The Cancer Genome Atlas' 2nd Annual Scientific Symposium
 
 
Agenda

The Cancer Genome Atlas' 2nd Annual Scientific Symposium:
Enabling Cancer Research Through TCGA
November 27-28, 2012
Crystal City, Virginia

*This agenda is currently a rough draft and is subject to change.

*The content of talks for the scientific sessions will be determined by Abstract submissions from participants.

Tuesday, November 27

7:00 a.m. - 8:30 a.m. Registration - Salon IV Foyer
8:30 a.m. - 8:40 a.m. Opening
Matthew Meyerson, M.D.
Dana-Farber Cancer Institute

Ilya Shmulevich, Ph.D.
Institute for Systems Biology

8:40 a.m. - 9:30 a.m. TCGA: Status Report and Insights From Leadership
Kenna Shaw, Ph.D.
The Cancer Genome Atlas Program

Stephen Chanock, M.D.
National Cancer Institute, NIH

Louis M. Staudt, M.D., Ph.D.
National Cancer Institute, NIH

9:30 a.m. - 11:25 a.m. Session I
Chair: Richard Gibbs, Ph.D.
Baylor College of Medicine
9:30 a.m. - 9:55 a.m. TCGA Clear Cell Renal Cell Carcinoma Project
Chad J. Creighton, Ph.D.
Baylor College of Medicine
9:55 a.m. - 10:10 a.m. Analysis of Somatic Mutations Across Many Tumor Types
Petar Stojanov
Dana-Farber Cancer Institute/Broad Institute
10:10 a.m. - 10:25 a.m. CRAVAT and muPIT: Web Services for High-Throughput Analysis of Sequence Variation in Cancer
Rachel Karchin, Ph.D., M.S.
Johns Hopkins University
10:25 a.m. - 10:40 a.m. Break
10:40 a.m. - 10:55 a.m. High-Grade Serous Ovarian Adenocarcinoma Transcriptome Sequencing
Andrew J. Mungall, Ph.D.
British Columbia Cancer Agency
10:55 a.m. - 11:10 a.m. Adverse Outcomes in Clear Cell Renal Cell Carcinoma With Mutations of 3p21 Epigenetic Regulators BAP1 and SETD2
Ari Hakimi, M.D.
Memorial Sloan-Kettering Cancer Center
11:10 a.m. - 11:25 a.m. Individual Patient Cancer Profiles in The Cancer Genome Atlas
Jianjiong Gao, Ph.D.
Memorial Sloan-Kettering Cancer Center
11:25 a.m. - 1:00 p.m. Lunch (on your own)
1:00 p.m. - 2:30 p.m. Poster Viewing - Salons C - H
2:30 p.m. - 4:10 p.m. Session II - Salons III - VI
Chair: Raju Kucherlapati, Ph.D.
Harvard Medical School
2:30 p.m. - 2:55 p.m. Comprehensive Genomic Characterization of Squamous Cell Carcinoma of the Head and Neck
David Neil Hayes, M.D.
The University of North Carolina at Chapel Hill
2:55 p.m. - 3:10 p.m. Genomic Characterization of Cancer-Adjacent Tissue: Evidence of Field Effects and Expression Subtypes
Melissa Troester, Ph.D., M.P.H.
The University of North Carolina at Chapel Hill
3:10 p.m. - 3: 25 p.m. Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer
Nicholas W. Knoblauch
Harvard Medical School
3:25 p.m. - 3:40 p.m. Pathway and Network Analysis of Somatic Mutations Across Cancer Types in TCGA
Ben Raphael, Ph.D.
Brown University
3:40 p.m. - 3:55 p.m. Detection and Diagnosis of Batch Effects in TCGA Data
Rehan Akbani, Ph.D.
The University of Texas MD Anderson Cancer Center
3:55 p.m. - 4:10 p.m. Papillary Thyroid Carcinoma Analysis
Thomas Giordano, M.D., Ph.D.
University of Michigan Medical School
4:10 p.m. - 4:30 p.m. Break/Workshop Setup
4:30 p.m. - 6:30 p.m. Hands-on Workshop Breakouts

Session 1: TCGA Data Access Committee - Salon A
Tamar Roomian
National Human Genome Research Institute, NIH

Session 2: Data Coordinating Center - Salon B
David Pot, Ph.D.
SRA International, Inc.

