2002 VCU CTRF Leadership Meeting October 7, 2002 Institutional Partners V C U G M U I N O V A 2002 VCU 9/09/02 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 Funding for CTRF 2002 VCU New Account Numbers for FY Torr Central Garrett INOVA Ginder GMU Buck Guiseppi-Eli New Account Numbers for CTRF 2002 VCU CTRF Grant Request for Year 2 Funds 2002 VCU Cost Sharing Report 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 Bookers office. (http://www.vcu.edu/finance/ In-kind%20Cost%20Sharing%Certification.pdf) Cost Share Expenses 2002 VCU Reminder Cost Share Form (VCU) 2002 VCU Website still incomplete; information regarding focus group activities is neededWebsite 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: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 2002 VCU VCU Tissue Bank 2002 VCU IRB has approved Tissue Acquisition at INOVA Consent form resubmitted to the IRB with changes to reflect the request that the consent would be signed after the biopsy was performed Marianne Smiths group has identified Eileen Kelley as coordinator for tissue acquisition project Study coordinator to obtain informed consent and acquisition INOVA CTRF Tissue Bank 2002 VCU Manual Form for Tissue Acquisition 2002 VCU Histopathologic Parameters 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 ( ) Update of Database for Histopathologic parameters of existing cases needed - Completed Tissue Acquisition Database 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 Elements (Update for October Meeting) 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 microarray data Clinical Data Model 2002 VCU Clinical Data Model - VCU Data Sources Tissue Bank/Primary Data (Questionnaire) Cancer Registry Claims Path LIS Shadow Creation of Database to house CTRF patients in progress (Muller, Miller, Cassel) (This includes specifications and refinement of data elements) 2002 VCU CTRF CA GENOMICS TISSUE UTILIZATION - PLAN 2002 VCU 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, -actin (ratio3'/5' = 1) low abundance genes (affy)ISGF-3A (ratio 3'/5' 3) Monitoring RNA Quality 2002 VCU cRNAyield (= g/cRNA/g 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 Labeling Process 2002 VCU Goal To assess the impact of sample RNA degradation on the gene expression data from microarrays Protocol Sample Type - Total RNA from the Ovary Sample (OV T) Degradation Experiment different degrees of degradation RNA Degradation and Gene Expression 2002 VCU Analysis of the sample RNA degradation reflected by rRNA 28S/18S ratio (Agilent Bioanalyzer, Denaturing Gel, etc) For Example : Agilent Ratio Sample Sample 21 Sample 30.5 Sample 40.1 RNA Degradation and Gene Expression 2002 VCU Microarray Data Analysis: Find a common parameter to compare data across platforms (Ratio between Control genes for all the platforms against 1 Control Gene within the linear range of the system) Check for changes in 35 ratios for Housekeeping genes Low and high abundance genes Check for changes in gene calls (P A) RNA Degradation and Gene Expression 2002 VCU Devitalization of Tissue Dr Nasim and Dr Grant 2002 VCU Ovarian 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. RNA extracted and analyzed by both VCU and GMU teams for integrity over the period of experimentation Tissue Devitalization 2002 VCU Control Genes (GMU & VCU) Data Analysis 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 #: ) ( 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 Directors 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 (lot number is ) Example Within Platform Quality Control Study for Affymetrix GeneChip System 2002 VCU GeneX 1.6v Meeting (Jae K. Lee) at UVA, at 9am at UVA Hospital West Complex ACHS Conference Room GeneX 2.0v Developer Meeting (J. Weller) at GMU Prince William Campus, at 8:30am Database Design/Data Analysis 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 2002 VCU 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 andaddress to the Program Director (C.Garrett) USE the listserv(s) to inform members of your activity or to seek advice from the members. LISTSERVS 2002 VCU 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. 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) 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 November 4, :30am Next Leadership Meeting 2002 VCU