DRAFT

Meeting Name: / CTRF Leadership Meeting
Date: / June 3, 2002
Location: / Video Teleconference at VCU/INOVA
Participants: / Carleton Garrett
Marianne Smith
Irene Gonzales
Alan Christensen
Curt Jamison
Geraldine Grant
Barrie Cook
Suhail Nasim
Lynne Penberthy
James Cooper
Vikas Chandhoke
Cynthia Losco
Andrea Ferreira-Gonzalez
Paula Spencer
Greg Buck
Meeting Minute Items

Approval of the Minutes of 5/6/2002

Minutes moved approval by Dr. Chandhoke and seconded by Dr. Christensen.

Funding

Ø  Documentation of Cost Share

·  Project PI’s reminded of necessity to document cost share

Ø  VCU use:

·  3rd Party/In Kind Cost Share form (http://www.vcu.edu/finance/Inkind%20Cost%20Sharing%20Certification.pdf)

*Please send original to Margie Booker with copy to Dr. Garrett/Jo Ann Breaux

Ø  FY02 Rollover

Ø  Justification and Carry-Forward Form to be submitted to Dr. Garrett by June 7, 2002

Ø  Expenses, Est. July Balance, and Matching Funds to date need to be collected for each account

Ø  INOVA to send documentation of spending

·  Automated Transaction System (FATS) request must be submitted between June 12th-14th

o  Summary of budget status (Carry-Forward Form)

o  Justification (Transaction Brief)

Ø  Justification (Transaction Brief)

Ø  FY03 Allocation

·  Submit record of expenditures and matching funds (FY02 Closeout)

·  Will need to submit progress indicating milestones achieved in FY02 (in-prep – Dr. Garrett)

Website Update

·  The URL is: www.ctrf-cagenomics.vcu.edu

·  Focus Groups Roles and Responsibilities still needed from Focus Group Leaders

·  CTRF “News and Updates” page will be added to site

Spin Research

·  Jo Ann Breaux receiving daily notices of grant opportunities

·  Compiling weekly document of relevant findings

·  Will be distributed over the CTRF LISTSERV and are located on website

·  Training is available: www.infoed.org/default.stm

Focus Group Updates

Tissue Bank

·  IRB has approved Tissue Acquisition at INOVA pending changes to Informed Consent

·  IRB to approve Informed Consent for tissue acquisition anticipated this week

·  VCU - CTRF will have direct contact to the study coordinator

·  Marianne Smith’s group has identified coordinator for tissue acquisition

·  Study coordinator to obtain informed consent and acquisition

·  Amy Ciccaro; Edwina Battle will be study coordinators for informed consent and acquisition with Erin Iturriaga overseeing process

·  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 completed

·  Tissue Bank Activities at VCU (Cynthia Losco)

·  Time sensitive issues to be resolved

·  Procedures established in Main OR and Ambulatory Surgery

·  Cynthia to be notified 30 minutes before specimen to be ready on cases identified for CTRF eligibility

·  In-service given to OR staff to address new procedure

·  Bone Marrow Biopsy patients will be consented directly after procedure

·  Specimens Acquired

·  Breast – 8; Bone Marrow – 14; Ovary – 3; Brain - 0

Tissue Acquisiton Database

·  Access Database

·  To Contain INOVA and VCU Cases

·  Demo held on June 3, 2002

Tissue Utilization – DRAFT Proposal

·  Non-Anonymized tissue samples are a form of patient medical record

·  The health system where the medical record is created is responsible for access and integrity

·  Personal identifying information should be maintained behind a health systems firewall

·  Each Health System which creates non-anonymized human tissue sample banks will:

·  Identify a guardian who is responsible for maintenance of the integrity of the collection and monitoring utilization

·  Establish a tissue utilization committee to formulate criteria for use of samples

·  For purposes of regulating utilization of all samples collected by the CTRF tissue collection personnel for the CTRF CA Genomics Project, it is assumed that:

