Purify Existing Viral Stock $53 $248 $495
Produce 500 ml viral stock $126 $450 $899
150 ml protein production $36 $162 $324
300 ml protein production $49 $176 $351
500 ml protein production $67 $199 $398
2.0 liter bioreactor $258 $470 $939
5.0 Liter bioreactor $428 $664 $1,328
Fusions
Mouse Injections and Bleeds/Animal $216 $286 $572
Fusion including ELISA screenings $541 $1,210 $2,421
Cloning of 1 positive hybridoma $117 $380 $760
Isotyping/hybridoma $2 $12 $24
Freeze additional 1 polyclonal-2
ampules
$43 $139 $279
Storage for 1 year of 6 ampules of 1
hybridoma
$16 $63 $126
Monoclonal Antibody Production
Produce 1-4 liters of hybridoma supt./
liter
$146 $348 $697
Produce 5 - 20 liters of hybridoma supt./
liter
$112 $179 $358
Hybridoma CL1000 Startup $162 $254 $508
Hybridoma CL1000 10weeks culture $1,066 $1,529 $3,059
Purification of hybridoma supt. for 1-4L $290 $484 $967
Purification of hybridoma supt 5L $557 $842 $1,685
Cell Culture
Freeze six ampule of 1 cell line $81 $180 $361
Cell lines - live cultures $51 $124 $248
Cell lines - frozen ampule $17 $65 $130
Mycoplasma Test $24 $45 $90
Mammalian Transfection and Large Scale Cell
Culture
Mammalian Cell Stable Transfection $270 $627 $1,254
Freeze down of additional 1
Mammalian Stables
$60 $132 $264
Cloning of 1 positive Mammalian
Stables
$203 $473 $947
Produce 1-4 liters of cell culture/liter $187 $287 $574
Produce 5-20 liters of cell culture/liter $90 $152 $305
CL1000 Flask Start up $259 $305 $609
CL1000 culture/week $84 $166 $331
Prices effective 07/01/08-06/30/09
Protein Production/MoAB/Tissue Culture Shared Core Service (UCCC)
From: Nordeen, Steve
Sent: Friday, October 02, 2009 2:46 PM
a) How is the quality of your measurements evaluated – quality control?
We provide more product than measurements and most of the evaluation of
that is done by the end users since each it specific for the individual lab and
project.
b) What is the turn-a-round time for the service you provide?
From consultation with the core and submission of the request projects are
begun from one day to 4-6 weeks depending on the project. The longer times
are for production of protein via baculovirus and we have purchased new
equipment and hired a part time technician recently in order to decrease the
waiting time on these projects. The actual projects may take less than a day
to 3 or 4 months depending on the project.
c) Who documents the data provided and signs off on the data?
Data is collected by the technical staff doing the production.
d) Have you had experience providing data for industry?
We have several industrial clients.
e) Do you have a standard operating procedure manual?
Yes
f) How will you track billing and financial aspects of your core?
The Lab Manager fills out the invoices and the Cancer Center administration
does the billing. We work closely with the Cancer Center administrative
staff on our budgets.
price list:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/tissue-
culture/prices.aspx
Mass Spectrometry/Proteomics Core Facility and Cancer Center
Proteomics Shared Core Service
Contacts:
Mark Duncan, PhD
Co-Director
[email protected]
303-724-3343
Natalie Ahn, PhD
Co-Director
[email protected]
303-492-4799
Kirk Hansen, PhD
Anschutz Facility Core
Manager
[email protected]
303 724-3325
Website:http://www.uccc.info/for-healthcare-professional/cancer-
center/cores/proteomics/index.aspx
The University of Colorado Cancer Center's Proteomics Shared Core Service aims to provide the
expertise, technical resources, training and collaborative interactions that enable Cancer Center
members to undertake detailed proteomic studies.
Cancer Center members have access to proteomics labs on two campuses:
• Anschutz Medical Campus
• Boulder Campus -http://www.colorado.edu/Chemistry/masspec/
Overview
The goal of the Proteomics Facility is to provide investigators with the capabilities to identify,
characterize and quantify the proteins present in tissues, cells and biological fluids. Through the
development of advanced methods, the Facility aims to assist members with solving difficult or
previously intractable problems in biomedical research. Methods for protein and peptide
isolation, separations, quantification, identification and bioinformatics analysis, together with
expert guidance in study design, are integrated into expertise offered by the Facility. The Facility
has access to several analytical technologies thereby allowing investigators to adopt multiple
strategies and to independently verify their findings. The Facility also provides training in
proteomics analysis and experimental design
Facility Fees
A charge is applied to all users of the resource to offset, the running costs associated with
maintaining this facility. Details of the fees are given in the following table.
Trained Individuals may use equipment in the facility at the following rates:
Equipment Usage (Trained Personel) Cancer
Center
Member
Non-
Member
2D Gel Electrophoresis Contact Facility
Protein Chromatography $55 $80
MALDI-TOF (per hr) $25 $35
LC/MS/MS ion trap (per hr) $58 $80
LC/MS/MS Qq-TOF (per hr) Contact Facility
Analysis Cancer
Center
Member
Non-
Member
Sample Preparation $18 $283
Protein Separation 1D-GE $25 $111
Protein Seperation 2D-GE $200 $588
Protein Separation 2D-LC $34 $211
Protein ID by Peptide Mass ID-MS $10 $78
Protein ID by Tandem Mass ID-MSMS $58 $200
Protein Molecular Weight Determination $44 $191
RADScIence Clinical Trial Physics Support
Ann Scherzinger, PhD
Chief, Division of Radiological Sciences
Department of Radiology, C-278
U of Colorado Denver, School of Medicine, Anschutz Medical Campus
Aurora, CO 80045
303-724-3766http://www.uchsc.edu/ucbirl/index.php
If your core business isn’t the assessment of radiological images or the use of radiation, how
do you effectively evaluate a centralized radiology reading center, provide IRBs and
regulatory agencies with safety information, or assess novel imaging techniques or analyses?
What HIPAA issues and technology hurdles will impact your operations and data submission
timelines? RadScience can provide valuable insight during the due diligence and startup
processes.
DCE-MRI, TOF PET, fMRI....
If you're awash in a sea of strange acronyms and technology, we can help. RadScience
provides quality educational services to transform even the most daunting technologies into a
concise, comprehensible framework. Whether you need support for your clinical development
group, CRAs, medical writers or investigators, trust RadScience to keep you informed and
educated in the fast-paced world of medical imaging and radiation technology.
Protocol Development and Quality Control
A new imaging technique looks promising for your clinical study. But what are the pitfalls of
implementing it in a multi-site environment? What factors may bias the results or drown out
that important signal with noise? If you’re going to invest in an imaging biomarker, consult
with RadScience regarding protocol feasibility, optimization and quality control issues and
services.
Dosimetry Services
Don’t try looking it up in a book. With the advent of multi-slice CT, dual modality systems
and increasingly complicated imaging protocols, estimating patient radiation dose can be a
daunting task. RadScience provides concise, accurate dose estimates for your imaging studies
that can be submitted for IRB and regulatory review.
Risk Analysis
So you know the radiation dose, but what does that mean? Age, organ type, exposure duration
and frequency are just some of the factors that can influence health risks. Know the risks
associated with your imaging study so you can better inform your subjects and comply with
GCP requirements.
Fees:
Under Construction
Research Design and Analysis Core
Contacts:
Samantha MaWhinney, ScD
Core Director
303-724-4368
[email protected]
Website:http://www.uchsc.edu/ccfar/cores/virology.htm
The Research Design and Analysis Core (RD&A) within the Colorado Center for AIDS
Research (CFAR) provides assistance with HIV/AIDS-related grant applications. Limited
statistical consulting is available to CFAR members for $75 per hour. Overflow is directed to
the Colorado Biostatistics Consortium for $125 per hour. Statistical training and mentoring
opportunities include short courses, lectures and online tutorials. The RD&A Core is in the
process of integrating these educational programs with the Colorado CTSI.
The overall goal of the CFAR Research Design and Analysis Core is to assist researchers across
a wide range of specialties in their goal of a scientifically rigorous approach to understanding
and preventing HIV-1 disease. Assistance will be provided through consulting, training,
communication and research collaboration. We will employ the most appropriate methods
combined with graphical summaries to aid interpretation. We strive to enhance the biostatistical
contribution to HIV/AIDS research within the Colorado CFAR through better understanding of
HIV/AIDS immunology, virology and laboratory assays. We will develop new methods and
pursue new research agendas in Epidemiology and Community Health to increase the quality and
breadth of HIV/AIDS research in Colorado.
The Research Design and Analysis Core will expand the range of Biostatistical, Epidemiological and
Community Health services for D-CFAR investigators. We will offer educational opportunities,
training and mentoring to junior faculty; and provide leadership in research design and analysis in
concert with a public health perspective to the overall D-CFAR. Motivated by interdisciplinary work
we will develop innovative analytic approaches to identify research gaps and further HIV/AIDS
research in Colorado.
The Research Design and Analysis Core (RD&A) within the Colorado Center for AIDS
Research (CFAR) provides assistance with HIV/AIDS-related grant applications. Limited
statistical consulting is available to CFAR members for $75 per hour. Overflow is directed to
the Colorado Biostatistics Consortium for $125 per hour. Statistical training and mentoring
opportunities include short courses, lectures and online tutorials. The RD&A Core is in the
process of integrating these educational programs with the Colorado CTSI.
Research Design & Analysis Core (CFAR)
From: MaWhinney, Sam
Sent: Monday, November 09, 2009 2:35 PM
For the CFAR Research Design and Analysis Core (Sam MaWhinney, Core Director)
a) How is the quality of your measurements evaluated – quality control?
