CTRF Leadership Meeting

April 1, 2002

Institutional Partners

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

Funding From CTRF

CTRF Funding - Monitoring Expenses

$ Data acquired from two accounting sources (Focus & FRS)

$ Need to identify keys to link data sets$ Automating data acquisition and

linkage remains major challenge

Reminder - Cost Share Form (VCU)

Cost share expenditures not paid from cost share linked ledger 4 account must be documented using ‘In Kind/3rd Party Cost Share form’ obtained from Margie Booker’s office.

CTRF Funding

CTRF Budget Reductions

• Budget passed by the General Assembly reductions in the CTRF of $1.25 million for 2003 and $1.5 million for 2004 (9% and 19%)

• This is not yet the final budget - the final version will not be passed until the April 17 reconvened session

CTRF Budget Reductions

• DPB gathering information for the Governor on the potential impact of these reductions.

• Any details you can provide about specific implications - how a reduction of this magnitude would affect your project, the impact on agreements you have in place with industry or academic partners, or on personnel you have brought on board - will be helpful in clarifying the consequences of a reduction in funding for existing projects.

• Please send this information by early next week if at all possible.

Website Update

Website is up and running; site is under construction

The URL for site is www.ctrf-cagenomics.vcu.edu

Content is still needed

Completion of site by mid April

Website Update - Home Page

Website Update - PI Page

Website Update - Focus Groups Page

Website Update - Focus Groups Page

SPIN Research

Jo Ann Breaux receiving daily notices of grant opportunities

Compiling weekly document of relevant findings

Will be distributed over the CTRF LISTSERV

1. Breast Cancer Research Program--Exploration Awards2. Breast Cancer Research Program--Physician-Scientist Training Awards3. Breast Cancer Research Program--Biotechnology Clinical Partnership Awards4. Breast Cancer Center of Excellence Awards5. Breast Cancer Research Program--HBCU/MI Partnership Training Awards6. Breast Cancer Research Program--Collaborative-Clinical Translational

Research Awards7. Ovarian Cancer Research Program--Institutional Training Grants8. Ovarian Cancer Research Program--Idea Development Awards9. RFP--Department of Defense Prostate Cancer Research Program (PCRP) for

Fiscal Year 200210. NCI--Specialized Programs of Research Excellence (SPOREs) in Pancreatic

Cancer for the Year 200211. NCI--Institutional Clinical Oncology Research Career Development Program12. NCI--Cancer Education and Career Development Program13. NHGRI--Technologies for Genomic Mapping, Sequencing & Analysis Program14. NHGRI--Pilot Projects or Feasibility Studies for Genomic Analysis15. RFA-HG-02-002--Developing Robust Components for Model Organism

Databases16. RFA-LM-02-001--NLM Internet Access to Digital Libraries Grants17. AHRQ--AHRQ Health Services Research18. Partnerships for Innovation (PFI)

SPIN Research

Tissue Bank Clinical and Pathology Laboratory

Data Database Design Data Analysis Quality Assurance in Microarray

Analysis (Chip Fabrication - proposed)

Focus Group

Focus Group Leaders

GMU

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)J a m e s B u rge s s ( I no va)

B a rr ie C o o k ( I n o va)

C linP 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 ataA nalysis

A la n C h r is ten s en ( G M U )A n d re a F e rre ira - G o n z ale z (V C U )

Q A / LQ C

VCU I nova

Focus Group Leaders

• Meeting March 5, 2002 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 (delat 5-10min)

• Protocol handling for Bone Marrow Aspirates not yet specified

• Tissue is not to leave Inova until surg path written report is completed

CTRF - Tissue Bank

CTRF - Tissue Bank

• Tissue Acquisition Protocol - Reviewed by VCU IRB - minor revisions requested (approval anticipated by May)

• Tissue Bank Staff Activities (Cynthia Losco)

– Improving current tissue storage system

– Meeting with pathologists and MCC faculty

• tissue handling

• breast clinic scheduler

– Developing expertise at cutting frozen section and microdissection

– developing database fields necessary for Tissue Bank

• Attending weekly Breast Conference to identify potential cases

• Data Sources– Clinical - MCCIS, Pathology, INOVA

• Desirable Info - Contains financial treatment and outcomes• If clinical identifiers present, must be behind firewall• Histopathology currently text format only

– Microarray Data

• Data Warehouse– Initial plan - include extensive clinical information including

therapies– ?Role of hypothesis’ in design of functional data warehouse

Database Design/Clinical InfoDatabase Design Meeting at GMU

(3/6/02)

Database Design/Clinical Info

Test Installation of GeneX up and Running (3/5/02)

Created And Instantiated A Schema For A Row-modeled Clinical Database (3/5/02)

Creating A Linking Table To Span The Two Databases (3/5/02)

GMU

Database Design/Clinical InfoVCU

MCC Registry (ERS) New system with cross platform connectivity ERS Company interested in assisting in data transfer issues

Pathology Shadow Database Contains all Pathology reports in text format and SNOMED

codes SNOMED Accuracy - an issue

Examined 95 breast cases accessioned 12/11/01-1/16/02 1 of 48 cases with cancer not coded for malignancy 9 cases coded as infiltuating duct but actually DCIS Other problems Automatic coding system and changes to dictionary planned

with expected improvement of accuracy

“Terabyte” Database - Questions associated analysis tools access issues capacity for incorporating clinical data advantages over open source databases

such as Gene-X

Data Analysis

GMU

Data Analysis

GeneX Database Set up at both institutions associated analysis tools ?status regarding Affymetrix Data

compatibility platform compatibility (?Unix based

only)

VCU

Meeting with Focus Group took place on March 21st

Major issues Quality Parameters needed to judge integrity of

tissue, RNA, and within platform and cross platform performance

Tissue Quality - percent tumor (frozen section); specimen handling - time to freezing; RNA integrity and changes in gene expression

RNA Quality - integrity (electropherogram); labeling; quantitation (real-time PCR)

Reference Material Commercial RNA prep (Dr. Christensen); other

QA/QC

Establish Standing Weekly or Biweekly Meeting Dates and Times

Complete the Milestone Updates

Document Discussions and Progress Using Listservs

REMINDER

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

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 Business

Intellectual property reporting - licenses, patents, etc

Publications

New applications identified - 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

Any other discoveries

Federal money leveraged

Private research money leveraged

Advancement of technology and economic development in VA

CTRF - Specific Reportables

- - Reminder - -

Monday

May 6, 2002

9:30 am