Focus


Focus on TCGA Pan-Cancer Analysis

Genomic alterations in diverse cell types at different sites in the body give rise to hundreds of different forms of cancer and the ways in which these changes give rise to tumors with different biology, pathology and treatment strategies are beginning to be characterized. The Cancer Genome Atlas Research Network has catalogued the aberrations in the DNA, chromatin and RNA of the genomes of thousands of tumors relative to matched normal cellular genomes and have analyzed their epigenetic and protein consequences. Here, the Pan-cancer initiative examines the similarities and differences among the genomic and cellular alterations found in the first dozen tumor types to be profiled by TCGA. This first look across cancer offers new tools in genomics and bioinformatics and the prospect of repurposing targeted therapies directed by the molecular pathology of the tumors in addition to their clinical classification.

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Editorial

Focus on TCGA Pan-Cancer Analysis

Targeting molecular tumor types p1103

doi:10.1038/ng.2780

In this issue, the Focus on Pan-Cancer Analysis examines the similarities and differences among the genomic and cellular alterations found in the first dozen tumor types to be profiled by The Cancer Genome Atlas (TCGA) Research Network. This first look across cancers offers new tools in genomics and bioinformatics and the prospect of repurposing targeted therapies to be directed by the molecular pathology of tumors in addition to their clinical classification.


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Commentaries

Focus on TCGA Pan-Cancer Analysis

The Cancer Genome Atlas Pan-Cancer analysis project Open pp1113 - 1120

The Cancer Genome Atlas Research Network, John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander & Joshua M Stuart

doi:10.1038/ng.2764


Focus on TCGA Pan-Cancer Analysis

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas Open pp1121 - 1126

Larsson Omberg, Kyle Ellrott, Yuan Yuan, Cyriac Kandoth, Chris Wong, Michael R Kellen, Stephen H Friend, Josh Stuart, Han Liang & Adam A Margolin

doi:10.1038/ng.2761


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Analysis

Focus on TCGA Pan-Cancer Analysis

Emerging landscape of oncogenic signatures across human cancers Open pp1127 - 1133

Giovanni Ciriello, Martin L Miller, Bülent Arman Aksoy, Yasin Senbabaoglu, Nikolaus Schultz & Chris Sander

doi:10.1038/ng.2762


Focus on TCGA Pan-Cancer Analysis

Pan-cancer patterns of somatic copy number alteration Open pp1134 - 1140

Travis I Zack, Steven E Schumacher, Scott L Carter, Andrew D Cherniack, Gordon Saksena, Barbara Tabak, Michael S Lawrence, Cheng-Zhong Zhang, Jeremiah Wala, Craig H Mermel, Carrie Sougnez, Stacey B Gabriel, Bryan Hernandez, Hui Shen, Peter W Laird, Gad Getz, Matthew Meyerson & Rameen Beroukhim

doi:10.1038/ng.2760


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Threads

Focus on TCGA Pan-Cancer Analysis

Thread 1: Mutational drivers

 Open

Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, Adam Margolin, Li Ding, Dmitry Gordenin & Myles Axton

doi:10.1038/ng.2786


Focus on TCGA Pan-Cancer Analysis

Thread 2: Network models

 Open

Jüri Reimand, Gary Bader, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John N Weinstein, Joshua Stuart & Myles Axton

doi:10.1038/ng.2787


Focus on TCGA Pan-Cancer Analysis

Thread 3: Environmental exposure and pathogens

 Open

Dmitry Gordenin & Myles Axton

doi:10.1038/ng.2788


Focus on TCGA Pan-Cancer Analysis

Thread 4: Data discovery, transparency and visualization

 Open

Nuria Lopez-Bigas, Melissa Cline, Bradley Broom, Adam Margolin, Larsson Omberg, John Weinstein & Myles Axton

doi:10.1038/ng.2789


Focus on TCGA Pan-Cancer Analysis

Thread 5: Future directions

 Open

Adam Margolin, John Weinstein, Joshua Stuart & Myles Axton

doi:10.1038/ng.2790


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