Biostatistical Services: Not applicable
b) What is the turn-a-round time for the service you provide?
Services related to study design for grants get priority, but we try to meet with
investigators within a few days of receiving requests. Projects then range from a
few hours to months.
c) Who documents the data provided and signs off on the data?
The primary investigator for the project is responsible for data integrity. We
generally do logical checks and graphical analyses to identify data outliers, which
will be double checked for accuracy.
d) Have you had experience providing data for industry?
Not through the CFAR RD&A core
e) Do you have a standard operating procedure manual?
No
f) How will you track billing and financial aspects of your core?
We have a charge back system.
Rodent Neurophysiology
Contact:
Yogendra Raol, PhD
Director
University of Colorado Denver- Anschutz Medical Campus
303-724-4257
[email protected]http://www.uchsc.edu/peds/research/cores/RIVNC.pdf
The UCD Rodent I n Vivo Neurophysiology Core
The c ore f acility p rovides c ontinuous r odent be havioral a nd ne urophysiological/EEG
monitoring ( including c erebral e lectrical pa tterns dur ing w aking a nd s leep, he art r ate,
respiration, E MG). T his t ype o f mo nitoring will p ermit in vestigators a t U CD to mo re
thoroughly ph enotype t he r odents t hey are us ing i n t heir r esearch a nd s pecifically address
issues of whether they have abnormalities of neurophysiological functioning such as interictal
epileptiform di scharges, s leep di sturbances and s eizures. T his c an be i mportant f or t he
characterization of translational models of nervous system disorders including stroke, epilepsy,
head trauma, neurodegenerative, psychiatric, genetic and developmental disorders. Equipment
available i n t he R odent In V ivo N europhysiology M onitoring C ore f acility i ncludes a n
inhalational anesthesia system, Angle 2 stereotactic apparatus with rat and mouse at lases and
video microscope for electrode placement and cerebral injections, microinfusion pump, and 48
cages ( 32 r at a nd 16 m ouse) e quipped f or vi deo_EEG m onitoring ( Stellate a nd P innacle
systems).
Core Personnel
Yogendra H. Raol, PhD (Director) is an Assistant Professor in the Department of Pediatrics,
School of Medicine. Dr. Raol has over 14 years of experience with in vivo neurophysiological
recording in rodents. Dr. Raol is responsible for the management of the daily operations of the
core facility, and training and supervision of the technicians.
Doron Shmueli, is a technician for the core. He obtained his BS degree i n Engineering from
the University o f Colorado. Doron i s a n e xpert i n i ntracranial electrode i mplantation, EEG
recording an d an alyses and was t rained with n eurologist Dr. Andy White a t University of
Colorado Denver.
Services Rate
Neurophysiology/EEG monitoring $8.35/day
Electrode implantation surgery $140/procedure
(surgery performed by core personnel)
Use of surgical supplies/facilities for $46/procedure
electrode implantation
(surgery perform by investigator)
1
Shared Analytical Service Laboratory (SASL)
J eff Boon
Laboratory Manager
303-556-2964
J [email protected]
http://thunder1.cudenver.edu/clas/sasl/index.html
Oversight Committee:
Dr. Dave Albeck, Department of Psychology
Dr. Larry Anderson, Department of Chemistry
Dr. Timberly Roane, Department of Biology
- Mission Statement -
The Shared Analytical Services Laboratory provides basic and analytical chemistry related
resources, including advanced analytical instrumentation. With the increase in the
interdisciplinary nature of research, the SASL supports the analytical chemistry needs across all
scientific disciplines. Additionally, the continuing effort to more efficiently use University
resources has created a demand for sharing resources.
The SASL allows researchers from a variety of disciplines to utilize analytical tools without
having to invest time, money, or resources towards maintaining the effort in their own research
groups. At the same time, the Laboratory allows faculty the freedom from duplicating
instrumentation and other resources that are used only peripherally. Finally, the SASL works to
support the efforts of the other colleges of the UCD, and to support the wider community.
- Instrumentation -
The following instrumentation is available for use in the Shared Analytical Service Laboratory.
While this equipment is fully functional, in some cases, like the gas and ion chromatographs and
the Hitachi GFAA, instruments have been shut down to save on the cost of the consumables.
Restarting the instrument may take several days before it would be ready for analytical use.
Perkin Elmer Model 5000 Flame Atomic Absorption Spectrophotometer – The flame
AA is a quick, easy, and inexpensive method to determine the concentration of a metal in
a liquid sample. The detection limits for the AA are dependent on the desired analyte and
the sample matrix, but are typically in the low parts-per-million range. Solid samples,
and some samples with complex matrices (i.e. blood), must be digested prior to
performing the analysis.
Hitachi Z-8270 Polarized Zeeman Graphite Furnace Atomic Absorbance
Spectrophotometer - Like the PE 5000 AA, the Hitachi GFAA is used to determine the
2
concentration of a metal in a sample. Unlike the PE 5000, which uses a flame to atomize
the metal species, the Hitachi uses an electrically heated graphite tube to turn the solvated
metal species into gaseous metal atoms, for analysis. The Hitachi uses a very small
aliquot of the sample (20 microliters for most analysis) and has detection limits in the low
parts-per-billion range.
Leeman Labs, Inc. PS 200 II Automated Mercury Analyzer – It is very difficult to
analyze for mercury using either the PE 5000 AA or the Hitachi GFAA. Sample prep is
time consuming, the instruments must be reconfigured, and either result in poor detection
limits. To address these shortcomings, Leeman Labs created their dedicated mercury
analyzer. The mercury analyzer combines an aliquot of the sample with tin chloride to
convert all of the mercury containing species in the sample and liberates ground state
gaseous mercury. This gaseous mercury is then analyzed in a manner similar to the PE
5000 and the Hitachi. Depending on how the instrument is configured, the detection
limits for the mercury analyzer can be in the low parts-per-trillion range.
HP 5890 Gas Chromatograph fitted with both a Perkin Elmer ATD 4000 Thermal
Desorption Sampling System and a Dynatech DynaSoils Purge and Trap Sampling
System. – The combination of these three instruments allow for the determination of
volatile and semi-volatile organic compounds in either gaseous or liquid samples. Bothe
systems are fitted with autosamplers for more convenient sample analysis. The HP 5890
uses a flame ionization detector which offers very good detection limits but doesn’t allow
for the analyte confirmation that the GC-MS would.
Applied Biosystems 4000 Q Trap Triple Quad Mass Spectrometer coupled with an
Eksigent Temp nano MDLC (LC-MS) – The LC-MS is the newest instrument in the
lab. The LC-MS is used to separate and identify mixtures of organic compounds that
would be too big for analysis by the GC-MS. The liquid chromatograph separates a
mixture of compounds which are then introduced into the mass spectrometer as they elute
off of the end of the LC column. The LC-MS has a wide range of applications, ranging
from the analysis of proteins in a cell to the identification of drugs in forensic toxicology,
to the determination of organic pollutants in environmental monitoring. The LC is a
“nano” scale chromatograph, meaning that it uses extremely small amounts of sample
(about 1 microliter) and small eluant flow rates (typically 250 nanoliters per minute).
The mass spectrometer is a triple-quad, meaning that as the compound comes off of the
chromatographic column and into the MS, the compound is ionized. The instrument can
either display all of the produce ions, or one ion can be selected for further fragmentation.
These subsequent fragments can be displayed or further fragmented. The multiple
fragmentations can be used to isolate one compound out of a complex mixture.
Dionex 4500i Ion Chromatograph – The IC allows for the separation and quantitation
of ionic species in a liquid matrix. Most frequently this involves the determination of
anions such as fluoride, chloride, nitrate, nitrite, sulfate, and sulfite, or cations such as
ammonium, sodium calcium, and potassium. The IC is equipped with both conductivity
and pulsed electrochemical detectors.
3
Hewlett-Packard 5890 Gas Chromatograph coupled with a Hewlett Packard Model
5970B Mass Selective Detector. This system, most commonly referred to as a GC-MS
is used to separate and quantify the volatile chemical compounds in a liquid sample. The
GC-MS is a commonly used instrument with a wide range of columns available for the
analysis of different classes of compounds. In some instances sample preparation or
method development can be time consuming.
Tekmar Model 6000 Thermal Desorption System – The Tekmar is a sampling system
attached to the Hewlett Packard GC-MS discussed above, and allows for the
determination of volatile and semi-volatile species in a gaseous sample. Unlike the ATD
400 discussed above, the Tekmar is a single-tube system, requiring the analyst to
physically mount and remove each of the sample for analysis.
Technicon TRAACS 800 Continuous Flow Analytical System – The Techincon is
typically used by engineers and industry to monitor a range of inorganic species. The
system adds a series of reagents to a portion of the sample to create a color change in the
sample. The intensity of the color is an indication of the concentration of the species in
the sample. A series of analyte-specific modules are installed in the instrument for each
analysis. Some of the possible analytes include nitrogen species, some of the industrial
important metals, and a range of water-quality related ions.
Thermo Separations Products P4000 Liquid Chromatograph and UV1000 Detector
(LC) – The LC is a widely used instrument for the separation of organic compounds that
are too big to be determined by the GC or GC-MS. After separation, the compounds are
passed through the UV detector where any compounds with a UV absorbance are
detected. Currently the LC is set up for the separation and determination of the tricyclic
antidepressants, but through the installation of the appropriate column most organic
compounds can be determined with the LC. Without the presence of a mass spectrometer,
the identification of the eluting species is determined by the time it takes the species to
come off of the column. Because of this lack of verification, a careful method
development cycle is important for any analysis.
