ctrf leadership meeting n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
CTRF Leadership Meeting PowerPoint Presentation
Download Presentation
CTRF Leadership Meeting

Loading in 2 Seconds...

play fullscreen
1 / 44

CTRF Leadership Meeting - PowerPoint PPT Presentation


  • 82 Views
  • Uploaded on

Institutional Partners. CTRF Leadership Meeting. Cancer Genomics and Development. of Diagnostic Tools and Therapies. March 3, 2003. 2/3/03. Minutes. Corrections Approval.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'CTRF Leadership Meeting' - priscilla-fox


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
ctrf leadership meeting

Institutional Partners

CTRF Leadership Meeting

Cancer Genomics and Development

of Diagnostic Tools and Therapies

March 3, 2003

minutes
2/3/03Minutes

Corrections

Approval

principal objective
Develop Infrastructure and Intellectual Property that Enhances the Competitiveness of the Partners for Clinical and Extramural Funds Principal Objective
slide4
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
slide10

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

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

slide11

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)

slide12

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
slide14

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
slide15

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
slide16

Tissue Bank

Clinical & Pathology Laboratory Data

Database Design

QA/QC

Data Analysis

Chip Fabrication

Focus Groups

slide18

VCU Tissue Bank

Tissue Type Specimen Count

slide19

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
slide20

INOVA Tissue Bank

  • INOVA has begun accessioning tissue samples and obtaining consents.

Tissue Type Specimen Count

Brain 2

Breast 2

slide21

Tissue Acquisition Database

  • Access Database
    • VCU linked by LAN for several users
    • Computer at INOVA to be upgraded and VPN software to be installed
slide25

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

slide26

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

slide31

Gene Expression

Data Analysis

slide33

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.
slide36

CTRF – Promoting Focus Group Activity

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

Complete the Milestone Updates

slide37

Communication Amongst Members and Focus Groups

8 - 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
  • CG-FBCHP: Chip Fabrication
slide38

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
slide42
Old Business
  • New Business
slide43

Next Leadership Meeting

Will be held:

Monday, April 7, 2003 at 9:30am