This is the agenda of the recent TCGA steering committee meeting, with links to the presentations made at that meeting:

National Cancer Institute and National Human Genome Research Institute National Institutes of Health

The Cancer Genome Atlas (TCGA) Steering Committee Meeting

December 3-4, 2008, Bethesda North Marriott Hotel & Conference Center

Bethesda, Maryland

PRESENTATIONS

Wednesday, December 3

8:30 a.m. - 8:40 a.m. Opening Remarks

Anna D. Barker, Ph.D., National Cancer Institute, NIH

Alan E. Guttmacher, M.D., National Human Genome Research Institute, NIH

8:40 a.m. - 10:40 a.m. Center Presentations

Report on data generation and analysis; presenter should include brief comment on status of ovarian project (10 minutes each)

Moderator: Bruce E. Johnson, M.D., Dana-Farber Cancer Institute

a. Cancer Genome Characterization Centers

University of North Carolina at Chapel Hill D. Neil Hayes, M.D.

Memorial Sloan-Kettering Cancer Center Marc Ladanyi, M.D.

Lawrence Berkeley National Laboratory Elizabeth Purdom, Ph.D.

Johns Hopkins/University of Southern California Peter W. Laird, Ph.D.

HudsonAlpha Institute of Biotechnology Devin Absher, Ph.D.

Harvard Medical School Peter J. Park, Ph.D.

Broad Institute of MIT and Harvard Gad Getz, Ph.D.

b. Genome Sequencing Centers

Washington University School of Medicine Li Ding, Ph.D.

Broad Institute of MIT and Harvard Michael S. Lawrence, Ph.D.

Baylor College of Medicine David A. Wheeler, Ph.D.

11:00 a.m. - 12 noon Analysis Working Group Reports

Moderator: D. Neil Hayes, M.D. University of North Carolina at Chapel Hill

Publications Using Integrated Data

Expression Analysis and GBM Subtypes (15 minutes) Roel G.W. Verhaak, Ph.D. Broad Institute of MIT and Harvard

Integrative Copy Number Analysis (15 minutes) Terrence P. Speed, Ph.D. (presented by E. Purdom) University of California, Berkeley

State of Ovarian Cancer Genomics (Literature Review) Paul T. Spellman, Ph.D., Lawrence Berkeley National Laboratory

c. Planning for the Ovarian Analysis Jamboree (15 minutes) Gad Getz, Ph.D., Broad Institute of MIT and Harvard

1:15 p.m. - 2:45 p.m. Technology Development (10 minutes each + 5-minute discussion)

Moderator: Robert H. Waterston, M.D., Ph.D. University of Washington

TCGA R21 Technology Development Grantees

Cytosine methylation and mammary carcinoma Timothy Bestor, Ph.D. Columbia University

Methylation Profiling of Normal and Cancer Genomes Gerd P. Pfeifer, Ph.D., City of Hope

Allele-Specific DNA Methylation in Normal and Cancer Tissues Benjamin Tycko, M.D., Ph.D., Columbia University

Detecting Structural Mutations in Cancer Genomes by Long-Range End-Tag Profiling

Aleksandar Milosavljevic, Ph.D., Baylor College of Medicine

Microarray Sequence Capture for Large-Scale Targeted Sequencing of Cancer Genomes Thomas Albert, Ph.D., Roche/Nimblegen Systems

Targeted Genomic Circularization for Cancer Genome Resequencing, Hanlee Ji, M.D., Stanford University School of Medicine

3:00 p.m. - 3:30 p.m. Technology Development of the CGCCs (10 minutes each)

RNA Profiling Via High-Throughput DNA SequencingJonathan G. Seidman, Ph.D., Harvard Medical School

Detecting Gene Rearrangement Associated with Intragenic CNA, Cameron W. Brennan, M.D., Memorial Sloan-Kettering Cancer Center

3:30 p.m. - 5:30 p.m. GSC Technology Implementation

Moderator: Mark S. Chee, Ph.D., Prognosys Biosciences, Inc.

Results From Pilots, Planning for 2009, Discussion

Richard A. Gibbs, Ph.D., Baylor College of Medicine

Stacey Gabriel, Ph.D. & Gad Getz, Ph.D., Broad Institute of MIT and Harvard

Elaine R. Mardis, Ph.D., Washington University School of Medicine

Thursday, December 4

8:30 a.m. - 10:00 a.m. Discussion: Cancer Genomics, Biology, and Translation

Moderators: Ronald A. DePinho, M.D. & Geoffrey Duyk, M.D., Ph.D.

What are the predictions for cancer genomics in 2 years? In 5 years?

What are the key challenges in technology? In analysis? In translation?

What are the expectations for diagnostic markers? For therapeutic targets?

How should cancer research communities be preparing for the influx of new findings?

10:10 a.m. - 11:45 a.m. Analyzing and Applying TCGA Data (15 minutes each)

Moderator: Sean Eddy, Ph.D., Janelia Farm Research Campus

caBIG® and TCGA, Kenneth H. Buetow, Ph.D., National Cancer Institute, NIH

Visualizing Cancer Genome Data, Jill P. Mesirov, Ph.D., Broad Institute of MIT and Harvard

UCSC Cancer Genomics Browser for TCGA Data, David Haussler, Ph.D., M.S., University of California, Santa Cruz

TCGA Functional Analysis Protein Mutations & Pathways Chris Sander, Ph.D., Memorial Sloan-Kettering Cancer Center

Analysis of mRNA Expression Data from TCGA and non-TCGA Glioma Samples, Kenneth D. Aldape, M.D., University of Texas M.D. Anderson Cancer Center

11:45 a.m. - 12:30 p.m. Samples Update

Samples Update: A Cautionary Tale (25 minutes), Carolyn C. Compton, M.D., Ph.D., National Cancer Institute, NIH

Breast Cancer Samples from SPORES (5 minutes), Charles M. Perou, Ph.D., University of North Carolina at Chapel Hill

12:30 p.m. Closing Remarks and General Adjournment

Alan E. Guttmacher, M.D.

Anna D. Barker, P