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: listname@VENUS.VCU.EDU

Unsubscribe to the listserv by submitting a message with the words SIGNOFF listname to: LISTSERV@VENUS.VCU.EDU

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