Cary 1E UV-Vis Spectrophotometer – The Cary is a general purpose UV-Vis
spectrophotometer, designed to show which wavelengths of ultra-violet and visible light
are absorbed by a compound. It is typically used for the characterization of a compound
prior to analysis by another technique, or to follow the process of a reaction, where one of
the reactants or products absorbs in the UV-Vis region.
Nicolet Analytical Instruments MX-S Infrared Spectrophotometer (FTIR) – Like the
Cary, the FTIR is a general purpose spectrophotometer, but instead of the UV-Vis region,
the Cary determines the absorption characteristics of a compound in the IR region of the
spectrum. The Nicolet FTIR is a general use instrument and not necessarily a “research-
grade” instrument.
4
The following pieces of instrumentation are currently in various states of repair. All are
expected to become operational as time and money for repairs are available.
Thermo Jarrell Ash ICAP 61 Inductively Coupled Argon Plasma
Spectrophotometer (ICP) – The ICP is used for the observation and quantitation of
metals in a liquid matrix. The ICP has detection limits that are significantly better than
the PE 5000 flame AA and slightly better than the Hitachi GFAA. Like the AAs,
detection limits vary from element to element. The ICP requires a large amount of argon
for operation, so the cost per sample is relatively high.
Perkin Elmer ELAN 6000 Inductively Coupled Argon Plasma Mass Spectrometer
(ICP-MS) – The ICP-MS is very comparable to the ICP, but instead of optically
determining the presence of a metal, the ICP-MS determines the presence of a metal by
observing the masses of the ions coming out of the plasma. There are several major
benefits to observing the masses of the ions. First, the ICP-MS has better detection limits
than the ICP for virtually all elements. Second, the ICP-MS is capable of analyzing for
all of the metallic elements simultaneously. Finally, the ICP-MS is capable of observing
and determining the concentrations of the different isotopes of a particular element. With
this capability, it is possible to perform experiments like carbon 14 dating. Like the ICP,
the ICP-MS uses a lot of argon, so the cost per sample is high.
JEOL 5300 Scanning Electron Microscope (SEM) – The SEM is a microscope that can
observe small samples at up to 200,000 X magnification. The stage of the SEM is only
about 2” x 2”, and must be evacuated, so the type of samples can be limited.
Mattson Polaris Fourier Transform Infrared Spectrophotometer (FTIR) – The
Mattson is a “research-grade” instrument that provides the same basic information as the
Nicolet described above. The Mattson is designed to be fitted with an external long path
gas cell for the determination of atmospheric species.
5
Administration - Pricing
Note - The charging mechanisms used by the Centers and Service Units of the University of
Colorado Denver (UCD) are currently being reviewed and revised. These revisions are required
to adhere to new policies instituted by several federal granting agencies. Our revised pricing
schedule will be published to this page once the new policies have been finalized. Until that time
the current schedule is in use and any pricing questions should be directed to the Laboratory
Manager.
The price schedule for analytical services or use of the Laboratory is based on the affiliation of
the customer to the University and to the College of Liberal Arts and Sciences. The charge to
faculty is based on the cost of performing the analysis. These costs are calculated from the
analyst cost, instrument depreciation, and the cost of the materials and supplies consumed to
perform the analysis. Typically, the analyst cost is the major expense in an analysis. It is possible
to decrease the cost of the analysis by using either a student working for the Laboratory, or an
acceptable qualified and trained student of the faculty member. Costs associated with particular
instrumentation can be found under the instrumentation section.
Since the budget for the Laboratory is provided by the College of Liberal Arts and Sciences,
CLAS Faculty pay 150 percent of the cost of the analysis. In some cases, the costs of a short
study to investigate the feasibility of a procedure, with an eye towards submitting a grant
proposal using the method, may be underwritten by the Laboratory.
Non-CLAS Faculty are charged 250 percent of the cost of the analysis. As with CLAS faculty,
the cost of the analysis can be minimized by using a student analyst.
The Laboratory actively seeks and invites industrial use of the Laboratory. Because of issues
regarding tax-payer funded competition with private laboratories, we are required to charge a
minimum of 95% of the cost for a comparable analysis performed by a private laboratory. If
trade secrecy aspects and time frame required for the analysis permit, we encourage industry to
perform the analysis as a research contract with the University. In this mode, the analysis would
be performed by a student, under the oversight of the Laboratory Manager and a responsible
faculty member. This type of interaction enhances the education of the student while, at the same
time, providing a cost effective analysis to the client.
Finally, we recognize the connection of the University to the community in which we live. The
Laboratory supports small, limited scale work to the general community. In practice this has
involved helping primary students with some chemical aspects of their science fair projects.
Contact the Laboratory Manager for pricing and a complete listing of services.
Statistical Consulting Service
Contact:
Loren Cobb, PhD
Director
303-880-8279
[email protected]
Statistical Consulting Service
Department of Mathematical & Statistical Sciences
CU Building, Sixth Floor
The Statistical Consulting Service (SCS) of the University of Colorado Denver in the
Department of Mathematical and Statistical Sciences provides quantitative consulting of many
kinds to the university community, to industry and government in the Denver metropolitan area,
and to state, federal, and international agencies. For university graduate students engaged in
thesis research this service is free, all others pay on a sliding scale. Our consultants range from
university professors with thirty years of consulting experience, to PhD- and MS-level graduate
students who work on selected projects under faculty supervision.
SCS offers the services of professionals who have experience with both statistical analysis and
mathematical modeling in many areas, as described below.
Statistical Analysis
Research design
Factorial designs, blocking, split-plot designs, randomization, power analysis, contrasts,
multiple comparison adjustments, response surface designs, repeated measures and
covariates, cross-over and time series designs, retrospective studies, prospective single-
and double-blind studies, case control studies, cohort studies, quasi-experimental designs.
Sampling
Probability sampling: random, systematic, stratified, size, cluster, and multistage
sampling; non-probability sampling: quota, purposive, and accidental sampling; political
polling; census methods; sampling for industrial quality control; bootstrap resampling
techniques.
Measurement
Validity and reliability of existing and proposed measures; bias and error patterns in
measurement; dimensionality reduction; performance improvement; measurement
instrument evaluation; latent trait analysis; vector and field measures; transformations;
frequency-domain measurement techniques (spike separation, signal processing,
wavelets, filtering).
ANOVA-related methods
Univariate and multivariate analysis of variance, analysis of covariance, ANOVA with
repeated measures, ANOVA for complex experimental designs.
Regression-related methods
Multiple, polynomial, logistic, weighted, and nonlinear regression; data mining; survival
analysis; principal components and factor analysis; errors-in-variables models; path
analysis; Bayesian regression; robust and non-parametric regression; splines; time series
analysis; spectral and cross-spectral analysis; forecasting.
Genomics and informatics
DNA and RNA microarray analysis; BLAST-like algorithms; structural genomics; Monte
Carlo methods; error modeling and analysis.
Filtering and image methods
Kalman filtering; signal processing; image analysis and pattern recognition; ensemble
and particle filters for spatial filtering, spatial kriging.
Computational statistics
Assistance with R, SAS, MatLab/Maple, Mathematica, Data Desk, and SPSS; numerical
methods; statistical modeling and simulation; genetic algorithms; neural networks;
hierarchical, partition, and spectral clustering; data fusion; dynamic and persistent
statistical databases.
Mathematical statistics
Creation of maximum likelihood and Bayesian estimators; tests of convergence;
nonparametric and robust statistics in Hilbert space; stochastic calculus; stochastic
differential and integral equations; stable distributions; multimodal distributions; implicit
equation models; statistical theory for differential topology; statistical theory for
nonlinear and chaotic systems; fuzzy statistics.
Modeling
Business and industrial operations
Mathematical models of industrial processes, product and process failure models,
information and decision flow, network modeling, catastrophic event models, stochastic
control theory, supply chain modeling, scheduling and queueing, pricing formulas,
predictive models.
Finance
Risk modeling, asset price models, cash flow models, stock price and volatility models,
investment screen development, pooled investment models, survival and actuarial
models, rare event models, econometrics.
Social Science
We offer decades of experience with mathematical modeling in all of the social sciences,
including anthropology, clinical psychology, communication, demography, economics,
education, geography, history, law, linguistics, military science, political science, public
administration, psychology, social work, and sociology.
Biology and Medicine
Genomics modeling, pharmacokinetics, enzyme kinetics, tumor growth models,
competing risks models, ecosystem modeling, fluid flow and transport models,
evolutionary games, epidemic models, population dynamics, spatial models, swarm
models, cellular automata, fishery dynamics, limit cycles and chaos.
Physical Science
Ordinary, partial, and stochastic differential and difference equations, numerical analysis,
statistical error propagation models, thermodynamic models.
Engineering and applied math
Linear and nonlinear systems, stochastic systems, graph and network models, operations
analysis, optimization, numerical analysis, queueing models.
Military
Models of peacekeeping, peace enforcement, and humanitarian operations, post-conflict
stabilization, asymmetric and irregular conflict, national security models, refugee and
displaced-person models, nation-building, satellite coverage optimization, cellular
automata models, models of information warfare.
Fee Schedule (draft-under review)
Client type Consultant type Hourly rate
UC Denver graduate thesis Any FREE
Any Graduate student
under supervision
$50
Unfunded faculty research Math faculty $100
Funded faculty research Math faculty $135 and up
State of Colorado Math faculty $135 and up
Industry Math faculty $150 and up
All rates are negotiable. Call Dr. Cobb for more information: 303-890-8279.
Version of August 2009.
Statistical Consulting Service
Loren Cobb, PhD, Director
a)
We have not yet established a quality control system. We may set up a feedback and
comment system in the future.
How is the quality of your measurements evaluated – quality control?
b)
When a client asks for a statistical analysis, our turn-around time is typically one to seven
days.
