Focus
Focus on TCGA Pan-Cancer Analysis
- Focus issue:
- October 2013 Volume 45, No 10
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.
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.
Abstract - | Full Text - Targeting molecular tumor types | PDF (111 KB) - Targeting molecular tumor types
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
Abstract - | Full Text - The Cancer Genome Atlas Pan-Cancer analysis project | PDF (608 KB) - The Cancer Genome Atlas Pan-Cancer analysis project
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
Abstract - | Full Text - Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas | PDF (758 KB) - Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas | Supplementary information
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
Abstract - | Full Text - Emerging landscape of oncogenic signatures across human cancers | PDF (1,828 KB) - Emerging landscape of oncogenic signatures across human cancers | Supplementary information
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
Abstract - | Full Text - Pan-cancer patterns of somatic copy number alteration | PDF (883 KB) - Pan-cancer patterns of somatic copy number alteration | Supplementary information
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
First Paragraph - Thread 1: Mutational drivers | Full Text - Thread 1: Mutational drivers | Supplementary information
Focus on TCGA Pan-Cancer Analysis
Thread 2: Network models
OpenJüri 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
First Paragraph - Thread 2: Network models | Full Text - Thread 2 Network models | Supplementary information
Focus on TCGA Pan-Cancer Analysis
Thread 3: Environmental exposure and pathogens
OpenDmitry Gordenin & Myles Axton
doi:10.1038/ng.2788
First Paragraph - Thread 3: Environmental exposure and pathogens | Full Text - Thread 3: Environmental exposure and pathogens | Supplementary information
Focus on TCGA Pan-Cancer Analysis
Thread 4: Data discovery, transparency and visualization
OpenNuria Lopez-Bigas, Melissa Cline, Bradley Broom, Adam Margolin, Larsson Omberg, John Weinstein & Myles Axton
doi:10.1038/ng.2789
First Paragraph - Thread 4: Data discovery, transparency and visualization | Full Text - Thread 4: Data discovery, transparency and visualization | Supplementary information
Focus on TCGA Pan-Cancer Analysis
Thread 5: Future directions
OpenAdam Margolin, John Weinstein, Joshua Stuart & Myles Axton
doi:10.1038/ng.2790
First Paragraph - Thread 5: Future directions | Full Text - Thread 5: Future directions | Supplementary information
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