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CTRF Leadership Meeting
July 1, 2002
Institutional Partners
V C U G M U I N O V A
6/03/02
Minutes
Corrections
Approval
Develop Infrastructure and Intellectual
Property that Enhances the Competitiveness of the Partners for Clinical and Extramural Funds
Principle Objective
Evaluate gene expression (and genetic changes) in human brain, ovarian, breast and hematopoetic cancers
Link gene expression (and genetic changes) to clinical findings and clinical laboratory findings (including histopathological diagnoses) in a common database
Evaluate linked data using bioinformatics
Research Objective
ChandhokeGrant
ChristensenFryxell
Jamison
Torr (Central Admin)GinderGarrettBuck
Guiseppe-ElieAbraham
Cooper
Year 1 Year 1 Year 1
$325,000 $582,000 $93,000
Total (3 yrs) Total (3 yrs) Total (3 yrs)
$975,000 $1,734,603 $290,397
Year 2 Year 2 Year 2
$325,000 $578,191 $96,809
Funding From CTRF
FY02 Budget Rollover Report
(M. Newsome)
Reminder - Cost Share Form (VCU)
Estimated Cost Share
Account PIAccoun
t #
Comm’d Cost Share
(Direct Cost Only)
Yr to Date as of
5/31/02Variance
Admin2-90000 97,500 81,347 (16,153)
Garrett4-12310 326,595 274,705 (51,890)
Guiseppi-Elie
1-37100 217,950 148,679 (69,271)
Buck1-30139 138,144 124,375 (13,769)
Ginder4-12320 98,750 48,548 (50,202)
Inova 211,070
GMU 177,226
Cost share expenditures not paid from cost share linked accounts must be documented using ‘In Kind/3rd Party Cost Share form’ obtained from Margie Booker’s office.
Cost Share Expenses
(http://www.vcu.edu/finance/In-kind%20Cost%20Sharing
%Certification.pdf)
FATS Table
Justification (Transaction Brief)
• Reason for year-end balance– Project began late– Delay in recruitment of key personnel– IRB approval
• Need for carry-forward funds– Use of the unexpended funds are essential to
continue the project and carry out the programmatic aims of the grant
– Matching funds have already been obligated– No alternative funds
• How the funds will be used– Personnel– Supplies/Maintenance/travel
FY 03 Allocation• [Submit record of expenditures and
matching funds (FY02 Closeout)] (Mike Newsome)
• Progress Report indicating milestones achieved sent to Mike Newsome
• Need to spend down carry over before new appropriations justified (J. Heiman)
Website Update
“News & Updates” page added
Focus Group roles and responsibility still needed from Focus Group Leaders
Pages have been amended and new links have been added
SPIN Research Jo Ann Breaux receiving daily notices of
grant opportunities Compiling weekly document of relevant
findings Will be distributed over the CTRF
LISTSERV
SMART documents currently on the CTRF website
• Training is available: http://www.InfoEd.org/default.stm
Tissue Bank Clinical and Pathology Laboratory Data Database Design Data Analysis Quality Assurance in Microarray Analysis (Chip Fabrication - proposed)
Focus Group
Focus Group LeadersFocus Group Leaders
G MU
G e rald in e G ran t ( G M U )S u ha il N as im ( V C U )B a rr ie C o o k ( I n o va)
Tissue Bank
L yn ne P en b e rth y (V C U )S u ha il N as im ( V C U )
J a m e s C o op e r ( I n o va)
ClinP ath
C u rtis J am is on ( G M U)L yn ne P en b e rth y (V C U )
G re g M ille r (V C U )M ike S he ride n ( I no va)
D B D esign
V ika s C h an d h oke ( G M U )G re g B u ck ( V C U )
D ataAnalysis
A la n C h ris ten s en ( G M U )A n d re a Fe rre ira - G o n z ale z (V C U)
S u ha il N as im ( V C U )G e rald ine G ra n t
Q A/ LQ C
Anthony Guiseppi-E lieA lan Christensen
Chip Fabrication
VCU I nova
• IRB approval at INOVA
• Tissue Acquisition person to be hired and managed by Marianne Smith
– Inova to work out process for obtaining necessary informed consent
• Tissue Bank person to go to OR area with pathologist responding to request for frozen section and take tissue at that time
• Ideal procedure is unclear at this time for tissue acquisition unclear:
– Cut and freeze a piece of tissue at the OR (most rapid)
– Perform a frozen section on a block and then drop the latter into liquid nitrogen (delay 5-10min)
• Protocol handling for Bone Marrow Aspirates not yet specified
• Tissue is not to leave Inova until surg path written report is completed
INOVA -CTRF - Tissue Bank
VCU - Tissue Bank
• TAS approved by IRB 4/15/02
• Tissue Bank Staff Activities (Cynthia Losco)
– Procedures Established in Main OR and Ambulatory Surgery
– Cynthia to be notified 30 minutes before specimen to be ready on cases identified for CTRF eligibility
– In-service given to OR staff to address new procedure
– Bone Marrow Biopsy patients are being consented directly after procedure
Specimens Acquired
Organ Number of Specimens
Breast 12
Bone Marrow 29
Ovary 5
Brain 0
Manual Form for Tissue Acquisition
Histopathologic Parameters
Tissue Acquisition Database
• Access Database– Computer has been installed at VCU– Database has been installed on
machine at VCU– PC Anywhere software sent to Inova
• To Contain Inova and VCU Cases
Tissue Utilization(1)
Non-anonymized tissue samples are a form of patient medical record
The health system where the medical record is created is responsible for access and integrity.