What is the turn-a-round time for the service you provide?
c)
We don't provide data; we offer advice on research design, measurement, models, and
analysis. When these services are provided by graduate students, then they do so under
my close supervision. In that restricted sense, I (Loren Cobb) am the person ultimately
responsible.
Who documents the data provided and signs off on the data?
d)
Again, we don't provide data. But yes, we have one or two industrial or business clients
every semester. They come seeking advice on research design, measurement, models, and
analytical methods.
Have you had experience providing data for industry?
e)
No. However, I am teaching a seminar on statistical consulting, and the notes from that
seminar will become the foundation for a consulting manual.
Do you have a standard operating procedure manual?
f)
For each paying client, I record billable hours in a simple spreadsheet. Once a month I
send out an invoice. The majority of our clients are graduate students working on thesis
research, for which our services are free.
How will you track billing and financial aspects of your core?
University of Colorado Cancer Center Small
Animal Imaging Core
Contact:
Natalie Serkova, PhD, Director
Associate Professor, Dept. of Anesthesiology and Radiology
303-266-2910 pager
[email protected]
303-724-1086 phone
303-359-6574 cell
Radiologist Technologist: Kendra Hasebroock (pager 303 266 2247)
Website:http://www.uccc.info/for-healthcare-professional/cancer-center/cores/small-animal-
imaging/index.aspx
The major goal of the small animal imaging program is establishment of novel imaging
approaches to cancer and cancer experimental therapeutics using animal models and
pharmacodynamic endpoints. State-of-the-art imaging facilities are extremely expensive and
require advanced technical personnel. Modern non-invasive imaging technologies include:
• Magnetic Resonance Imaging (MRI for anatomic, physiologic, and molecular imaging)
• Computed Tomography (CT for anatomic imaging)
• Positron Emission Tomography (PET for metabolic and molecular imaging)
• Optical Imaging (Bioluminescence, Fluorescence)
• Ultrasound
Our Small Animal Imaging Core is a developing resource that includes three areas:
• MRI/CT/PET, supervised by Natalie Serkova, PhD (Anesthesiology/ Radiology)
• VisualSonic Ultrasound, supervised by Peter Buttrick, MD (Cardiology)
• IVES (bioilluminescence), supervised by Chuan Li, PhD (Radiation Oncology)
• Irradiation, supervised by David Raben, MD (Radiation Oncology)
MRI/CT/PET Services
The University of Colorado Cancer Center Small Animal Imaging Core offers MRI, CT and PET services to
members and non-members.
Facility
Our facility is fully equipped for magnetic resonance imaging and proton spectroscopy (MRI/
MRS) studies on small animals. All 18FDG-PET and bone- and coft-tissue (enhanced) CT
protocols are available. All standard operating procedures (SOP) for animal imaging are in place.
The facility is currently comprised of approximately 660 sq ft of laboratory space, in which are
housed three imaging modalities (MRI, PET and CT), animal anesthesia equipment, one
physiological monitoring system, animal warming equipment, and computers and data
processing systems.
• The Small Animal Imaging has been in existence since 2005 and is in a nascent stage of
development.
• The MR scanner was purchased in 2005 with support from an NIH-sponsored Shared
Instrumentation grant (PI: N. Serkova).
• The combined microPET/CT system was purchased in July 2007 from collaborative internal grant
to the School of Medicine (PI: N. Serkova, supported by the Cancer Center, Depts. Radiology,
Anesthesiology, the National Jewish Center as well as the Dean Office).
• All equipment maintenance, protocol development, quality controls, as well as assistance
provided to users of the resource is performed by the Dr. Serkova and Radiologist Technologist
Kendra Hasebroock (B.S., MRT).
Equipment
The facility is fully equipped for all aspects of MRI, PET and CT evaluations on small animals,
ex vivo specimens and vivo cell models:
• 4.7 Tesla Bruker Pharmascan MRI/MRS scanner with 1H resonance frequency of 200 MHz, RT
bore without shims 160 mm. The system is equipped with an actively shielded gradient system I
(90 mm inner diameter: x,y,z with 3 mT/m/A); maximum gradient strength 300 mT/m.
• Three volume transmitter/ receiver coils of different diameters (from 22 to 68 mm diameters).
• Siemens Inveon microPET (field of view 12 cm allowing for one-bed position for the whole-body
mouse scan).
• Siemens Inveon microCT (to be installed in February 2008).
• Bruker computer platform is equipped with a high-performance MR-workstation X2000 for use
with Bruker MR softwares (NMR SUITE and PARAVISIONTM 3.0). The PC is configured with Intel
Pentium 1.5 Hz, 1 Gbyte RAM, SCSI Controller Adaptec 29160, 73 GByte Disk, Red Hat LINUX,
20” TFT LCD monitor with graphics 1024, HP printer, Ethernet card etc. ×resolution of 1280
• Anesthesia machines, physiological monitoring system, warming pads and fans, as well as other
additional accessories are available in the animal preparation room.
Prices
Metabolics Core Pricing FY2009/2010
Full Service Self Service
Service Description
Member
Rate
Non Member
Rate
Member
Rate
Non Member
Rate
Biopsy $116 $144 $69 $70
Blood $59 $80 $23 $23
Cell Culture $324 $405 $188 $193
Quality Control (HSQC) $185 $190 $185 $190
Other - Minimum
Processing
$43 $54 $24 $24
* only experienced NMR/ Radiologist scientists after on-site training by Dr. Serkova
$
additional costs for radioactive glucose: $50 per animal
How to Use the Core
To schedule an appointment for animal MRI-, PET- and CT-based studies, please
contact Dr. Natalie Serkova. You must have an approved animal protocol, including
animal imaging procedure, for all imaging-based animal studies. Please contact Dr.
Serkova to discuss your animal protocol approval application and/or incorporating
imaging SOP into an amendmentSmall Animal & Cell Radiation Sciences Shared Core
Service
The Radiation Sciences Core supports radiation biology studies of cell cultures and small
animals receiving moderate-dose radiation. We also enable investigators to study low dose-rate
irradiation in cell culture. And we provide irradiation services for investigators who need this
tool in support of other efforts, such as using total body irradiation for immunosuppression of
animals before stem cell transplantation.
Services We Offer
• Project design and consultation, including advice on radiation delivery to in vitro experiments
and animal models
• Design assistance for single or fractionated radiation protocols and study duration
• Radiation safety training (all users) and radiation operation training (advanced users)
• Animal tumor and partial-body irradiation at doses comparable to external beam radiotherapy
• Cell suspension irradiation
• High-dose irradiation to sterilize implant material
• Dosimetry calculation
• Calibration in support of stem cell research
• Blocking cellular division in in vitro cell cultures
• Immune function assays
• Radiation-induced DNA damage repair studies
• Data analysis an publication preparation assistance
Equipment
• Cesium Irradiator, which allows for deep tissue irradiations with notable accuracy
• Electronic Monitoring System for tracking and recording system use
Prices
The Radiation Sciences Core offers a discounted rate for UCCC members. Non-members are
welcome to use our services as well, but we give members scheduling priority. We issue all users
a key card that operates the equipment and tracks your time for easy billing.
Time is charged in one-minute increments, including warm-up time, regardless of the number of
samples irradiated.
• Member price per minute: $1
• Non-member price per minute: $2
How to Use the Core
• All users must undergo radiation safety training. To schedule your training, contact Chastiti
Vetter.
• Please contact Dr. Angela Hu or Francis Newman to schedule irradiator time or for help
designing and implementing your irradiation experiment.
In Vivo Optical Gene Service
The In Vivo Optical Gene Imaging Facility offers UCCC members and other investigators the
tools to image biological processes in live experimental animals based on powerful, non-invasive
bioluminescence and fluorescence imaging. We use a state-of-the-art Xenogen IVIS200 imaging
device that is specifically designed to visualize genetically labeled cells, such as tumor cells, and
proteins, such as those that stimulate cancer growth in live animals. It does so by recording light
emitted from the genetic labels, such as firefly luciferase, located within the animals.
Requirements for Animal Protocols
All animal studies using using the Xenogen IVIS200 must have an approved animal protocol.
Please visit the Institutional Animal Care and Use Committee website or Dr. Margaret Turner for
more information.
Dr. Fang Li can help you prepare your IACUC submission. She will give you PQ forms for
imaging personnel who will be conducting scans.
How to Use the Core
1. Have your animal protocol approved
2. Arrange for instrument training with Dr. Fang Li .
3. Dr. Li will then give you a key card to access the instrument, and assign each user group (PI) a
user ID for the computer system attached to the Xenogen system.
4. Request user time via email to Dr. Li. Please understand that you are not automatically
guaranteed you will get the dates and times you request. Please place your request several days
in advance to make sure your requested slot is available.
5. We will email you when your request is approved.
Prices (effective 7/1/08)
• Member: $63.35 per hour
• Non-Member: $86.13 per hour
D-luciferin
• $25/ml from the facility
• $800/gram directly from Caliper Life Sciences
Leadership & Staff
Chuan-Yuan Li, PhD
Director
[email protected]
303-724-1542
Fang Li, PhD
Manager
[email protected]
303-724-1625
Ultrasound Service: the fee schedule is under
construction
Small Animal Imaging Core (UCCC)
From: Serkova, Natalie
Sent: Thursday, October 01, 2009 2:26 PM
a) How is the quality of your measurements evaluated – quality control?
CT and PET calibration using manufacturer’ phantoms i s performed every 1-2 months;
MRI phantoms are run every 3 months.
b) What is the turn-a-round time for the service you provide?