·  The VCU and INOVA tissue utilization committees agree to follow the criteria and decisions regarding tissue utilization as determined by the CTRF CA Genomics Project Tissue Utilization Group

CTRF CA Genomics Project Tissue Utilization Group

·  Project PIs

·  Tissue Guardians

·  ?Other Project Leadership

·  Issues

·  QA Program

·  Pre-Analytical Tissue Handling

·  Storage Conditions (Freezer Monitoring, etc)

·  Manner in which tissue is supplied

·  Storage and availability of data

·  Will meet within next few weeks

Database Design/Clinical Info Update

·  VCU - Database Design/Clinical Info

·  CTRF Leadership needs to define minimal set of common clinical data elements; Initial choice to be the elements required to be sent to state cancer registry

·  Data elements will have to be built into CTRF Database – no resolution as to where data will be held

· 

·  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 Status

·  Jae K. Lee is currently running tests at UVA – almost ready to load it at VCU soon (2wks)

·  Dr. Buck has talked to Jae K. Lee, Weller and GeneX people for update

·  Late June would like to initiate visit to UVA

·  Identified person for Software/System Analyst onsite in a week or two

·  LabBook – Sean Green (CEO) contacted and meeting to be set up with Bill Plank (Assoc. VP of UVA)

·  GMU Update

·  Implementation changes have been made and completed

·  Biostatisticians have approved schema

·  Will be running in a week or two

QA/QC Updates

Ø  VCU Pathology – supplies on order to perform 16 Chip Schema to test

·  Test for inter-run Variation

·  Chip-Chip

·  Labeling

·  Buffers

·  Modules (4)

Ø  VCU C3B Schema (Presented by Scott Taylor)

Method / Description
Arabidopsis / The MWG 10K human oligo set comes with arabidopsis controls for hybridization verification. Positive controls for hybridization.
Housekeeping / Genes spotted to determine the basal level of expression
Pin Normalization / To normalize the variation in deposition of oligos by the spotting pins
Spiking / Known amounts of labeled oligo, which are specific for a subset of arrayed probes, are included in the hybridization fluid.
3’5’ Ratio / The 3’ and 5’ end of certain defined genes will be arrayed. The ratio of the intensities will be taken as an indication of the mRNA degradation
Global / The global intensity average will be used to normalize the intensity of the individual spots.
Dynamic Range / A subset of oligos are spotted in a concentration gradient, and the hybridization buffer is spiked with the labeled complement. The resulting intensity gradient yields information on hybridization uniformity, sensitivity, and dynamic range. The dynamic range yields info on validity of signal as a function of the signal to noise ratio.
Yellow Slide / An mRNA sample is labeled with both Cy3 and Cy5 in equal ratios. After hybridization the slide is used to balance the laser power.
Two Slides/Flip / Each microarray experiment will be done on 4 slides. mRNA (Sample and Control) is each labeled with two dyes. 2 slides are hybridized with RED Sample and GREEN Control, 2 slides are hybridized with GREEN Sample and RED Control.

Ø  GMU Update

·  Stratagene (ref RNA) being used

·  20 spotted arrays (6000 genes per slide) tested

·  Printed 100 sets of 40,000 genes (cDNA) each (20,000 genes per chip)

· 

Promoting Focus Group Activity

·  Establish standing weekly meetings or biweekly meeting dates and times

·  Complete milestone updates

·  Document discussion and progress using LISTSERVS

CTRF – Specific Reportables

Old Business
·  INOVA to send documentation of spending
New Business

·  C3B Presentations at BECON 2002 Symposium

·  Scott Taylor presented summary of studies to define optimum conditions to make custom spotted arrays with oligonucleotides (See Attachments)

1_Bioinformatics and Pharma_Taylor_Abstract_3_age.htm

BECON2002_Taylor_Abstract_3_age.htm