Computational approaches to identify functional genetic variants in cancer genomes

Journal name:
Nature Methods
Volume:
10,
Pages:
723–729
Year published:
DOI:
doi:10.1038/nmeth.2562
Received
Accepted
Published online

Abstract

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.

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Author information

  1. These authors contributed equally to this work.

    • Abel Gonzalez-Perez,
    • Ville Mustonen,
    • Boris Reva &
    • Graham R S Ritchie

Affiliations

  1. Research Unit on Biomedical Informatics, University Pompeu Fabra, Barcelona, Spain.

    • Abel Gonzalez-Perez &
    • Nuria Lopez-Bigas
  2. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Ville Mustonen,
    • Graham R S Ritchie,
    • Adam Butler &
    • Serge Dronov
  3. Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

    • Boris Reva &
    • Chris Sander
  4. Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Graham R S Ritchie &
    • Paul Flicek
  5. Cellular Signal Integration Group, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.

    • Pau Creixell &
    • Rune Linding
  6. Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

    • Rachel Karchin &
    • Hannah Carter
  7. Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.

    • Miguel Vazquez &
    • Alfonso Valencia
  8. Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland, Australia.

    • J Lynn Fink,
    • Karin S Kassahn &
    • John V Pearson
  9. The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.

    • Gary D Bader,
    • Jüri Reimand &
    • Lincoln D Stein
  10. Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

    • Paul C Boutros,
    • Lakshmi Muthuswamy &
    • B F Francis Ouellette
  11. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

    • Paul C Boutros &
    • Lakshmi Muthuswamy
  12. Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.

    • Paul C Boutros
  13. Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.

    • B F Francis Ouellette
  14. Division of Cancer Genomics, National Cancer Center, Chuo-ku, Tokyo, Japan.

    • Tatsuhiro Shibata
  15. Spanish National Bioinformatics Institute, Madrid, Spain.

    • Alfonso Valencia
  16. Cambridge Research Institute, Cambridge, UK.

    • Nick B Shannon
  17. The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.

    • Li Ding
  18. Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, USA.

    • Li Ding
  19. Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.

    • Josh M Stuart
  20. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA.

    • Josh M Stuart
  21. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

    • Lincoln D Stein
  22. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.

    • Nuria Lopez-Bigas

Consortia

  1. the International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group

    • 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 D Stein &
    • Nuria Lopez-Bigas

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

Author details

Supplementary information

PDF files

  1. Supplementary Text and Figures (129.3 KB)

    Supplementary Tables 2–4

Excel files

  1. Supplementary Table 1 (11.2 KB)

    Sequence Ontology (SO) terms used to describe the effect of mutations.

Additional data