10-30 m in pe r a nimal; for a s ingle s tudy, t he pr oject pe riod c an b e up t o 1 ye ar
(longitudinal studies on animals).
c) Who documents the data provided and signs off on the data?
The Core Director provides monthly reports to the Cancer Center based on the data from
the staff.
d) Have you had experience providing data for industry?
Yes, we run 5-10 industry sponsored studies per year.
e) Do you have a standard operating procedure manual?
Yes, per requested, approved by the IACUC.
f) How will you track billing and financial aspects of your core?
We do it already for the past 3 years: Cancer Center provides us with our cost study every
fiscal year. It is posted on our website.
Transgenic and Gene Targeting Core
Core Personnel:
Peter J. Koch, Ph.D.
Associate Professor of Dermatology
Director, Transgenic and Gene Targeting Core
Charles C. Gates Regenerative Medicine and Stem Cell Biology Program
University of Colorado Denver
(P) 303 724 0051
E-Mail: [email protected]
Joseph Anderson, M.S., Laboratory Manager
Senior PRA
Embryo Manipulation Services
E-Mail: [email protected]
Ling Wang, M.D.
PRA
Gene targeting in ES cells
E-Mail: [email protected]
Wallace Chick, Ph.D.
Instructor
Transgene and Gene Targeting Vector Design
E-Mail: [email protected]
Shawna Johnson, B.S.
PRA
Breeding and maintenance of genetically engineered mouse lines
E-Mail: [email protected]
Abby Knight, CVT, RLAT
PRA
Colony and Data Management
E-Mail: [email protected]
Website:http://www.uchsc.edu/stemcell/resources/transgenic.htm
Message from the Director:
A new "Transgenic and Gene Targeting Core" has been established in the Charles C. Gates
Regenerative Medicine and Stem Cell Biology Program at UCD. Our core facility replaces the
Transgenic/Knockout Core that was part of the UCD Cancer Center. We are committed to
provide the UCD research community with state-of-the-art services. Our goal is to assist PIs in
designing and generating genetically engineered mouse lines to further biomedical research.
Our services include pronuclear injections (conventional and BAC transgenic mice), ES cell
injections (e.g. knockout and knockin mice), cryo-preservation of embryos and embryo re-
derivation (see below for a detailed
Embryonic stem Cell Iinjections (courtesy of Eppendorff Inc.)
list of services and prices). We also conduct gene targeting experiments. The PIs will provide the
gene targeting construct and test ES cell clones for homologous recombination. We will conduct
the entire cell culture work and inject recombinant ES cell clones into mouse embryos to
generate chimeric mice. If requested, we will breed these chimeras to test for germline
transmission of mutant alleles.
Pronuclear DNA Injection (Courtesy of Eppendorff Inc.)
We also provide consultation services for the UCD community. Usually, we discuss
experimental design before we actually initiate the project. The goal is to ensure that the
experimental strategy employed is likely to result in the successful generation of the desired
mouse line. The initial consultation (usually a one hour meeting) is provided free of charge.
Further consultations and assistance in designing the experimental strategy to generate and
analyze mouse lines will be provided on a fee-for-service basis.
To streamline our communication with PIs, we have established an e-mail account that should be
used to schedule services and to request consultations ([email protected]). All core
members have access to this e-mail account. To facilitate correct routing of your requests, please
include the PI name and the requested service in the header of your e-mail (e.g. John Doe
“schedule transgene injection"; John Doe “schedule consultation"). We will then route the
request to the appropriate core member.
We are planning to introduce new services to accommodate the needs of our research
community. This might include the generation of transgenic rats, and the use of retroviral vectors
to generate transgenic mice. We will evaluate requests for services from the research community
for new services on a regular basis.
We are also planning to provide you with transgene and gene targeting vector design and
construction services in the near future. Please stay tuned. I will need your feedback with respect
to the introduction of new services. Feel free to drop me an e-mail at
[email protected]
Lastly, our core services are partially supported by a grant from the SOM dean. We are planning
to become self-sufficient within three years. This will not be possible without your support.
Please use our services and provide us with feedback so that we can continue to improve our
services and help you to achieve your research goals.
Peter J. Koch
To request or schedule services please send an e-mail to:
[email protected]
Please include the PI name and the type of service requested in the subject line.
Information and Protocols:
Producing Fertile Embryos for Cryopreservation and Rederivation
Information and requirements for producing embryo donors and breeder males for
optimal embryo production for efficient cryopreservation and rederivation of investigator
colonies.
DNA preparation for Microinjections
DNA preparation for Gene Targeting
BAC DNA Construct Preparation
Please contact [email protected]
Re-derivation and Cryopreservation Information
This information pertains to the TGTC standard rederivation and cryopreservation
procedures and is not part of the VC sponsored rederivation project. These two
procedures are separate. Crypreservation provides for long-term storage of mouse lines
and rederivation is the means to regenerate these lines. Cryopreserved embryos can also
be shipped directly to other institutions without the complicated regulations needed for
live animal shipments.
Application Forms:
Note: Please use the latest versions of application forms from this list. Outdated forms will be returned to the
investigator and resubmission on the current appropriate forms required.
Vice Chancellor's Cryopreservation and Rederivation into RC-2
Use for Vice Chancellor's rederivation project.
Standard TGTC Cryopreservation or Rederivation
The application allows separate selections of cryopreservation for storage and/or
rederivation for colony speed expansion and rederivation without the need for prior
cryopreservation.
DNA Constuct Microinjection
Your DNA construct will be validated for microinjection by our personnel and the
application forwarded to TGTC for scheduling. The TGTC will inform you by email
when your microinjections are scheduled.
Embryonic Stem Cell Services
Used to submit your DNA to the Cell Services Lab, where it will be processed for stem
cell injections. Please follow the instructions on the form. Following completion of
processing, you will be notified.
Stem Cell Injection
Please use this form to apply for ES cell injections. You will be notified when the
injections are scheduled.
Terms of Service Agreement
Please review this agreement prior to utilizing the services of the TGTC and the stem cell
facility.
Approval to Generate Genetically Engineered Mice
Note: you must have an approved Production and Experimental I ACUC protocol in order to produce transgenic
animals.
Please visit the Institutional Animal Care and Use Committee (IACUC) web page for
information regarding the approval of animal experimentation at UC Denver.
Transgenic & Gene Targeting Core Pricing, 2008-2009
Prices subject to change.
Gene Targeting Service Price
Electroporation/Drug Selection (First 288 clones) $2,863
Additional Clones (Per 96 well plate) $600
Clone Expansion (Per Clone) $371
Karyotyping (cost per clone) [mandatory before blastocyst injection] $390
Removal of loxP- or FRT-flanked genomic sequences by transient transfection
of ES cell clones with Cre expression plasmids or FLPE expression plasmids
(contact us at [email protected] for details)
$2,863
Gene Targeting Consultation with Peter Koch, PhD. (per hour) $100
Chimeric Mouse Model Development $1543
Listed price inlcludes Injections (~50 blasts minimum), minimum of three
recipient females and embryo transfer surgeries. Additional
recipients/surgeries extra.,
Embryo donor purchase and estimated per diems included in listed price.
These charges billed separately through CCM.
Transgenic Mouse Model Development $1693
Price includes construct microinjections, minimum of three recipient females
and embryo transfer surgeries. Additional recipients/surgeries extra.
Embryo donor purchase and estimated per diems included in listed price.
These charges billed separately through CCM.
Strain Rederivation (per line) $1,765
Price includes minimum of three recipient females and embryo transfer
surgeries. Additional recipients/surgeries extra.
45 day of animal per diems included (billed separately through OLAR).
Embryo Cryopreservation (per transgenic line) $540
Line regeneration charges will be dependent upon the recipient female costs,
embryo transfer surgery costs and facility per diems in effect on that date.
Miscellaneous Services
DNA Purification $163
Pseudopregnant Recipient Females - each $65
Embryo Transfer Surgeries - each $106
Mating, Weaning, Tagging, Biopsies $21
Weaning Only $13
Repeat Biopsies $26
Timed Pregnancies $33
Miscellaneous Services hourly rate, (billed in 15 minute increments) $35
PCR Genotyping of Mice (per 10 PCR reactions) $33
Consultation with TGTC personnel (per hour) $51
The Transgenic and Gene Targeting Core can test your chimeras or
transgenic founder mice for germline transmission of the desired mutations.
Please contact the Core ([email protected]) for details. These
experiments will be conducted in our own animal room, which is shielded from
the general mouse population at CCM to ensure that your mice are efficiently
protected from common mouse pathogens.
The prices listed above are charged to investigators affiliated with UCD who
conduct non-commercial basic or clinical research. For prices charged to
commercial entities, please contact us at [email protected]
Response form the Transgenic and Gene Targeting Core
From: Koch, Peter
Sent: Monday, October 05, 2009 1:37 PM
a) How is the quality of your measurements evaluated – quality control?
Internal quality control procedures:
- Pronuclear Injections (conventional and BAC transgenes): Periodic injections of
control constructs (e.g. CMV-GFP) into fertilized eggs. Determine the recovery of
life embryos with integrated and expressed transgene. Compare efficiency of two
senior embryologists.
- ES Cell Injections, surgical procedures: Compare success rate of two embryologists
to identify techniques that can be improved/optimized.
- Transgene generation: Collect data on the percentage of transgene-positive founders
generated by us (information provided by our customers).
- Gene targeting and ES cell injections: Collect data on the number and quality of
chimeras produced by us (% chimerism, germline transmission of mutations)
b) What is the turn-a-round time for the service you provide?
- Most services are initiated within 2-3 weeks (gene targeting in ES cells, pronuclear
injections of conventional or BAC transgenes; ES cell injections; cryo-
preservations).