Session 3: CGHub - Salon K
Chris Wilks, M.S.
University of California, Santa Cruz

Session 4: Regulome Explorer - Salon J
Richard Kreisberg, M.S.
Institute for Systems Biology

Session 5: Integrated Genomics Viewer - Salon I
James Robinson, Ph.D.
Broad Institute

Session 6: Stratome X - Salon II
Nils Gehlenborg, Ph.D.
Harvard Medical School

Session 7: cBio Portal at MSKCC - Alexandria Room
Nikolaus Schultz, Ph.D.
Memorial Sloan-Kettering Cancer Center

Session 8: Firehose - Salons III and IV
Michael S. Noble, R.A.
Broad Institute

6:30 p.m. Adjourn Day 1

Wednesday, November 28

7:00 a.m. - 8:30 a.m. Registration - Salon IV Foyer
8:30 a.m. - 10: 10 a.m. Session III - Salons III - VI
Chair: John N. Weinstein, M.D. Ph.D.
The University of Texas MD Anderson Cancer Center
8:30 a.m. - 8:55 a.m. The Bladder Cancer Analysis Working Group (BLCA AWG): A Progress Report
John N. Weinstein, M.D., Ph.D.
The University of Texas MD Anderson Cancer Center
8:55 a.m. - 9:10 a.m. Identification of Gene Fusions Using RNA Sequencing Data
Siyuan Zheng, Ph.D.
The University of Texas MD Anderson Cancer Center
9:10 a.m. - 9:25 a.m. Comparative Mutational Analysis in Frozen and FFPE Tumor Samples
Kristin Ardlie, Ph.D.
Broad Institute
9:25 a.m. - 9:40 a.m. Structural Variant Detection in Colorectal Cancer
Evert van den Broek, M.D., Ph.D.
VU University Medical Center Amsterdam
9:40 a.m. - 9:55 a.m. FGFR2 and FGFR3 Mutations in Lung Squamous Cell Carcinoma Are Sensitive to Inhibition by Targeted Therapies
Rachel G. Liao
Harvard University
9:55 a.m. - 10:10 a.m. Analysis of 3,000 Cancer Exomes to Identify Novel Cancer Drivers and Therapeutic Opportunities
Nickolay Khazanov, Ph.D.
Compendia Bioscience
10:10 a.m. - 10:25 a.m. Break
10:25 a.m. - 12:05 p.m. Session IV
Chair: Charles Perou, Ph.D.
The University of North Carolina at Chapel Hill
10:25 a.m. - 10:50 a.m. Integrated Genomic Characterization of Endometrial Carcinoma
Douglas A. Levine, M.D.
Memorial Sloan-Kettering Cancer Center
10:50 a.m. - 11:05 a.m. Assessing Tumor Heterogeneity and Tracking Clonal Evolution Using Whole Genome or Exome Sequencing
Christopher A. Miller, Ph.D.
The Genome Institute at Washington University
11:05 a.m. - 11:20 a.m. TCGA Benchmark 4: Evaluating SV and SNV Calls Using Cell Line Genomes
Adam Ewing, Ph.D.
University of California, Santa Cruz
11:20 a.m. - 11:35 a.m. Polymerase Epsilon Mutations Accelerate Mutation Rates in Colorectal and Endometrial Cancer
David A. Wheeler, Ph.D.
Baylor College of Medicine
11:35 a.m. - 11:50 a.m. The Somatic Genomic Landscape of Glioblastoma Multiforme
Roel Verhaak, Ph.D.
The University of Texas MD Anderson Cancer Center
11:50 a.m. - 12:05 p.m. Network-Based Stratification of Tumor Mutations
Matan Hofree, M.S.
University of California, San Diego
12:05 p.m. - 1:30 p.m. Lunch (on your own)
1:30 p.m. - 3:10 p.m. Session V
Chair: Louis M. Staudt, M.D., Ph.D.
National Cancer Institute, NIH
1:30 p.m. - 1:55 p.m. Comprehensive Analysis of Lung Adenocarcinoma
Matthew Meyerson, M.D.
Dana-Farber Cancer Institute
1:55 p.m. - 2:10 p.m. Predicting Time to Ovarian Carcinoma Recurrence Using Protein Markers
Ji-Yeon Yang, Ph.D.
The University of Texas MD Anderson Cancer Center
2:10 p.m. - 2:25 p.m. The Molecular Diversity of Luminal A Breast Tumors
Giovanni Ciriello, Ph.D.
Memorial Sloan-Kettering Cancer Center
2:25 p.m. - 2:40 p.m. Virus Analysis in Head and Neck and Bladder Cancers
Michael Parfenov, M.D., Ph.D., M.S.
Harvard Medical School
2:40 p.m. - 2:55 p.m. GeneSpot: A Portal for Interactive Gene-Centric Exploration of The Cancer Genome Atlas
Brady Bernard, Ph.D.
Institute for Systems Biology
2:55 p.m. - 3:10 p.m. Functional Characterization of KEAP1 TCGA Mutants in Squamous Cell Carcinoma
Bridgid E. Hast
The University of North Carolina at Chapel Hill
3:10 p.m. - 3:25 p.m. Break
3:25 p.m. - 4:15 p.m. Keynote Talk
William Sellers, M.D.
Novartis Institutes for BioMedical Research, Inc.
4:15 p.m. - 4:30 p.m. Closing Remarks
Matthew Meyerson, M.D.
Dana-Farber Cancer Institute

Ilya Shmulevich, Ph.D.
Institute for Systems Biology

4:30 p.m. Adjourn Day 2
 
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The Cancer Genome Atlas' 2nd Annual Scientific Symposium