The Cancer Genome Atlas' 1st Annual Scientific Symposium: Enabling Cancer Research Through TCGA - November 17-18, 2011
 
 
Agenda

The Cancer Genome Atlas' 1st Annual Scientific Symposium:
Enabling Cancer Research Through TCGA
November 17-18, 2011
National Harbor, Maryland

Please note that we will be unable to provide Internet services at this symposium.

Thursday, November 17, 2011
7:00 a.m. - 8:00 a.m. Registration and Breakfast-Potomac C&D
8:00 a.m. - 8:15 a.m. Opening
Lynda Chin, M.D.
University of Texas M.D. Anderson Cancer Center
8:15 a.m. - 9:15 a.m. Keynote and Q&A
Eric S. Lander, Ph.D.
Broad Institute
9:15 a.m. - 11:15 a.m. Session I-Potomac C&D
Chair:  Peter W. Laird, Ph.D., M.S.
University of Southern California Epigenome Center
9:15 a.m. - 9:45 a.m. Lead Talk
Peter W. Laird, Ph.D., M.S.
University of Southern California Epigenome Center
9:45 a.m. - 10:00 a.m. Predicting Patient Outcomes With Chained Biological Concept Classifiers
K. James Durbin
University of California, Santa Cruz

Daniel Edward Carlin, M.S.
University of California, Santa Cruz

10:00 a.m. - 10:15 a.m. Lessons Learned From 24 Completely Sequenced AML Genomes
Timothy Ley, M.D.
Washington University in St. Louis
10:15 a.m. - 10:30 a.m. Break
10:30 a.m. - 10:45 a.m. LRpath Analysis Reveals Common Pathways Dysregulated via DNA Methylation Across Cancer Types
Maureen A. Sartor, Ph.D., M.S.
University of Michigan
10:45 a.m. - 11:00 a.m. Multi-Cancer Mutual Exclusivity Analysis of Genomic Alterations
Giovanni Ciriello, Ph.D.
Memorial Sloan-Kettering Cancer Center
11:00 a.m. - 11:15 a.m. Genome-Wide Co-Localization of Somatic Copy Number Alterations and Germline Common Variant Risk Loci in Cancer
Marcin Imielinski, M.D., Ph.D.
Broad Institute
11:15 a.m. - 11:30 a.m. Correlating Protein Phosphorylation With Genomic Alterations in Cancer
Jianjiong Gao, Ph.D.
Memorial Sloan-Kettering Cancer Center
11:30 a.m. - 12:30 p.m. Poster Viewing
12:30 p.m. - 1:30 p.m. Lunch(and continued poster viewing)
1:30 p.m. - 3:30 p.m. Session II -Potomac C&D
Chair:  Ilya Shmulevich, Ph.D.
Institute for Systems Biology
1:30 p.m. - 2:00 p.m. Lead Talk
Ilya Shmulevich, Ph.D.
Institute for Systems Biology
2:00 p.m. - 2:15 p.m. Absolute Quantification of Somatic DNA Alterations in Cancer Reveals Frequent Genome Doublings in Human Cancers
Scott L. Carter, Ph.D.
Broad Institute
2:15 p.m. - 2: 30 p.m. Predicting the Impact of Mutations in Cancer Using an Integrated Pathway Approach
Sam Ng
University of California, Santa Cruz
2:30 p.m. - 2:45 p.m. TCGA Computational Histopathology Pipeline Reveals Subtypes and Their Molecular Signature
Hang Chang
Lawrence Berkeley National Laboratory

Bahram Parvin, Ph.D., M.S.
Lawrence Berkeley National Laboratory

2:45 p.m. - 3:00 p.m. Algorithms for Automated Discovery of Mutated Pathways in Cancer
Ben Raphael, Ph.D.
Brown University
3:00 p.m. - 3:15 p.m. The Spectra of Somatic Mutations Across Many Tumor Types
Michael S. Lawrence, Ph.D.
Broad Institute
3:15 p.m. - 3:30 p.m. An Integrated View Into Multivariate Associations Inferred From TCGA Cancer Data
Richard Kreisberg, M.S.
Institute for Systems Biology
3:30 p.m. - 4:00 p.m. Break/Workshop Setup
4:00 p.m. - 5:00 p.m. Hands-on Workshop Breakouts
  Session 1: Nature Genetics Editorial Process-Potomac 1
Pamela Feliciano, Ph.D., M.S.
Nature Publishing Group
  Session 2: The Integrative Genomics Viewer-Potomac 2
James Robinson, Ph.D.
Broad Institute
  Session 3: cBio Portal at MSKCC-Potomac 3
Nikolaus Schultz, Ph.D.
Memorial Sloan-Kettering Cancer Center

