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
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