©2002 VCU

CTRF Leadership Meeting

November 4, 2002

Institutional Partners

V C U G M U I N O V A

©2002 VCU

10/07/02

Minutes

Corrections

Approval

©2002 VCU

Develop Infrastructure and Intellectual

Property that Enhances the Competitiveness of the Partners for Clinical and Extramural Funds

Principal Objective

©2002 VCU

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

©2002 VCU

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 for CTRF

©2002 VCU

FY02 Funds Pending

•Email was sent to Judy Heiman on status of FY02 CTRF Funds on October 28, 2002

•The FATS transaction for transfer of funds to VCU for year 2 is apparently still pending DPB approval.

•Funds needed to conduct analysis of accrued specimens

©2002 VCU

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.

(http://www.vcu.edu/finance/In-kind%20Cost%20Sharing

%Certification.pdf)

Cost Share Expenses

©2002 VCU

Matching

PI Acct

MatchingRequirement

9/30/2002FRS Actual In-Kind

Total Matching (Surplus) Shortage

Garrett 290000 97,500 117,493 - 117,493 (19,993)Garrett 412310 326,595 73,246 273,553 346,799 (20,204)Buck 130139 138,144 - 150,854 150,854 (12,710)Ginder 412320 98,750 98,750 - 98,750 0Guiseppi-Eli 137100 217,950 148,679 - 148,679 69,271

878,939 438,168 424,407 862,575 16,365

GMU 345,651 - 385,472 385,472 (39,821)INOVA 364,536 - 9,936 9,936 354,600

710,187 - 395,408 395,408 314,779

Total 1,589,126 438,168 819,815 1,257,983 331,144

Cost Sharing Report

©2002 VCU

Reminder Cost Share Form (VCU)

©2002 VCU

Website still incomplete; information regarding focus group activities is needed

www.ctrf-cagenomics.vcu.edu

Website Update

©2002 VCU

Jo Ann Breaux receiving daily notices of grant opportunities

Compiling weekly document of relevant findings

Monthly SMART documents currently on the CTRF website

• Training is available: http://www.InfoEd.org/default.stm

SPIN Research

©2002 VCU

Focus Groups

Tissue Bank

Clinical & Pathology Laboratory Data

Database Design

Chip Fabrication

QA/QC

Data Analysis

©2002 VCU

Focus Group Leaders

G MU

G e rald in e G ran t ( G M U)S u ha il N as im ( VC 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 ( VC U)

J a m e s C o op e r ( I n o va)

C linP ath

C u rtis J am ison ( 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 ataA nalysis

A la n C hris ten sen ( G M U)A n d re a Fe rre ira -G o n zale z (V C U)

S u ha il N as im ( VC U)G e rald ine G ra nt

Q A / LQ C

A ntho ny Gu isepp i-E lieA lan Christensen

Chip Fabrication

VCU I nova

Focus Group Leaders

©2002 VCU

Organ Number of Specimens

Breast 26

Bone Marrow 87

Ovary 10

Brain 0

Lymph Node 3

VCU Tissue Bank

©2002 VCU

•IRB approval status for Tissue Acquisition at INOVA

•Coordinator status (?)

INOVA – CTRF – Tissue Bank

©2002 VCU

• Access Database– Computer has been installed at INOVA– Database has been installed on machine

at VCU– INOVA connected to database at VCU

using PC Anywhere (8-20-02)

• Update of Database for Histopathologic parameters of existing cases needed - Completed

Tissue Acquisition Database

Leukemia – Diagnosis Distribution

Diagnosis

# Patien

ts Total

# Patients Diagnos

tic

# Patients Remissi

on

# Patients Remission Post BM

Transplant

# Patien

ts Relap

se

# Patient

s Unkow

nMultiple Myeloma 2

Lymphoid Leukemia, acute

1

Lymphoid Leukemia, chronic

2

Myeloid Leukemia, acute 10

Myeloid Leukemia, chronic

5

Monocytic Leukemia 1

Monocytic Leukemia, acute

2

Anemia, unspecified 1

Sideroblastic Anemia 1

Other Lymphomas 3

Ovarian Diagnosis Distribution

Diagnosis#

Patients Total

Grade 1/2

Grade 3/4

Pathological Stage

1/2

Pathological Stage

3/4

Invation

Positive

Breast Diagnosis Distribution

Diagnosis

# Patien

ts Total

Grade 1/2

Grade 3/4

Lymph Node

Dissected

Lymph Node Positi

ve

Estrogen

Receptor

Positive

Progesterone

Receptor Positive

Her-2/ne

©2002 VCU

• 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

CTRF Ca Genomics Project Tissue Utilization Group

©2002 VCU

Clinical Data Model

• Minimum Data Set = State Cancer Registry Fields

• Data Sources– Tissue Bank/Primary Data (Questionnaire)– Cancer Registry– Claims (VCU)– Path LIS Shadow (VCU)

