The Cancer Genome Atlas Research Network Symposium Meeting
In November 2011, The Cancer Genome Atlas (TCGA) Research Network held its first open scientific symposium in Washington, D.C. TCGA researchers and outside investigators from around the world presented results on the use of TCGA data to make biological discoveries about cancer. The two-day meeting included lectures, collaborative workshops and poster sessions. The lectures are made freely available here and on NHGRI's YouTube channel, GenomeTV.
The National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), two of the National Institutes of Health's 27 institutes and centers, jointly fund TCGA to use genome analysis technologies, including large-scale genome sequencing, to accelerate the understanding of the molecular basis of cancer.
Available in the table below are videos and accompanying slides from the symposium.
Also available as a video playlist on GenomeTV
Thursday, November 17, 2011
1 | OpeningVideo |
Lynda Chin, M.D. University of Texas M.D. Anderson Cancer Center |
2 | Keynote and Q & A Video | Slides not available |
Eric S. Lander, Ph.D. Broad Institute |
3 | Session I - Lead Talk Video | Slides |
Peter W. Laird, Ph.D., M.S. University of Southern California Epigenome Center |
4 | Predicting Patient Outcomes With Chained Biological Concept Classifiers Video | Slides |
K. James Durbin University of California, Santa Cruz Presenter: Daniel Edward Carlin, M.S. |
5 | Lessons Learned From 24 Completely Sequenced AML Genomes Video | Slides |
Timothy Ley, M.D. Washington University in St. Louis |
6 | LRpath Analysis Reveals Common Pathways Dysregulated via DNA Methylation Across Cancer Types Video | Slides |
Maureen A. Sartor, Ph.D., M.S. University of Michigan |
7 | Multi-Cancer Mutual Exclusivity Analysis of Genomic Alterations Video | Slides |
Giovanni Ciriello, Ph.D. Memorial Sloan-Kettering Cancer Center |
8 | Genome-Wide Co-Localization of Somatic Copy Number Alterations and Germline Common Variant Risk Loci in Cancer Video | Slides |
Marcin Imielinski, M.D., Ph.D. Broad Institute |
9 | Correlating Protein Phosphorylation With Genomic Alterations in Cancer Video | Slides |
Jianjiong Gao, Ph.D. Memorial Sloan-Kettering Cancer Center |
10 | Session II - Lead Talk Video | Slides not available |
Ilya Shmulevich, Ph.D. Institute for Systems Biology |
11 | Absolute Quantification of Somatic DNA Alterations in Cancer Reveals Frequent Genome Doublings in Human Cancers Video | Slides |
Scott L. Carter, Ph.D. Broad Institute |
12 | Predicting the Impact of Mutations in Cancer Using an Integrated Pathway Approach Video | Slides |
Sam Ng University of California, Santa Cruz |
13 | TCGA Computational Histopathology Pipeline Reveals Subtypes and Their Molecular Signature Video | Slides |
Hang Chang Lawrence Berkeley National Laboratory Presenter: Bahram Parvin, Ph.D., M.S. |
14 | Algorithms for Automated Discovery of Mutated Pathways in Cancer Video | Slides |
Ben Raphael, Ph.D Brown University |
15 | The Spectra of Somatic Mutations Across Many Tumor Types Video | Slides |
Michael S. Lawrence, Ph.D. Broad Institute |
16 | An Integrated View Into Multivariate Associations Inferred From TCGA Cancer Data Video | Slides |
Richard Kreisberg, M.S. Institute for Systems Biology |
Wednesday, November 18, 2011
17 | Session III - Lead Talk Video | Slides |
Marco Marra, Ph.D. British Columbia Cancer Agency |
18 | RetroSeq: A Tool To Discover Somatic Insertion of Retrotransposons Video | Slides |
Elena Helman Broad Institute |
19 | Patient-Specific Pathway Analysis Using PARADIGM Identifies Key Activities in Multiple Cancers
Video | Slides |
Josh Stuart, Ph.D. University of California, Santa Cruz |
20 | Morphologic Analysis of Glioblastoma Identifies Morphology-Driven Clusters and Molecular Correlates Associated With Patient Survival
Video | Slides |
Lee Cooper, Ph.D. Emory University |
21 | Validated Targets Associated With Curatively Treated Advanced Serous Ovarian Carcinoma Video | Slides |
Douglas A. Levine, M.D. Memorial Sloan-Kettering Cancer Center |
22 | Massively Parallel Validation of Cancer Mutations and Other Variants Identified by Whole Cancer Genome and Exome Sequencing
Video | Slides |
Georges Natsoulis, Ph.D. Stanford University |
23 | SuperPathway Analyses of Luminal and Basaloid Breast Cancers From The Cancer Genome Atlas Program Video | Slides not available |
Christopher Benz, M.D. Buck Institute for Research on Aging |
24 | Session IV - Lead Talk
Video | Slides |
David Haussler, Ph.D. University of California, Santa Cruz |
25 | RF-ACE for Uncovering Nonlinear Associations From Heterogeneous Cancer Data
Video | Slides |
Timo Erkkilä, M.S. Institute for Systems Biology |
26 | Supporting Subtype Characterization Through Integrative Visualization of Cancer Genomics Datasets
Video | Slides |
Nils Gehlenborg, Ph.D. Harvard Medical School |
27 | Uncovering the Pseudo-Subclonal Structure of Tumor Sample With Copy Number Variation Analysis of Next-Generation Sequencing Data
Video | Slides |
Yi Qiao Boston College |
28 | Comparison and Validation of Somatic Mutation Callers Video | Slides |
Andrey Sivachenko, Ph.D. Broad Institute |
29 | Post-Transcriptional Regulators of microRNA Biogenesis Regulate Pathogenesis of Cancer Video | Slides |
Pavel P. Sumazin, Ph.D. Columbia University |
30 | Neuroimaging Predictors of Survival, Pathology, and Molecular Profiles in TCGA Glioblastomas Video | Slides |
David Gutman, M.D., Ph.D. Emory University |
31 | Closing Video | Slides |
Elaine Mardis, Ph.D. Washington University School of Medicine |
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Last Reviewed: March 21, 2012
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Rao Divi (December 7, 2011, 15:28)
Disproportionately high C/T transition in heterogeneous tumor tissue is very surprising. The predominant C/T transition observed in TCGA samples may be a sequence specific pre-analytical artifact. If not all, some of them may be systematic pre-analytical artifacts. The artifact may be generated by deaminases or other biomolecules present in nucleus or cytosol that deaminate 5-methylcytosine to thymidine during cell lysis and DNA extraction. For every C/T transition, investigators should try confirming it by sequencing complementary strand. Endogenous mutation will show as G/A transition in opposite strand, whereas the C/T artifact transition shows 'G' opposite T. The high degree of C/T transition may be a function of deaminase levels/activity in vitro. When isolating DNA from human samples, nucleoside deaminase inhibitors, nitric oxide scavengers, and thymine-DNA glycosylase inhibitors may be included in buffers used for cell lysis and DNA extraction to prevent C/T transition artifact. Uracil-DNA glycosylase is included in PCR buffers to prevent C/U transition from thermal deamination during DNA amplification, but inclusion of deaminase inhibitors and TDG-inhibitors in DNA extraction buffers may be equally important to prevent artifacts.
Thanks for making all of these resources available.