Computational approaches to identify functional genetic variants in cancer genomes.
Abel Gonzalez-Perez,Ville Mustonen,Boris Reva,Graham R. S. Ritchie,Pau Creixell,Rachel Karchin,Miguel Vazquez,J. Lynn Fink,Karin S. Kassahn,John V. Pearson,Gary D. Bader,Paul C. Boutros,Lakshmi Muthuswamy,B. F. Francis Ouellette,Jüri Reimand,Rune Linding,Tatsuhiro Shibata,Alfonso Valencia,Adam Butler,Serge Dronov,Paul Flicek,Nick B. Shannon,Hannah Carter,Li Ding,Chris Sander,Josh M. Stuart,Lincoln Stein,Nuria Lopez-Bigas +27 more
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TLDR
The result of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy is presented, and computational techniques to annotate somatic variants and predict their impact on cancer phenotype are recommended.Abstract:
International Cancer Genome Consortium members review and recommend computational approaches for identifying mutations that drive cancer progression from among the many sequence variants present in tumor genomes.read more
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The Ensembl Variant Effect Predictor.
William M. McLaren,Laurent Gil,Sarah E. Hunt,Harpreet Singh Riat,Graham R. S. Ritchie,Anja Thormann,Paul Flicek,Fiona Cunningham +7 more
TL;DR: The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
Journal Article
Patterns of Somatic Mutation in Human Cancer Genomes
TL;DR: In this paper, the coding exons of the family of 518 protein kinases were sequenced in 210 cancers of diverse histological types to explore the nature of the information that will be derived from cancer genome sequencing.
Journal ArticleDOI
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Matthew H. Bailey,Collin Tokheim,Eduard Porta-Pardo,Sohini Sengupta,Denis Bertrand,Amila Weerasinghe,Antonio Colaprico,Michael C. Wendl,Jaegil Kim,Brendan Reardon,Patrick Kwok Shing Ng,Kang Jin Jeong,Song Cao,Zixing Wang,Jianjiong Gao,Qingsong Gao,Fang Wang,Eric Minwei Liu,Loris Mularoni,Carlota Rubio-Perez,Niranjan Nagarajan,Isidro Cortes-Ciriano,Daniel Cui Zhou,Wen-Wei Liang,Julian M. Hess,Venkata Yellapantula,David Tamborero,Abel Gonzalez-Perez,Chayaporn Suphavilai,Jia Yu Ko,Ekta Khurana,Peter J. Park,Eliezer M. Van Allen,Eliezer M. Van Allen,Han Liang,Michael S. Lawrence,Adam Godzik,Nuria Lopez-Bigas,Josh Stuart,David A. Wheeler,Gad Getz,Ken Chen,Alexander J. Lazar,Gordon B. Mills,Rachel Karchin,Li Ding +45 more
TL;DR: This study reports a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations, identifying 299 driver genes with implications regarding their anatomical sites and cancer/cell types.
Journal ArticleDOI
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Jüri Reimand,Jüri Reimand,Ruth Isserlin,Veronique Voisin,Mike Kucera,Christian Tannus-Lopes,Asha Rostamianfar,Lina Wadi,Mona Meyer,Judy M. Y. Wong,Chao Xu,Daniele Merico,Gary D. Bader +12 more
TL;DR: This protocol describes pathway enrichment analysis of gene lists from RNA-seq and other genomics experiments using g:Profiler, GSEA, Cytoscape and EnrichmentMap software, and describes innovative visualization techniques.
Journal ArticleDOI
Comprehensive identification of mutational cancer driver genes across 12 tumor types
David Tamborero,Abel Gonzalez-Perez,Christian Perez-Llamas,Jordi Deu-Pons,Cyriac Kandoth,Jüri Reimand,Michael S. Lawrence,Gad Getz,Gary D. Bader,Li Ding,Nuria Lopez-Bigas,Nuria Lopez-Bigas +11 more
TL;DR: The combination of complementary methods allows identifying a comprehensive and reliable list of cancer driver genes and the methodology presented here open new avenues to better understand the mechanisms of tumorigenesis.
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