- The turnaround time depends on the service requested:
ES cell targeting: 4-6 weeks after initiation of ES cell work
Pronuclear and ES cell injection: One day after initiation; turn around time from
service request to generation of pups: 6-7 weeks
Rederivation 6-8 weeks
c) Who documents the data provided and signs off on the data?
Database manager (Abby Knight, Shawna Johnson) in conjunction with the Core
Manager (Joseph Anderson). Evaluation of efficiency and trouble-shooting is done
collaboratively with the Core Director (Peter J. Koch)
d) Have you had experience providing data for industry?
So far we had one request from a small biotech company. Our main customer basis is
the University of Colorado (Denver and Boulder campuses) as well as a few out of state
Universities (e.g. University of Alabama).
e) Do you have a standard operating procedure manual?
We have standard operating procedures for repetitive procedures, such as the
rederivation program sponsored by the Vice Chancellor of Research. All SOPs are
updated regularly to ensure the best practices.
f) How will you track billing and financial aspects of your core?
Core prices are based on a cost analysis which is revised twice a year. Detailed reports
of monthly revenue are kept both electronically and as a paper copy. All services are
charged though Granite and additional reports are available upon request from
Carolyn Russell.
Translational Neuroscience Nexus Core (IDDRC)
Website:http://www.ucdenver.edu/academics/colleges/medicine/Centers/IDDRC/research/translational/Pa
ges/default.aspx#directors
Mission
The Translational Nexus (Nexus) is a database, patient registry and biological sample bank
focused on pediatric neurological, cognitive and behavioral disorders (IDD). Its major goal is to
advance research on neurodevelopmental disabilities (i) by linking human neurological,
cognitive, behavioral phenotypes to biological samples, especially DNA, and (ii) by facilitating
access to appropriate patient cohorts for clinical trials.
IDDRC members are invited to learn more about the services available from the Translational
Neuroscience Nexus core by watching a short video.
Staffing
Core Experts: Elaine Spector, PhD; Scott Lucia, MD
System Managers: Tom Yaeger, BS (consultant)
Technical Personnel: Katrina Merrion, MS, CGC; Kathy Acha, MS
Because of the special nature of the functions of the Nexus, a special 7-member Steering
Committee oversees the development and operation of the Nexus. The Steering Committee
represents the various user groups (programs, departments) and is composed of:
a. IDDRC director
b. The Nexus director and Nexus co-director
c. The Study Coordinator and/or a genetic counselor
d. 1-2 IDDRC member investigators (appointed for a 2-year term)
e. A representative of the CCTSI-IT core
f. A laboratory coordinator
Director:
Cordelia Robinson, PhD, RN
303-724-7680
[email protected]
Associate-Director:
Gunther Scharer, MD, FACMG
303-724-1571
[email protected]
Services
1. IDD Clinical Data Registry (Nexus CDR). The Nexus CDR is an extension of the
Intellectual and Developmental Disabilities Registry, which is already IRB-approved. The
Registry is a standard-of-care protocol to be used with all individuals who present for
multidisciplinary evaluation services at one of the IDDRC participating clinics listed below.
Partnering clinics invite all appropriate individuals who present for care to enroll in the Nexus
Registry. Clinical data is collected from consenting individuals and entered into a
secure electronic enrollment list. Data is collected during every follow-up outpatient visit to
these clinics as well as to Adult General Psychiatry, Rehabilitation Medicine, and Assistive
Technology Partners for as long as the subject remains in the study.
Registry Entry Points
Clinical Service Clinicians in Charge (All IDDRC Members)
Child & Adolescent Psychiatry
Developmental and Behavioral Pediatrics
JFK Partners
Pediatric Neurology
Pediatric Clinical Genetics
Inherited Metabolic Disease Clinic
Pediatric Special Care Clinic
Adult Medical Genetics
R. Ross
A. Reynolds, N. Tartaglia
C. Robinson, S. Hepburn
T. Benke, A, Brooks-Kayal, G. Wilkening, A. Yee
G. Scharer
R. Gallagher
E. Elias
M. Taylor
IDDRC investigators interested in data from the Nexus-CDR for their research proposals submit
a data query request to the Nexus. If sufficient subjects are available and the Nexus Study
Selection Committee has confirmed the merit of the study, then the investigator is asked to
submit an IRB protocol (exempt, for de-identified data-sets; full review for data linked to PHI or
for human subject research). Upon approval, the IDDRC investigator then is given full access to
the requested information. Contact Cordelia Robinson at [email protected] or
303-724-7680.
2. Nexus Biobank (Nexus-BB) stores biological samples from individuals enrolled into the
Nexus-CDR, and who are consenting to collection of a venous blood sample (for lymphoblast
transformation and for serum), as well as a buccal smear, blood sample, or saliva sample for
DNA extraction. Other biological samples, such as urine may be collected. Biological samples
are stored secure in the UCD-Biorepository Core Facility. Sample access is monitored
electronically using tracking software (Freezerworks®).
IDDRC investigators interested in accessing the biobank for their research proposals will submit
a sample request to the Nexus. If sufficient biological samples are available and the Nexus Study
Selection Committee has confirmed the merit of the study, then the investigator is asked to
submit a COMIRB protocol (exempt, for de-identified samples; full review for samples linked to
Nexus-CDR data). Upon approval, the IDDRC investigator then is given aliquots of the
requested samples. Contact Gunter Scharer at [email protected] or 303-724-1571.
3. Clinical Study Design Assistance is available from the CCTSI. However, in addition to basic
design expertise there is the need for specific expertise regarding recruitment and retention of
individuals with IDD and their families as subjects. In that regard. the Nexus Director (C.
Robinson) and several of the JFK faculty, including Susan Hepburn and adjoint faculty member
William MacLean, are available to provide advice on study design. Senior investigators of the
IDDRC with specific content expertise will be consulted on an ad hoc basis. Contact Cordelia
Robinson at [email protected] or 303-724-7680.
4. Biostatistics Support for IDDRC investigators is available through the CCTSI design
biostatistics and clinical research ethics program (a consortium of nine programs across the
Schools of Medicine, Pharmacy, Nursing, The Children's Hospital, and National Jewish Health).
The following specific focus areas are available: statistical genetics, methods for analysis of
high-throughput data, design and analysis of classification and discrimination studies, modeling
of pharmacokinetic/pharmacologic dynamic statistics, clinical trials epidemiological methods,
design and analysis of community studies, and evidence-based practice and meta-analysis.
Access to the CCTSI consortium is through a single portal. Contact Gunter Scharer
at [email protected] or 303-724-1571.
5. IRB Protocol Consulting and support is provided by the Nexus research coordinator (K.
Merrion) and, when necessary, the Nexus-associate director (G. Scharer). This is intended to
facilitate access to the Nexus resources. For example a general research protocol covering the
policies and procedures of the Nexus is currently under review by the COMIRB. It was
developed by the directors of the Nexus with the support of the Nexus research coordinator.
Contact Katrina Merrion at [email protected] or 303-724-2349.
Fees for Services
Service Cost, annual
(IDDRC member)*
Cost, annual
(Non-member)*
Contact
1. Clinical Data
Registry
10 data-sets (free)
$ 800 (unlimited)
Subject to review
$1,200
C. Robinson
2. Biobank 10 samples (free)
$1,600 (per 80 samples)
$2,000 (combined with 1.)
Subject to review
$2,400
$3,000
G. Scharer
3. Clinical Study
Design Support
Included in IDDRC
membership
TBD
C. Robinson
4. Biostatistics
Support
Included in IDDRC
membership
TBD
G. Scharer
5. COMIRB Protocol
Consulting
Included in IDDRC
membership
TBD
K. Merrion
UCH CTRC Core Lab
Contacts:
Bryan Haugen, MD
Core Director
303-724-3921
Pamila Allen, MS, MT(ASCP)
Core Laboratory Supervisor
720.848.6665
Leprino Office Building
Room 327
Kayla Carstens, BS,
MT(ASCP)
Core Laboratory Supervisor
720.848.6877
Leprino Office Building
Room 327
Website:http://ctsa1.uchsc.edu/Research-Resources/Clinical-Research-
Resources/Pages/UCHCTRCCoreLab.aspx
UCH CTRC Core Lab Accreditations
CAP Accreditation
CLIA Accreditation: 06D0644347
Important Assay Information
PLEASE READ CAREFULLY
Currently available CTRC Core Laboratory assays have priority over newly developed assays.
Occasionally, the laboratory director will negotiate with the investigator to reduce the number of
requests for expensive or time-consuming assays. Assays which are not available in the routine
hospital lab or the CTRC Core Laboratory are generally expected to be paid for by the
investigator's individual research funds; although the CTRC Core Laboratory can often help with
sample processing. Any shipment of specimens to an off-site laboratory is the sole responsibility
of the investigator.
Results from routine assays completed in the hospital laboratory are available through Clinical
Workstation. Results from assays performed at the CTRC Core Laboratory are available through
a server. Tom Yaeger, Director of Research Informatics, will work with the investigator to set up
a system that works best for the research project.
Approval of additional assays (and requests for current assays) is based on scientific merit. The
investigator must initiate the request to add additional assays by writing a letter to the Laboratory
Administrator and Chairman of the Scientific Advisory and Research Committee (SARC).
Complex requests may need approval of the full SARC.
CCTSI Core Lab Assays
Discounted pricing may be available, please contact Pamila Allen at 720.848.6665
or Kayla Carstens at 720.848.6877 for pricing specific to your study.
CCTSI Core Lab Assays
Assay
Pricing
Manufacturer
8-Isoprostane, urine $45.75 Cayman
Adiponectin $7.25 Linco Research
Adrenocorticotropic Hormone (ACTH) $29.25 Siemens
Aldosterone $9.50 Diagnostic Products Corp.
