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; Ding Li; Chris Sander; Josh M. Stuart; Lincoln D. Stein; Nuria Lopez-Bigas

doi:10.1038/nmeth.2562

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 journal › Review article › peer-review

134 Scopus citations

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.

Original language	English
Pages (from-to)	723-729
Number of pages	7
Journal	Nature Methods
Volume	10
Issue number	8
DOIs	https://doi.org/10.1038/nmeth.2562
State	Published - Aug 2013

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Gonzalez-Perez, A., Mustonen, V., Reva, B., Ritchie, G. R. S., Creixell, P., Karchin, R., Vazquez, M., Fink, J. L., Kassahn, K. S., Pearson, J. V., Bader, G. D., Boutros, P. C., Muthuswamy, L., Ouellette, B. F. F., Reimand, J., Linding, R., Shibata, T., Valencia, A., Butler, A., ... Lopez-Bigas, N. (2013). Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods, 10(8), 723-729. https://doi.org/10.1038/nmeth.2562

@article{cb803f35eb5e440d8760efdb32a167e8,

title = "Computational approaches to identify functional genetic variants in cancer genomes",

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.",

author = "Abel Gonzalez-Perez and Ville Mustonen and Boris Reva and Ritchie, {Graham R.S.} and Pau Creixell and Rachel Karchin and Miguel Vazquez and Fink, {J. Lynn} and Kassahn, {Karin S.} and Pearson, {John V.} and Bader, {Gary D.} and Boutros, {Paul C.} and Lakshmi Muthuswamy and Ouellette, {B. F.Francis} and J{\"u}ri Reimand and Rune Linding and Tatsuhiro Shibata and Alfonso Valencia and Adam Butler and Serge Dronov and Paul Flicek and Shannon, {Nick B.} and Hannah Carter and Ding Li and Chris Sander and Stuart, {Josh M.} and Stein, {Lincoln D.} and Nuria Lopez-Bigas",

year = "2013",

month = aug,

doi = "10.1038/nmeth.2562",

language = "English",

volume = "10",

pages = "723--729",

journal = "Nature Methods",

issn = "1548-7091",

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}

Gonzalez-Perez, A, Mustonen, V, Reva, B, Ritchie, GRS, Creixell, P, Karchin, R, Vazquez, M, Fink, JL, Kassahn, KS, Pearson, JV, Bader, GD, Boutros, PC, Muthuswamy, L, Ouellette, BFF, Reimand, J, Linding, R, Shibata, T, Valencia, A, Butler, A, Dronov, S, Flicek, P, Shannon, NB, Carter, H, Li, D, Sander, C, Stuart, JM, Stein, LD & Lopez-Bigas, N 2013, 'Computational approaches to identify functional genetic variants in cancer genomes', Nature Methods, vol. 10, no. 8, pp. 723-729. https://doi.org/10.1038/nmeth.2562

TY - JOUR

T1 - Computational approaches to identify functional genetic variants in cancer genomes

AU - Gonzalez-Perez, Abel

AU - Mustonen, Ville

AU - Reva, Boris

AU - Ritchie, Graham R.S.

AU - Creixell, Pau

AU - Karchin, Rachel

AU - Vazquez, Miguel

AU - Fink, J. Lynn

AU - Kassahn, Karin S.

AU - Pearson, John V.

AU - Bader, Gary D.

AU - Boutros, Paul C.

AU - Muthuswamy, Lakshmi

AU - Ouellette, B. F.Francis

AU - Reimand, Jüri

AU - Linding, Rune

AU - Shibata, Tatsuhiro

AU - Valencia, Alfonso

AU - Butler, Adam

AU - Dronov, Serge

AU - Flicek, Paul

AU - Shannon, Nick B.

AU - Carter, Hannah

AU - Li, Ding

AU - Sander, Chris

AU - Stuart, Josh M.

AU - Stein, Lincoln D.

AU - Lopez-Bigas, Nuria

PY - 2013/8

Y1 - 2013/8

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84881396090&partnerID=8YFLogxK

U2 - 10.1038/nmeth.2562

DO - 10.1038/nmeth.2562

M3 - Review article

C2 - 23900255

AN - SCOPUS:84881396090

SN - 1548-7091

VL - 10

SP - 723

EP - 729

JO - Nature Methods

JF - Nature Methods

IS - 8

ER -

Computational approaches to identify functional genetic variants in cancer genomes

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