CTRF Leadership Meeting

Presentation Transcript

Institutional Partners

Cancer Genomics and Development

of Diagnostic Tools and Therapies

March 3, 2003

2/3/03Minutes

Corrections

Approval

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

Funding for CTRF

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

Year 1 Account Balances as of 1/29/03 (Old Accounts)

YR 2 Account Balances as of 2/27/03

Cost Sharing Report YR 1

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.

(http://www.vcu.edu/finance/

In-kind%20Cost%20Sharing%Certification.pdf)

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

Reminder Cost Share Form (VCU)

Website Update

www.ctrf-cagenomics.vcu.edu

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

QA/QC

Data Analysis

Chip Fabrication

Focus Groups

Focus Group Leaders

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

Breast – Diagnosis Distribution

Ovary – Diagnosis Distribution

Hematopoietic Neoplasia – Diagnosis Distribution

Clinical Data Model (VCU) - Primary: Data Collection

AFFY

Study ID

Tissue ID

Sample ID

Sub-sample ID

TISSBK & 1oCLINICAL & Consent

Study ID

SSN

CERNER

REGISTRY

CLAIMS

PathShadw

MRN

SSN

Path Accsn

MRN

SSN

ACCSN

SEQ

MRN

SSN

PAN

Reg Shadw

SPOTTED

Histopath Risk Factors

Path Dx

Clin Lab

Study ID

Lab ID

Tissue ID

Run ID

Clinical Risk Factors

Treatments

Outcomes

Secondary: Queries, Data Reduction, Anonymization

GeneX

CEL file data

Spot data

Experimental

(Metadata)

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

Treatments

Outcomes

Expanded

GeneX

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.

CTRF CA GENOMICS TISSUE UTILIZATION - PLAN

QA Program

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)

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).

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

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 UpdateFebruary 27, 2003

C 3 B

Dr. Guiseppi-Elie

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.