Angiopoietin-2 $27.25 R&D Systems
Angiotensin II $29.00 Evaluating Data
Beta-Carotene $59.00
Bile Acid, Total $19.25 Diazyme
Bone Specific Alkaline Phosphatase $31.75 Quidell
Brain Naturetic Peptide (BNP)
Bronchoalveolar Lavage Fluid $59.75
Caffeine $14.25 Siemens
Cell Culture
Cell Isolation
Cell Staining
Cholesterol $3.25 Olympus America
Coenzyme Q10 $35.50
Cortisol, serum/plasma $5.00 Beckman Coulter
Cortisol, urine Beckman Coulter
Cotinine $27.25 Siemens
Cotinine, salivary $16.00 Salimetrics
C-Peptide $6.50 Diagnostic Products Corp (DPC)
Creatinine, serum/plasma $3.25 Roche Diagnostics Systems
Creatinine, urine $3.75 Roche Diagnostics Systems
CRP-hs $5.75 Olympus America
DHEA $16.50 Diagnostics Systems Lab (DSL)
DHEA-S $14.25 Diagnostic Products Corp (DPC)
Differentials $64.75
DNA Extraction, >10 $40.00
DNA Extraction, blood $75.00
DNA Extraction, other $75.00
DNA Extraction, saliva $50.00
DNA Sequencing (PCR fragment) $50.00
EGF $27.00 Milliplex
Elastase, Free (neutrophil) $17.00
Elastase, PMN $19.25 ALPCO
Endoglin $28.00
Endothelin-1 $14.50 Peninsula Labs (Antibody)
Eosinophil Cationic Protein $23.00 Siemens
Epinephrine $14.50 BioRad
E-Selectin Milliplex
Estradiol $12.00 Diagnostic Systems Laboratories (DSL)
Estrone $13.25 Diagnostics Systems Lab (DSL)
Exotaxin $27.00 Milliplex
F-Actin, sputum $200.00 Cytoskeleton/BioRad
Ferritin $17.75 Siemens
FGF-2 $27.00 Milliplex
Flow Cytometry
FLT-1 (sVEGF R1) $27.25 R&D Systems
Flt-3Li $27.00 Milliplex
Fractalkine $27.00 Milliplex
Free Fatty Acid $3.50 WaKo Chemicals USA
FRO $27.00 Milliplex
FSH $5.25 Beckman Coulter
Galactose $8.50 R-Biopharm
G-CSF $27.00 Milliplex
Genotyping (PCR, digest) $50.00
Genotyping (PCR, sequencing) $90.00
Ghrelin $7.50 Linco Research
Glucagon $5.25 Linco Research
Glucagon-Like Peptide-1
Glucose $3.25 Olympus America
Glutathione Peroxidase $5.25 Randox Laboratories
Glycerol $4.00 R-Biopharm
GM-CSF $27.00 Milliplex
HDL-C, direct $6.00 Olympus America
HDL-Sub 3 $6.00 Warnick and Co.
HDL-T (Prec) $6.00 Warnick and Co.
ICAM-1 Milliplex
IFN-alpha2 $27.00 Milliplex
IGF-1 $21.50 Diagnostic Systems Lab (DSL)
IGFBP-3 $21.50 Diagnostic Systems Lab (DSL)
IL-1 alpha $27.00 R&D Systems or Milliplex
IL-1 beta $27.00 R&D Systems or Milliplex
IL-10 R&D Systems or Milliplex
IL-11 $24.25 R&D Systems
IL-12p40 Milliplex
IL-12p70 Milliplex
IL-13 Milliplex
IL-15 $27.00 Milliplex
IL-17 $27.00 Milliplex
IL-18 $25.50 R&D Systems
IL-1ra $27.00 R&D Systems or Milliplex
IL-2 $27.00 R&D Systems or Milliplex
IL-23 $27.25 R&D Systems
IL-3 R&D Systems or Milliplex
IL-4 R&D Systems or Milliplex
IL-5 R&D Systems or Milliplex
IL-6 $25.50 R&D Systems
IL-7 R&D Systems or Milliplex
IL-8 R&D Systems or Milliplex
IL-9 R&D Systems or Milliplex
Immunoreactive Trypsinogen $24.50 DiaSorin
INSULIN $5.25 Diagnostic Systems Lab (DSL)
IP-10 $27.00 Milliplex
LACTATE $4.00 Olympus America
Lactulose/Mannitol Ratio $87.50
LEPTIN $7.25 Linco Research, Inc.
LH $5.25 Beckman Coulter
Lymphocyte Proliferation $214.00
Macrophage Inhibitory Factor $27.25 R&D Systems
Matrix Metalloproteinase-7 $40.50 R&D Systems
Matrix Metalloproteinase-9 $40.50 R&D Systems
MCP-1 Milliplex
MCP-3 Milliplex
MDC $27.00 Milliplex
Micro Total Protein $9.00 Sigma
Microalbumin, urine $13.25 Siemens
Microcarotenoids $77.50
MIP-1 alpha $27.00 Milliplex
MIP-1 beta Milliplex
MLPA
Myeloperoxidase $44.50 Prognostix
Nitrates/Nitrites $84.25 Waters
Nitrogen, urine $43.50 Antek
Norepinephrine, plasma $14.50 BioRad
Norepinephrine, urine $40.50 BioRad
N-Telopeptide, urine $75.00 Wampole Osteomark
NT-pro BNP $27.50 Milliplex
OXI-LDL $33.00 ALPCO Diagnostics
Parathyroid Hormone (PTH) $31.25 Siemens
PBMC Isolation $43.25
PCR (no set-up, fragment) $40.00
PCR (set-up/exon, fragment) $100.00
PCR multiplex (set-up) $500.00
PDGF-AA $27.00 Milliplex
PDGF-AB/BB $27.00 Milliplex
PROGESTERONE $8.75 Diagnostic Products Corp (DPC)
PROLACTIN $5.25 Beckman Coulter
PYY $8.25 Linco Research, Inc.
RANTES $27.00 Milliplex
RENIN (PRA) $16.50 Diasorin
Retinal Binding Protein $17.25 Siemens
RNA Extraction, blood $80.00
sCD40L $27.00 Milliplex
Secretory Leukocyte Protease Inhibitor $24.25 R&D Systems
SHBG $21.50 Diagnostics Systems Lab
sIL-2Ra $27.00 R&D Systems or Milliplex
Sputum Processing $80.00 TDN Protocol
sTransferrin Receptor $19.00 Siemens
T3-UPTAKE Beckman Coulter
T4, FREE $6.50 Beckman Coulter
TAS $12.50 Randox Laboratories
TESTOSTERONE $6.00 Beckman Coulter
TGF-alpha $27.00 Milliplex
TGF-Beta 1 $29.00 Milliplex
Tissue Inhibitor of Metalloproteinase $23.25 R&D Systems
TNF-a $26.00 R&D Systems
TNF-beta IFN-y $27.00 Milliplex
TOTAL T3 $4.25 Beckman Coulter
TOTAL T4 Beckman Coulter
TRIGLYCERIDE $3.25 Olympus America, Inc.
TSH $5.50 Beckman Coulter
URINE NITROGEN See link below
VCAM-1 Milliplex
VEGF Milliplex
Vitamin A $50.25
Vitamin D 1,25 diOH $48.50 DiaSorin
Vitamin D 25OH $37.50 DiaSorin
Vitamin E $49.25
X-inactivation
Fees are not guaranteed
UCH CTRC Core
From: Carstens, Kayla for Bryan Haugen, MD (Director)
Sent: Monday, November 02, 2009 2:53 PM
Our core is the Laboratory. Our director is Dr. Bryan Haugen. Managers are Pamila Allen and
Kayla Carstens
a) How is the quality of your measurements evaluated – quality control?
For every assay that is performed here, quality control samples are assayed along with the
unknown samples. The controls are either purchased separate from the instrumentation
or kits, from an outside source, or for some of our kits, the quality control is provided.
For our more routine chemistries, quality control is assayed once a day, otherwise it is
run when the assay is performed. Other quality control measures include, but are not
limited to, refrigerator/ freezer monitoring, centrifuge calibration, electrical safety checks
on all equipment, instrument maintenance and function checks, pipette calibrations,
reagent performance checks, deionized water quality, safety inspections, etc.
b) What is the turn-a-round time for the service you provide?
For our more routine chemistries, such as lipids, glucose, and TSH, we assay these 2-3
times per week. Most of our researchers need these for screening purposes. Other assays
are performed on a batch basis whereby we wait until we have enough samples to justify
setting up the assay or when our researchers need the data. Most of our turn-around-time
is driven by our researchers and the cost to run the assay.
c) Who documents the data provided and signs off on the data?
Data generated from our lab is entered into our Access database by the technologist
performing the assay. The data is verified before release by one of the core lab
managers. This is documented on every assay worksheet.
d) Have you had experience providing data for industry?
For industry studies, we offer specimen processing and temporary storage, but have not
provided any data.
e) Do you have a standard operating procedure manual?
Our core lab has a standard operating procedure manual (we call it “Global Procedures”),
procedures for all of our assays, safety procedures, processing procedures, etc. We are
certified by the College of American Pathologists (CAP) and CLIA both of whom require
procedure manuals for nearly all aspects of laboratory work.
f) How will you track billing and financial aspects of your core?
We are currently in the process of setting this up with our administrative group. Our
administrative contact is Pat Kittelson.