Ethan Cerami, Ph.D.
Memorial Sloan-Kettering Cancer Center

  Session 4: UCSC Cancer Genome Browser-Potomac 4
Jingchun Zhu, Ph.D.
University of California, Santa Cruz
  Session 5: Steps To Get Controlled Access Data-Potomac 5
Vivian Ota Wang, Ph.D., M.S.
National Human Genome Research Institute, NIH
  Session 6: Firehose-Potomac 6
Douglas Voet
Broad Institute
  Session 7: Oncomine-Chesapeake 2&3
Paul Williams, Ph.D.
Compendia Bioscience
  Session 8: Getting To Know TCGA DCC-Azalea 2
Anna Chu
SRA International, Inc.
5:00 p.m. - 6:00 p.m. All Hands-on Workshops Repeat
6:00 p.m. Dinner on Your Own
Friday, November 18, 2011
7:30 a.m. - 8:30 a.m. Registration and Breakfast
8:30 a.m. - 10: 30 a.m. Session III -Potomac C&D
Chair:  Marco Marra, Ph.D.
British Columbia Cancer Agency
8:30 a.m. - 9:00 a.m. Lead Talk
Marco Marra, Ph.D.
British Columbia Cancer Agency
9:00 a.m. - 9:15 a.m. RetroSeq: A Tool To Discover Somatic Insertion of Retrotransposons
Elena Helman
Broad Institute
9:15 a.m. - 9:30 a.m. Patient-Specific Pathway Analysis Using PARADIGM Identifies Key Activities in Multiple Cancers
Josh Stuart, Ph.D.
University of California, Santa Cruz
9:30 a.m. - 9:45 a.m. Morphologic Analysis of Glioblastoma Identifies Morphology-Driven Clusters and Molecular Correlates Associated With Patient Survival
Lee Cooper, Ph.D.
Emory University
9:45 a.m. - 10:00 a.m. Validated Targets Associated With Curatively Treated Advanced Serous Ovarian Carcinoma
Douglas A. Levine, M.D.
Memorial Sloan-Kettering Cancer Center
10:00 a.m. - 10:15 a.m. Massively Parallel Validation of Cancer Mutations and Other Variants Identified by Whole Cancer Genome and Exome Sequencing
Georges Natsoulis, Ph.D.
Stanford University
10:15 a.m. - 10:30 a.m. SuperPathway Analyses of Luminal and Basaloid Breast Cancers From The Cancer Genome Atlas Program
Christopher Benz, M.D.
Buck Institute for Research on Aging
10:30 a.m. - 11:00 a.m. Break
11:00 a.m. - 1:00 p.m. Session IV -Potomac C&D
Chair:  David Haussler, Ph.D.
University of California, Santa Cruz
11:00 a.m.  - 11:30 a.m. Lead Talk
David Haussler, Ph.D.
University of California, Santa Cruz
11:30 a.m. - 11:45 a.m. RF-ACE for Uncovering Nonlinear Associations From Heterogeneous Cancer Data
Timo Erkkilä, M.S.
Institute for Systems Biology
11:45 a.m. - 12 noon Supporting Subtype Characterization Through Integrative Visualization of Cancer Genomics Datasets
Nils Gehlenborg, Ph.D.
Harvard Medical School
12 noon - 12:15 p.m. Uncovering the Pseudo-Subclonal Structure of Tumor Sample With Copy Number Variation Analysis of Next-Generation Sequencing Data
Yi Qiao
Boston College
12:15 p.m. - 12:30 p.m. Comparison and Validation of Somatic Mutation Callers
Andrey Sivachenko, Ph.D.
Broad Institute
12:30 p.m. - 12:45 p.m. Post-Transcriptional Regulators of microRNA Biogenesis Regulate Pathogenesis of Cancer
Pavel P. Sumazin, Ph.D.
Columbia University
12:45 p.m. - 1:00 p.m. Neuroimaging Predictors of Survival, Pathology, and Molecular Profiles in TCGA Glioblastomas
David Gutman, M.D., Ph.D.
Emory University
1:00 p.m. Closing
Elaine Mardis, Ph.D.
Washington University School of Medicine
1:30 p.m. Lunch and Poster Take-Down
 

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The Cancer Genome Atlas' 1st Annual Scientific Symposium: Enabling Cancer Research Through TCGA - November 17-18, 2011