CTRF Leadership Meeting

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CTRF Leadership Meeting

• April 1, 2002

Cancer Genomics and Development
of Diagnostic Tools and Therapies
Institutional Partners
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Principle Objective

• Develop Infrastructure and Intellectual Property
  that Enhances the Competitiveness of the Partners
  for Clinical and Extramural Funds

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Research 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

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

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Reminder - Cost Share Form (VCU)
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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 Bookers 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

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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

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Website Update - Home Page
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Website Update - PI Page
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Website Update - Focus Groups Page
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Website Update - Focus Groups Page
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SPIN Research

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

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SPIN Research
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Focus Group

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

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Focus Group Leaders
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CTRF - Tissue Bank

• 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

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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

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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

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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)

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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

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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

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Data Analysis
VCU

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

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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

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QA/QC Update Sheet
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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

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Communication Amongst Members and Focus Groups
7 - 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

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LISTSERVS

• Address messages to listname_at_VENUS.VCU.EDU
• Unsubscribe to the listserv by submitting a
  message with the words SIGNOFF listname to
  
  
  
  
  
  LISTSERV_at_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.

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• Old Business
• New Business

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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

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Next CTRF Leadership Meeting
Monday May 6, 2002 930 am
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Serous Carcinoma of Ovary