Vivarium Animal Facility
Office of Laboratory Animal Resources Recharges and
Per Diem Rates For Fiscal Year 2008-2009
Contact:
Jori Leszczynski, DVM DACLAM
303-724-3987
[email protected]
Website:http://www.uchsc.edu/animal/
OLAR i s obl igated to recover t he cos ts a ssociated with the procurement and car e of and use o f
animals. These costs are billed to investigators monthly. Per di em rates f or animal care or di rect
charges for personnel costs and supplies are based on a cost analysis and recovery program outlined
by NIH Cost Analysis and Rate Setting Manual for Animal Resource Facilities.
The following t able gives t he per diem r ates for the care and housing of laboratory animals. Per
diems cover these basic services: feed, special diets, health checks, cage changes and cleaning.
Cost Center Per Diems Current Rate
Cat Per Diem Per animal 3.68
Chinchilla Per Diem Per animal 3.44
Dog Per Diem Per animal 18.93
Ferret Per Diem Per animal 3.24
Fish Aquarium Per Diem Per aquarium .45
Frog Tank Per Diem Per tank 3.24
Frog Tank-Maller Per Diem Per tank 3.43
Gerbil Per Diem Per Cage .58
Ground Squirrel Per Diem Per Cage 1.07
Hibernating Ground Squirrel Per Diem Per Cage .52
Guinea Pig Per Diem Per Cage 1.64
Hamsters Per Diem Per Cage 1.62
Mouse Autoclave Per Diem Per Cage 1.00
Mouse Microisolator Per Diem Per Cage .57
Mouse Quarantine Per Diem Per Cage .66
Mouse Quarantine Static Per Diem Per Cage .76
Mouse Static Per Diem Per Cage .67
Opossum Per Diem Per Cage 1.27
Pig Per Diem Per animal 23.74
Rabbit Per Diem Per Cage 3.71
Rat Autoclave Per Diem Per Cage 1.66
Rat Microisolator Per Diem Per Cage 1.15
Rat Quarantine Per Diem Per Cage 1.37
Rat Quarantine Static Per Diem Per Cage 1.47
Rat, Metal Suspended Per Diem Per Cage .39
Rat Static Per Diem Per Cage 1.25
Zebrafish Per Diem Per Rack 2.94
Zebrafish(Shared) Per Diem Per Rack 1.46
Animal Administrative Purchasing Fee I Per Animal Order 20.00
Denver Health
Denver Health Mouse Per Diem Per Cage .69
Denver Health Rat Per Diem Per Cage 1.46
Technician Fees
Animal Care Tech Time Tech Time Per Hour 16.17
Vet Tech Time Tech Time Per Hour 18.15
Surgery Fees
Table Charge Internal Customer Per Event 120
Table Charge External Customer Per Event 289
Anesthesia Per Hour 22.27
Admin Charge External Customer Per Event 140.00
Special Order Goods Per Item Cost
Veterinarian Time Per Hour 69.23
Vivarium – Animal Housing & Care
From: Leszczynski, J ori
Sent: Thursday, October 01, 2009 9:29 PM
a) How is the quality of your measurements evaluated – quality control?
We monitor all housing rooms for temperature, humidity, and light cycle.
The system will alarm if there are any issues. All equipment is calibrated on
a set schedule. Cage changing is handled on a specific basis. All treatments
and husbandry procedures are accurately recorded. This is checked on a
regular basis by supervisors.
b) What is the turn-a-round time for the service you provide?
This depends on what type of service the PI is looking for. The specific
service due dates are negotiated with each PI.
c) Who documents the data provided and signs off on the data?
This could be the PI, the veterinary staff or the animal care staff depending
on the information required. At this point we are not performing GLP
studies which would require a study director and other more formal data
reporting requirements.
d) Have you had experience providing data for industry?
There are people in the organization that have experience with providing
data for industry. We currently are not set up as a GLP lab though. We
would require prep time to be able to do this. However if someone needs to
do pre-GLP discovery work, we can definitely provide this service.
e) Do you have a standard operating procedure manual?
Yes, we can make this available
f) How will you track billing and financial aspects of your core?
We use the Granite system by Topaz Technologies. We can accept checks
or charge by credit card.
X-Ray Core Facility
Contacts:
Mair Churchill, PhD
Professor, Director of the X-ray core facility
Department of Pharmacology
University of Colorado Denver
12801 E. 17
th
Avenue, Mail Stop 8303
Aurora, CO 80045
Phone: 303-724-3670
Fax: 303-724-3663
Email: [email protected]
Sarah Roemer, PhD
Instructor, Facility Manager of the X-ray Core
Facility
Department of Pharmacology
12801 E. 17
th
Avenue, Mail Stop 8101
Aurora, CO 80045
Phone: 303-724-3672
[email protected]
Website:http://biomol.uchsc.edu/cores/xray/
The X-ray core facility was set up in 1999. The facility is fully equipped for biomolecular
crystallization, crystal screening, data collection, data processing, structure-determination and
model building. It currently has a Rigaku/MSC Ru-H3R X-ray generator, two Raxis IV++ area
detectors, and two X-stream cryo-cooling apparatus. The facility is located in RC1 South
Building Rm 1301. It is directed by Dr. Mair Churchill (Department of Pharmacology), and is
managed by Sarah Roemer (Department of Biochemistry and Molecular Genetics).
User Fees and Policies
For 2008-2009 the fees are:
Service
Cancer Center
Member-major
user
Cancer
Center
Member
Non Cancer
Member
Private
Sector User
Service contract $2500/yr 0 0 0
Data Collection $10 /hr $25 /hr $35 /hr $50/hr
Crystallization
access per quarter 0 $100 $250 $500
Alchemist (block w/own
reagents and supplies)
$2 $2 $4 $50
Alchemist (block
w/facility reagents and
supplies)
?$30 ?$30 ?$50 ?$75
Phoenix (tray w/own
reagents and supplies)
$2 $2 $4 $50
Phoenix (tray w/facility
reagents and supplies)
~$16 ~$16 ~$32 ~$64
Minstrel per image $2 $2 $4 $10
Materials at cost
Labor for service cost cost cost $50/hr
Crystal Screening $250 / half day
$250 /
half day
$500 / half
day
$1500 /
half day
Beamline usage
Crystal screening $25 $25 $25 N/A
Data set $100 $100 $100 N/A
*Price are subject to change
• Access to facility by other faculty, staff, postdoc and students: Facility open to all
UCHSC faculty, staff, postdocs and students, but need approval of the X-ray facility
steering committee to arrange details.
Services Currently Provided
• Project design and consultation: Assistance with starting projects includes advice on
protein expression and purification, and crystallization. Until now these services have
been provided in direct collaboration with the primary users. Since the manager has just
become available, these services will be more broadly available to all members of the
cancer center.
• Crystallization screening: Facilities for setting up crystal growth trays is available.
• Screening crystals: Crystal (diffraction) screening is available.
• Data collection: Data collection service is available.
X-Ray Crystallography
From: Mair Churchill [mailto:[email protected]]
Sent: Monday, November 02, 2009 11:04 AM
Structural Biology core UCCC core facility (X-ray)
a) How is the quality of your measurements evaluated – quality control?
Standard practices in Structural Biology
b) What is the turn-a-round time for the service you provide?
N/A
c) Who documents the data provided and signs off on the data?
The users
d) Have you had experience providing data for industry?
No but the facility can be used by industry users for a fee that is already set for each type
of service or access.
e) Do you have a standard operating procedure manual?
For safety protocols only.
f) How will you track billing and financial aspects of your core?
The core manager does this.
Zebrafish Transgenic Core
Contact:
Angie Ribera, PhD
Director
303-724-4517
[email protected]
http://www.uchsc.edu/neuroscience/Program/cores.htm
The NINDS P30 Center Zebrafish Core has three Specific Aims:
1. Create transgenic lines of zebrafish that express different fluorescent proteins in specific
populations of pre- and postsynaptic neurons
2. Create transgenic zebrafish strains that express genetically-encoded calcium indicator
dyes in specific neuronal populations
3. Maintain transgenic and wild type zebrafish strains for the UCD neuroscience community
During the first year of the grant, the fish facility at the Fitzsimons campus is being optimized
and we are focusing on Aim 3. In subsequent years, Aims 1 and 2 will be a priority. The Core
can cover the expenses associated with breeding wild type fish for pilot experiments. If you
would like to use zebrafish embryos for pilot experiments, please contact Angie Ribera
([email protected]) for further information.
Zebrafish transgenic lines express GFP in specific
neuronal subpopulations.
In the Figure, GFP expression is driven by the flh
promoter. (This transgenic line was developed by Drs.
Marnie Halpern and Josh Gamse - Carnegie Institute of
Washington). At 48 hours post fertilization, GFP
expression (green) is present in specific populations of
motor neurons that extend axons either ventrally (down,
asterisks) or dorsally (up, arrowhead). A subset of the
axons also expresses the zn-8 epitope (red). Zn-8 is a
marker for axons of later-born (secondary) motor
neurons.
Scale Bar: 25 µm.
Zebra Fish Transgenic
From: Ribera, Angie
Sent: Friday, October 02, 2009 10:10 AM
a) How is the quality of your measurements evaluated – quality control?
Quality is assured by two means: 1 – The RMNDC Steering Committee meets on a
regular basis to review Core performances. 2 – Users: most users come back and use
services again, meaning that they were at a minimum satisfied with previous use.
b) What is the turn-a-round time for the service you provide?
Depends on the Core and the request. For use of a microscope, turn around can be
immediate. For construction of gene targeting vector, turn around can be several months.
c) Who documents the data provided and signs off on the data?
Each Core’s Manager/Director.
d) Have you had experience providing data for industry?
NO
e) Do you have a standard operating procedure manual?
NO
f) How will you track billing and financial aspects of your core?
Each Core’s Manager/Director.
doc_396173378.pdf