Personal identifying information should be maintained behind a health systems firewall.
Tissue Utilization(2)
Each health system which creates non-anonymized human tissue sample banks will:ο Identify a guardian who is
responsible for maintenance of the integrity of the collection and monitoring utilization.
ο Establish a tissue utilization committee to formulate criteria for use of samples.
Institutional Tissue Utilization Committee
Formulate criteria for who is eligible to obtain human residual samples at the institution.ο Faculty status, IRB approval, ?
scientific validityο ?minimum QA requirementsο ?minimum data access
requirements Review requests for human tissue
utilization. Formulate criteria for the degree of
clinical information which can be provided with the samples.
Assess resources required to fill request and whether PI is prepared to provide them.
Tissue Utilization(3)
For purposes of regulating utilization of all samples collected by CTRF tissue collection personnel for the CTRF Ca Genomics Project, it is assumed that:ο the VCU and Inova tissue utilization
committees agree to follow the criteria and decisions regarding tissue utilization as determined by the CTRF Ca Genomics Project Tissue Utilization Group.
CTRF Ca Genomics Project Tissue Utilization
Group• Project Pis
– Garrett– Buck – Ginder– Guiseppi-Eli– Cooper– Chandhoke
• Tissue Guardians– Nasim – Grant– Cook
• Clinical Data Leadership– Penberthy– Smith
• Quality Assessment Leadership– Ferreira-Gonzales– Christensen– Taylor
• Issues– QA Program– Pre-Analytical Tissue
Handling• Storage Conditions
(Freezer Monitoring, etc)
– Manner in which tissue is supplied
– Storage and availability of data
Tissue Utilization Summary
VCU TissueCommittee
Inova TissueCommittee
CTRF TissueUtilization Group
Analyze Samples
Database Design/Clinical Info
Clinical Data ElementsDefine minimal set of common clinical
data elements; Initial choice to be the elements required to be sent to state cancer registry
Data elements should include MIAME (Minimum Information about a Microarray Experiment) for holding Expression Array Data
GeneX Database – Initial choice for storing project data
GeneX Database (Update) Version 1.5 UVA (Jae K. Lee)Version 2.0 GMU-VT (J. Weller)
“Terabyte” Database – (Update)GMU
LabBook (Update - Buck) VCU
Database Design/Data Analysis
Schema (VCU Preliminary) 16 Chips
Test for Variation Chip-Chip Labeling Buffers Modules (4)
Update – VCU/GMU
QA/QC
QA/QC – GMU Update
• GMU cDNA Microarrays– Check by hybridizing slides from each
batch• Composite probe - one cDNA from each plate• Sequential cDNAs selected
– 1A1, 2B2, 3C3, etc.• Labeled with fluorescent primer (FAM) and PCR• Hybridize and scan• Compare patterns: experimental vs. Expected
QA/QC – GMU Update• RNA
– Checked on gels– Amplified RNA also
checked
• Probe labeling• Determine incorporation of
fluorescent dye
• ~5,500 cDNAs printed one one microarray– Four printings - ~200
slides– ~40,000 cDNAs printed
on two slides– ~20,000 cDNAs per slide– 80 slides of each printed
• ~50 microarrays (~5500cDNAs) hybridized– reference RNA
(Stratagene)– experimental RNA
• Quality control - microarray manufacture– Correct orientation
and sequence of plates at all steps in manufacture process?