• Creation of Database to house CTRF patients in progress SQL2000 at VCU (Muller, Miller, Cassel)

(This includes specifications and refinement of data elements)

©2002 VCU

Clinical Data ElementsClinical Data Elements

• Interviews - demographics, risk factors, quality of life, function

• Cancer Registry/Path Shadow - histopathology, treatment, follow-up status, other cancers, other lab data

• Cancer Registry/Claims - history, co-morbidities, outcomes, side-effects, treatments

• Other Data Sources - Clinical Trials (tx detail, adverse events), BMT (degree of donor match)

Collection and StorageCollection and Storage

Low-level analysis - Low-level analysis - data from these sources joined and minedto create variables suitable for higher level analysis (ANOVA, MR)

Study IDTissue IDSample ID

Sub-sample ID

Study IDSSN

Data ModelData Model - Primary: Data Collection / Generation

Secondary: Queries, Data Reduction, Anonymization

Tertiary: Analysis & Hypothesis Testing

AFFYTISSBK & 1o CLINICAL & Consent

CERNER

PathShadw

REGISTRY CLAIMS

Clinical Data Repository

SPOTTED

Gene Expressio

n

Non-genetic

predictors

Treatments

Outcomes

MRN

SSN

ACCSN

SEQ

MRN

SSN

PAN

MRN

SSN

Path Accsn

Study ID

Lab ID

Tissue ID

Run ID

CEL file dataSpot data

Experimental(Metadata)

Reg Shadw

GeneX

Clinical Risk Factors

Treatments

Outcomes

Histopath Risk Factors

Path Dx

Clin Lab

ExpandedGeneX

Table: Consent

Info

Tables: Demogrph

s Risk Factrs

Nutirtion Comorbidt

y etc

Tables: Extract

Info StorageInfo Usage Info etc

Tables: Histopath parameters Path Dxs SNOMED

Text Repts

Tables: Tumor

info Treatment Follow-up

etc

Tables: Surg Tx Medical

Tx Radiatin Tx other

dxs

©2002 VCU

10-10-02 - GeneX 1.6v Meeting (Jae K. Lee) at UVA, at 9am at UVA Hospital West Complex – ACHS Conference Room

10-17-02 – GeneX 2.0v Developer Meeting (J. Weller) at GMU – Prince William Campus, at 8:30am

VCU – CDR being Developed SQL2000GeneX Database – Utility ?

AffymetrixIobionBiofortis

Database Design/Data Analysis

©2002 VCU

CTRF CA GENOMICS TISSUE UTILIZATION - PLAN

©2002 VCU

Puritycontaminants - DNA, Protein, phenol

DNA detect DNA via fluorescence

Protein 260/280 ratiophenol 270 absorbency

DNA Affy ribosomal genes (see Excel file:

uChipControlGenes.xls)

Integrity

18S/28S ratio PAGE, LabChip®-electropherogram

housekeeping genes (affy) GAPDH, β-actin (ratio3'/5' = 1)

low abundance genes (affy) ISGF-3A (ratio 3'/5' 3)

Monitoring RNA Quality

©2002 VCU

• cRNA yield (= μg/cRNA/μg total RNA)size range

• cRNA Fragmentation size range

• Labeling Efficiency spotted array -~1kbp DNA fragment of Lambda A DNA on

slides + include Lambda A polyA

RNA in labeling reactions

affy arrays - see gene list uChipControlGenes.xls

Labeling Process

©2002 VCU

Devitalization of Tissue

Dr Nasim and Dr Grant

©2002 VCU

• Breast samples collected VCU– Tissue to be snap frozen over a time

series• Immediate snap freezing (time 0)• Freeze extra pieces at 15, 30 and 60

and 120 minutes (from time 0).• Frozen sections will be performed to

monitor for purity of tumor. • Sections cut and placed directly in

TRIZOL and distributed.

