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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

Institutional Partners

CTRF Leadership Meeting

Cancer Genomics and Development

of Diagnostic Tools and Therapies

March 3, 2003




principal objective
Develop Infrastructure and Intellectual Property that Enhances the Competitiveness of the Partners for Clinical and Extramural Funds Principal 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

fy02 funds
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

Cost Sharing Report Yr 2 as of 1-29-03

Does Not include indirect cost or In-Kind cost sharing.


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.




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

Website Update


  • 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

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

Tissue Bank

Clinical & Pathology Laboratory Data

Database Design


Data Analysis

Chip Fabrication

Focus Groups


VCU Tissue Bank

Tissue Type Specimen Count


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

INOVA Tissue Bank

  • INOVA has begun accessioning tissue samples and obtaining consents.

Tissue Type Specimen Count

Brain 2

Breast 2


Tissue Acquisition Database

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

Clinical Data Model (VCU) - Primary: Data Collection


Study ID

Tissue ID

Sample ID

Sub-sample ID


Study ID








Path Accsn








Reg Shadw


Histopath Risk Factors

Path Dx

Clin Lab

Study ID

Lab ID

Tissue ID

Run ID

Clinical Risk Factors



Secondary: Queries, Data Reduction, Anonymization


CEL file data

Spot data



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






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.
results i
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.
results ii
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).
dr nasim and dr grant

Tissue Devitalization

  • Awaiting specimen of sufficient size to create multiple samples over time

Dr. Nasim and Dr. Grant


Gene Expression

Data Analysis


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.

ctrf update february 27 2003

CTRF UpdateFebruary 27, 2003

C 3 B

Dr. Guiseppi-Elie

progress report
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.

CTRF – Promoting Focus Group Activity

  • Establish Standing Weekly or Biweekly Meeting Dates and Times
  • Document Discussions and Progress Using Listservs

Complete the Milestone Updates


Communication Amongst Members and Focus Groups


  • CG-TISBK: Tissue Bank
  • CG-CLNDT: Clinical and Pathology Data
  • CG-DBDSN: Database Design
  • CG-ANLDT: Analyze Data (Data Analysis)
  • CG-LDRPI: Focus Group Leaders and PIs
  • CG-MEMBS: All Members
  • CG-FBCHP: Chip Fabrication

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
Old Business
  • New Business

Next Leadership Meeting

Will be held:

Monday, April 7, 2003 at 9:30am