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CTRF Leadership Meeting

Institutional Partners. CTRF Leadership Meeting. Cancer Genomics and Development. of Diagnostic Tools and Therapies. March 3, 2003. 2/3/03. Minutes. Corrections Approval.

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CTRF Leadership Meeting

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  1. Institutional Partners CTRF Leadership Meeting Cancer Genomics and Development of Diagnostic Tools and Therapies March 3, 2003

  2. 2/3/03 Minutes Corrections Approval

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

  4. 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

  5. Funding for CTRF

  6. FY02 Funds • 2nd half of the Year 2 CTRF CG Project allocation has been received. Virginia DPB asked VCU OFF BUDGETING & RESOURCE ANALYSIS on 1/21/03 to create the FATS request. VCU did so on 1/22/03 and it was approved by DPB on 1/29/03. State has approved a transfer of $500,000 to VCU for the new CTRF accounts

  7. Year 1 Account Balances as of 1/29/03 (Old Accounts)

  8. YR 2 Account Balances as of 2/27/03

  9. Cost Sharing Report YR 1

  10. Cost Sharing Report Yr 2 as of 1-29-03 Does Not include indirect cost or In-Kind cost sharing.

  11. Cost Share Expenses • 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)

  12. Cost Share Update • Meeting with all CTRF Fiscal Administrators took place on 12/12/2002 to review documents of CTRF Cost Sharing Accounts • For in deficit accounts, Fiscal Administrators to do IDTs. • Cost Sharing will be taken out of Ledger 1 Accounts and PAFs will be used to document Salaries • Cost sharing will be updated on a quarterly span

  13. Reminder Cost Share Form (VCU)

  14. Website Update www.ctrf-cagenomics.vcu.edu • Website has been updated in some areas • Information is still needed regarding various focus group activities • The CTRF Website is best viewed in Internet Explorer 5.0v or better

  15. SPIN Research • 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

  16. Tissue Bank Clinical & Pathology Laboratory Data Database Design QA/QC Data Analysis Chip Fabrication Focus Groups

  17. Focus Group Leaders

  18. VCU Tissue Bank Tissue Type Specimen Count

  19. INOVA – CTRF – Tissue Bank • Jean Donovan, RN has been hired at INOVA as new study coordinator • Colleen Gilmore, RN has also been hired as part-time coordinator • Training will begin next week for both coordinators

  20. INOVA Tissue Bank • INOVA has begun accessioning tissue samples and obtaining consents. Tissue Type Specimen Count Brain 2 Breast 2

  21. Tissue Acquisition Database • Access Database • VCU linked by LAN for several users • Computer at INOVA to be upgraded and VPN software to be installed

  22. Breast – Diagnosis Distribution

  23. Ovary – Diagnosis Distribution

  24. Hematopoietic Neoplasia – Diagnosis Distribution

  25. Clinical Data Model (VCU) - Primary: Data Collection AFFY Study ID Tissue ID Sample ID Sub-sample ID TISSBK & 1oCLINICAL & Consent Study ID SSN CERNER REGISTRY CLAIMS PathShadw MRN SSN Path Accsn MRN SSN ACCSN SEQ MRN SSN PAN Reg Shadw SPOTTED Histopath Risk Factors Path Dx Clin Lab Study ID Lab ID Tissue ID Run ID Clinical Risk Factors Treatments Outcomes Secondary: Queries, Data Reduction, Anonymization GeneX CEL file data Spot data Experimental (Metadata) Clinical Data Repository Table: Consent Info Tables: Extract Info StorageInfo Usage Info etc Tables: Histopath parameters Path Dxs SNOMED Text Repts Tables: Demogrphs Risk Factrs Nutirtion Comorbidty etc Tables: Tumor info Treatment Follow-up etc Tables: Surg Tx Medical Tx Radiatin Tx other dxs Tertiary: Analysis & Hypothesis Testing Gene Expression Non-genetic predictors Treatments Outcomes Expanded GeneX

  26. GMU Informatics Update • Create or Identify existing databases into which expression microarray data can be stored in electronic format in real time at this juncture. • Identified GeneX as candidate microarray database. • Worked with GeneX developers and UVA to modify GeneX to accept both cDNA and Affymetrix gene expression data • Instantiated new version of GeneX • Defined new LIMS schema for data management • Create or Identify existing databases into which clinical, laboratory, tissue bank information, and expression microarray can be stored in electronic format in real time at this juncture. • Examined several available clinical databases and found none to be sufficient in terms of performance and flexibility. • Used CGO as starting basis to generate new clinical schema. • Currently implementing clinical databases. • Create ODBC links between separate databases containing clinical, laboratory, and tissue bank data. • In progress.

  27. CTRF CA GENOMICS TISSUE UTILIZATION - PLAN QA Program

  28. Results (I) • By using TRIZOL we obtained undegraded RNA (28S/18S >1.5) but the cDNA synthesis was inhibited (accumulation of short, ~50 bp, molecules). • By cleaning up the RNA isolated using TRIZOL with the RNeasy cleanup protocol, we obtained cDNA molecules of greater size, with a max. peak at ~1,500 bp.

  29. Results (II) • By usingthe RNeasy RNA isolation protocol from breast tissue sections, we obtained total RNA with 28S/18S ratios << 1.5, and the cDNA molecules were shorter than expected (max. peak at ~500 bp). • Therefore, we decided to isolate the RNA using TRIZOL followed by the RNeasy cleanup protocol, to ensure cDNA molecules of greater size, (max. peak at ~1,500 bp).

  30. Tissue Devitalization • Awaiting specimen of sufficient size to create multiple samples over time Dr. Nasim and Dr. Grant

  31. Gene Expression Data Analysis

  32. Gene Expression Data Analysis of Breast & Ovary Tumors

  33. Gene Expression Data Analysis of Breast & Ovary Tumors Summary From the previous analysis we concluded that a good correlation between the histological classification and gene expression clustering could be accomplished among the cancer cases so far analyzed. Further associations between gene expression patterns and more complete histopathological and clinical data are now being analyzed intended to make gene expression profiles of tumor tissues an early predictive tool of good or bad outcome for cancer patients.

  34. CTRF UpdateFebruary 27, 2003 C 3 B Dr. Guiseppi-Elie

  35. Progress Report • Completed Printing ~200 C3B10k microarrays. • Hybridized Arabidopsis control oligos to 1 array from each of the four 50 slide batches to confirm viability. • Begun preliminary variability studies using Stratagene RNA, and RNA from human glioma cell lines. • Presented poster “Surface Chemistries and Blocking Strategies” at the annual AAAS meeting in Denver Feb 14-16. • Grant proposal for $200,000 for 2 years in preparation for submission to the Brain Tumor Society. • Cancer Treatment Research Fund identified for possible funding source, pregrant preparation in progress. • Exchange student Derk Bemeleit from the University of Bremen in Germany has joined the C3B lab to work on gene expression in glioma cell lines.

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

  37. Communication Amongst Members and Focus Groups 8 - 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

  38. CTRF - Specific Reportables • - Reminder - - • Intellectual property reporting - licenses, patents, etc • Publications • New applications • Federal money leveraged • Private research money leveraged • Advancement of technology and economic development in VA

  39. Publications & Presentations

  40. Publications & Presentations Con’t

  41. New Applications Identified

  42. Old Business • New Business

  43. Next Leadership Meeting Will be held: Monday, April 7, 2003 at 9:30am

  44. Mucinous Carcinoma (of the breast )

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