CTRF Leadership Meeting

1. CTRF Leadership Meeting Cancer Genomics and Development of Diagnostic Tools and Therapies April 1, 2002 Institutional Partners

2. Develop Infrastructure and Intellectual Property that Enhances the Competitiveness of the Partners for Clinical and Extramural Funds Principle Objective

3. 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

4. Funding From CTRF

5. 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

6. Reminder - Cost Share Form (VCU)

7. CTRF Funding • 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.

8. 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

9. 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.

10. 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

11. Website Update - Home Page

12. Website Update - PI Page

13. Website Update - Focus Groups Page

14. Website Update - Focus Groups Page

15. SPIN Research • Jo Ann Breaux receiving daily notices of grant opportunities • Compiling weekly document of relevant findings • Will be distributed over the CTRF LISTSERV

16. SPIN Research

17. Focus Group • Tissue Bank • Clinical and Pathology Laboratory Data • Database Design • Data Analysis • Quality Assurance in Microarray Analysis • (Chip Fabrication - proposed)

18. Focus Group Leaders

19. 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

20. 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

21. Database Design/Clinical Info Database Design Meeting at GMU (3/6/02) • 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

22. Database Design/Clinical Info GMU • 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)

23. Database Design/Clinical Info VCU • 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

24. Data Analysis GMU • “Terabyte” Database - Questions • associated analysis tools • access issues • capacity for incorporating clinical data • advantages over open source databases such as Gene-X

25. Data Analysis VCU • GeneX Database • Set up at both institutions • associated analysis tools • ?status regarding Affymetrix Data compatibility • platform compatibility (?Unix based only)

26. QA/QC • 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

27. QA/QC Update Sheet

28. CTRF - Promoting Focus Group Activity REMINDER • Establish Standing Weekly or Biweekly Meeting Dates and Times • Complete the Milestone Updates • Document Discussions and Progress Using Listservs

29. Communication Amongst Members and Focus Groups • 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 7 - LISTSERVS

30. LISTSERVS • Address messages to: listname@VENUS.VCU.EDU • Unsubscribe to the listserv by submitting a message with the words SIGNOFF listnameto: 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.

31. Old Business • New Business

32. CTRF - Specific Reportables - - Reminder - - • 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

33. Next CTRF Leadership Meeting Monday May 6, 2002 9:30 am

34. Serous Carcinoma of Ovary