– In Progress

Tissue Devitalization

©2002 VCU

• Each PI will perform quality assessment designed to measure the degree of variation due to each of the critical steps in the generation of results.

• PI Laboratories will use the Stratagene Human Reference mRNA (Product #: 740000-41) ( lot number 1000207 can be obtained from A. Christensen or A. Ferreira-Gonzalez)

• Written report summarizing findings will be prepared by PI laboratories

• Copy of report/manuscript will be provided to the Project Director’s Office

• Data for study to be treated as Project Data

Within Platform Performance Assessment

©2002 VCU

•All chips hybridized to cRNA prepared from Stratagene Human Reference mRNA is Product Number 740000-41 (lot number is 1000207)

Example Within Platform Quality Control Study for Affymetrix GeneChip System

number"Present" N probes % <.0001 <.001 <.01 <.1 NS % NS

0 6896 30.95 1 14 100 346 6435 93.31I 665 2.98 1 7 19 638 95.94

2 382 1.71 10 24 348 91.103 299 1.34 2 21 276 92.314 2252 1.13 2 I 8 241 95.635 194 0.87 3 9 182 93.816 185 0.83 2 11 172 92.977 186 0.83 2 6 178 95.768 179 0.80 2 4 173 96.659 161 0.72 3 7 151 93.79

10 185 0.83 3 15 167 90.2711 184 0.83 2 9 173 94.0212 225 1.01 3 12 210 93.3313 234 1.05 I 6 227 97.0114 316 1.42 3 14 299 94.6215 530 2.38 2 17 511 96.4216 11209 50.31 8 87 474 10640 94.92

22282 100.00 1 25 233 1002 21021 94.34

Probes p-value

Yi=day + day*module + module + module*frozen + frozen + E

©2002 VCU

Day1 vs Day2 variability -- essentially no effect on any Probe Set at p<0.0001

©2002 VCU

Module-to-Module variability -- essentially no effect on any Probe Set at p<0.0001 (Example plotted

module 1 vs module 2)

GMU - Quality Control Protocol for Custom Spotted Arrays (Process for Single Run)

Cy3 Cy5

Pool

1

2

3

4

5 5

4

3

2

1

cDNA

– 5000 Probes

- Probe Excess

- Includes Control Genes and Lambda

2 X 5 Labeling Reactions

B CA D E

Slides A thru E

Quality Control Protocol for Custom Spotted Arrays (Process for Single Run)

Slide A Slide B Slide C Slide D Slide E

Hybrid Chambers

Chamber

1Chamber

2Chamber

3Chamber

4Chamber

5

Hybridization Oven

Quality Control Protocol for Custom Spotted Arrays (Process for Single Run)

A B C

S C A N

Measures of Experimental Variances

Variance Comparison

Labeling Reaction Pooled Reactions vs. Individual Reactions

Slide Variation Changes between individual slides for pooled reactions (factoring in effect of different hybridization chambers over separate runs)

Hybridization Chamber Differences

Changes of mean between chamber hybridizations for multiple runs (factoring in effect of between slide variation).

Run to Run Variability factors: Wash solutions hybrid oven temp handling – other

Between run comparisons of gene expression intensities controlled for hybridization chamber over multiple runs

©2002 VCU

Establish Standing Weekly or Biweekly Meeting Dates

and Times

Complete the Milestone Updates

Document Discussions and Progress Using

Listservs

CTRF – Promoting Focus Group Activity

©2002 VCU

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

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.

10/01/02 – 1.5 Million – WT1 As A Determinate of Ovarian Cancer Cell Genotype

10/02 – $500,000 - “Genomics and Other Risk Factors for Oral Cancer Outcomes” (Penberthy)

1/1/02 – $42,000 – Gleevec/Novartis – “Phase I Label Study of Combination of Gleevec with Cisplatin and Etopside for Previously Untreated Extensive Stage Small Lung Cancer” (Nasim)

Any other discoveriesFederal 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 office

will 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

©2002 VCU

Old BusinessNew Business

Annual Report due December 31, 2002 – Infrastructure created Samples collectedSamples extracted & arrayedSamples analyzedPublicationsGrants submitted/awarded

©2002 VCU

Updates for Next Leadership

Meeting to Form Basis for Annual

Report

Monday

December 2, 2002

9:30am

Next Leadership Meeting

©2002 VCU