• VCU/MDx quality control: -chip/chip, run/run, fresh/frozen cRNA variation- Human Reference RNA (Stratagene)
200 g total RNA from 10 human cell lines
(additional aliquots to be shipped to GMU)Run day#1 Run day#2 Total
• 4 chips/ fresh cRNA• 4 chips/ frozen cRNA
• 4 chips/ frozen cRNA• 4 chips/ frozen cRNA 16 chips
QA/QC – VCU Update
Sample Quality:
• Bioanalyzer (28S/18S ratio)• Spectrophotometer (A260/A280)• 3’/5’ ratio for high abundant transcripts (GAPDH)• 3’/5’ ratio for low abundant transcripts (ISGF3A)
Quality Control Parameters
QA/QC – VCU Update
Preliminary analysis
18S
28S
Fluore
scen
ce
Time (seconds)
0
100
200
300
400
500
600
700
19 24 29 34 39 44 49 54 59 64 69
18S
28S
Fluore
scen
ce
Time (seconds)
0
10
20
30
40
50
60
70
80
90
100
110
120
19 24 29 34 39 44 49 54 59 64 69
Bioanalyzer (28S/18S ratio)
3’/5’ ratio (GAPDH) 3’/5’ ratio (ISGF3A)
0.76
1.83 1.09 3.68
1.06 9.36
Sample Quality:
QA/QC – VCU Update
Quality Control Parameters
• Noise (RawQ)• Scaling Factor (SF)• Number of Present genes (P/A)• Spike controls Linearity (BioB, BioC, BioD, CREX)• Signal intensities for housekeeping genes (GAPDH, -actin)
Chip Performance:
QA/QC – VCU Update
Preliminary analysis
•
Chip Performance:
QA/QC – VCU Update
Noise (RawQ) CV% < 4%
Scaling Factor (SF) CV% < 10%
Number of Present genes (P/A) ~ 60%
CV% < 2%
Signal intensities for housekeeping genes (GAPDH, -actin)
CV% < 7%
Preliminary analysis
• Spike controls Linearity (BioB, BioC, BioD, CREX) Run day#1 Run day#2
Spike Controls Linearity
1.E+00
1.E+01
1.E+02
1.E+03
1.E+04
BioB BioC BioD Cre
Lo
g o
f S
ign
al
Inte
ns
ity
Spike Controls Linearity
1.E+00
1.E+01
1.E+02
1.E+03
1.E+04
BioB BioC BioD CreL
og
of
Sig
na
l In
ten
sit
y
QA/QC – VCU Update
Establish Standing Weekly or Biweekly Meeting Dates and Times
Complete the Milestone Updates
Document Discussions and Progress Using Listservs
CG-TISBK: Tissue Bank CG-CLNDT: Clinical and Pathology Data CG-DBDSN: Database Design CG-ANLDT: Analyze Data (Data Analysis) CG-QAQC: QAQC CG-LDRPI: Focus Group Leaders and PIs CG-MEMBS: All Members CG-FBCHP: Chip Fabrication
Communication Amongst Members and Focus Groups
Address messages to: [email protected]
Unsubscribe to the listserv by submitting a message with the words SIGNOFF listname to: [email protected]
Subscribe to the listserv by asking the PI with whom you work to submit your name and E-mail address to the Program Director (C.Garrett)
USE the listserv(s) to inform members of your activity or to seek advice from the members.
LISTSERVS
Old Business
New Businesso Presentations by CTRF CaGenomic’s Members at Bioinformatic’s Symposium held on June 12-14, 2002
5/21/02 - 1 million (1yr) submission to VTSF (Penberthy-PI)
“Early Clinical Trials of Imaging Agents” –contract to permit the VCU Molecular Imaging Center to respond to subsequent specific RFPs for development of new imaging agents.
Any other discoveries
Federal money leveraged
Private research money leveraged
Advancement of technology and economic development in VA
CTRF - Specific Reportables - - Reminder - -Intellectual property reporting - licenses, patents, etc
Publications
New applications
CTRF Administrative officewill search for new funding opportunities (SPIN)
will collect CVs, other support, facilities, interest documents
goal - 4 - 8 million in D.C. from CTRF CG Project
Monday
August 5, 2002
9:30AM