CTRF Leadership Meeting August 5, 2002 Institutional Partners V C U G M U I N O V A

7/01/02 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

Funding From CTRF

FY02 Budget Rollover Report (M. Newsome)

New Account Numbers for CTRF New Account Numbers for FY Torr Central Garrett INOVA Ginder GMU Guiseppi-Eli

FY2002 Account Balances Accounts will be closed as of September 30, 2002

Estimated Cost Share Account PI Account # Comm’d Cost Share (Direct Cost Only) Yr to Date as of 5/31/02 Variance Admin ,50081,347(16,153) Garrett ,595274,705(51,890) Guiseppi-Elie ,950148,679(69,271) Buck ,144124,375(13,769) Ginder ,75048,548(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 ( In-kind%20Cost%20Sharing%Certification.pdf)

Reminder - Cost Share Form (VCU)

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  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:

 Tissue Bank  Clinical and Pathology Laboratory Data  Database Design  Data Analysis  Quality Assurance in Microarray Analysis  Chip Fabrication Focus Group

Focus Group Leaders

INOVA -CTRF - Tissue Bank IRB has approved Tissue Acquisition at INOVA pending changes to Informed Consent IRB to approve Informed Consent for Tissue Acquisition anticipated soon VCU – CTRF will have direct contact to study coordinator Marianne Smith’s group has identified Eileen Kelley as coordinator for tissue acquisition project –Study coordinator to obtain informed consent and acquisition At INOVA Tissue Bank person to go to OR area with pathologist responding to request for frozen section and take tissue at that time Protocol handling for Bone Marrow Aspirates not yet developed at INOVA Tissue acquired at INOVA is not to leave INOVA until Surg Path written report is complete

VCU Tissue Bank

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

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

 Temporary Storage (If appropriate)  -80°C freezer monitored 24hr X 7 days with daily recording of temperature; or, -80°C freezer monitored 5 days/wk with week day (including holiday) daily recording of temperatures and with liquid nitrogen back-up capable of maintaining -40°C for 72hr. (Note: liquid nitrogen back-up must include written quality assurance plan to insure that liquid N 2 maintained at satisfactory levels).  Permanent Storage  -80°C freezer maintained on an emergency power line (ie, line with back-up generator in case of system wide power loss) monitored 5 days/wk with week-day (including holiday) daily recording of temperatures and with liquid nitrogen back-up capable of maintaining -40°C for 72hr. (Note: liquid N 2 is maintained at satisfactory levels). Laboratory must have a plan for emergency storage of tissue specimens in the event of freezer failure including persons responsible to respond in the event of freezer failure and identification of alternative freezer space. Tissue Storage

 Amount of Tissue  Based on current accessioning practices – for solid tumors (ie, breast, ovary [no VCU experience yet with brain]) – it is anticipated that each specimen will consist of approximately 200mg total weight and will contain 0.5 – 2.5  g total RNA per mg of tissue for a total of  g total RNA per sample. GMU requires ~20  g per run. VCU requires ~10  g per run for the Affymetirx platform. Supplying Tissue to Project PI Labs

Preparation of Tissue Samples In order to minimize the chances for RNA degradation and to monitor percent tumor cellularity as well as other potential confounding morphological changes (ie, inflammation, necrosis, desmoplasia, etc), tissue will be handled as follows:  blocks of tissue will be maintained frozen at all times.  blocks of tissue will be sectioned (5 μ thick) on a cryostat.  no more than μ sections will be taken from any one sample without removal of a section for frozen section histology.  the tissue sections will be placed directly into cold Trizol, dispersed by vigorous shaking at the time of sectioning and maintained at -80 o C for storage and -37 o C (dry ice temp) for transportation. (Note: participating laboratories may request transportation solution other than Trizol based on their specific needs and experience.)  the standard sample will consist of Trizol with 40 section of tissue or the equivalent amount of total RNA.

Institutional Tissue Utilization Committee  Formulate criteria for who is eligible to obtain human residual samples at the institution. οFaculty status, IRB approval, ?scientific validity ο?minimum QA requirements ο?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 Summary VCU Tissue Committee Inova Tissue Committee CTRF Tissue Utilization Group Analyze Samples

CTRF CA GENOMICS TISSUE UTILIZATION - PLAN

Monitoring RNA Quality Purity contaminants - DNA, Protein, phenol DNAdetect DNA via fluorescence Protein260/280 ratio phenol270 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)

Labeling Process cRNAyield (= μg/cRNA/μg total RNA) size range cRNA Fragmentationsize range Labeling Efficiencyspotted 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

Data Analysis Control Genes (GMU & VCU) –see uChipControlGenes.xls

Within Platform Performance Assessment 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 #: ) ( lot number 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

Example Within Platform Quality Control Study for Affymetrix GeneChip System All chips hybridized to cRNA prepared from Stratagene Human Reference mRNA is Product Number (lot number is )

Database Design/Clinical Info  Clinical Data Elements  Define 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 Database Design/Data Analysis

 Establish Standing Weekly or Biweekly Meeting Dates and Times Don’t Forget!  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:  Unsubscribe to the listserv by submitting a message with the words SIGNOFF listname to:  Subscribe to the listserv by asking the PI with whom you work to submit your name and 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

 5/21/ 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 office  will search for new funding opportunities (SPIN)  will collect CVs, other support, facilities, interest documents  goal million in D.C. from CTRF CG Project

Monday September 9, :30AM