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 DronovPaul Flicek, Nick B. Shannon, Hannah Carter, Ding Li, Chris Sander, Josh M. Stuart, Lincoln D. Stein, Nuria Lopez-Bigas

Research output: Contribution to journalReview articlepeer-review

132 Scopus citations


The International Cancer Genome Consortium (ICGC) aims to catalog genomic abnormalities in tumors from 50 different cancer types. Genome sequencing reveals hundreds to thousands of somatic mutations in each tumor but only a minority of these drive tumor progression. We present 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, and recommend computational techniques to annotate somatic variants and predict their impact on cancer phenotype.

Original languageEnglish
Pages (from-to)723-729
Number of pages7
JournalNature Methods
Issue number8
StatePublished - Aug 2013
Externally publishedYes


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