Computational approaches to identify functional genetic variants in cancer genomes

被引：131

作者：

Gonzalez-Perez, Abel ^{[1
,2
,3
]}

Mustonen, Ville ^{[2
]}

Reva, Boris ^{[3
]}

Ritchie, Graham R. S. ^{[2
,4
]}

Creixell, Pau ^{[5
]}

Karchin, Rachel ^{[6
,7
]}

Vazquez, Miguel ^{[8
]}

Fink, J. Lynn ^{[9
]}

Kassahn, Karin S. ^{[9
]}

Pearson, John V. ^{[9
]}

Bader, Gary D. ^{[10
]}

Boutros, Paul C. ^{[11
,12
,13
]}

Muthuswamy, Lakshmi ^{[11
,12
]}

Ouellette, B. F. Francis ^{[11
,14
]}

Reimand, Jueri ^{[10
]}

Linding, Rune ^{[5
]}

Shibata, Tatsuhiro ^{[15
]}

Valencia, Alfonso ^{[8
,16
]}

Butler, Adam ^{[2
]}

Dronov, Serge ^{[2
]}

Flicek, Paul ^{[4
]}

Shannon, Nick B. ^{[17
]}

Carter, Hannah ^{[6
,7
]}

Ding, Li ^{[18
,19
]}

Sander, Chris ^{[3
]}

Stuart, Josh M. ^{[20
,21
]}

Stein, Lincoln D. ^{[10
,22
]}

Lopez-Bigas, Nuria ^{[1
,23
]}

机构：

[1] Univ Pompeu Fabra, Res Unit Biomed Informat, Barcelona, Spain

[2] Wellcome Trust Sanger Inst, Cambridge, England

[3] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10021 USA

[4] European Bioinformat Inst, Mol Biol Lab, Cambridge, England

[5] Tech Univ Denmark, Ctr Biol Sequence Anal, Dept Syst Biol, Cellular Signal Integrat Grp, DK-2800 Lyngby, Denmark

[6] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD USA

[7] Johns Hopkins Univ, Inst Computat Med, Baltimore, MD USA

[8] Spanish Natl Canc Res Ctr, Struct Biol & Biocomp Programme, Madrid, Spain

[9] Univ Queensland, Queensland Ctr Med Genom, Inst Mol Biosci, Brisbane, Qld, Australia

[10] Univ Toronto, Donnelly Ctr, Toronto, ON, Canada

[11] Ontario Inst Canc Res, Toronto, ON, Canada

[12] Univ Toronto, Dept Med Biophys, Toronto, ON, Canada

[13] Univ Toronto, Dept Pharmacol & Toxicol, Toronto, ON, Canada

[14] Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada

[15] Natl Canc Ctr, Div Canc Genom, Chuo Ku, Tokyo 104, Japan

[16] Spanish Natl Bioinformat Inst, Madrid, Spain

[17] Cambridge Res Inst, Cambridge, England

[18] Washington Univ, Sch Med, Genome Inst, St Louis, MO USA

[19] Washington Univ, Sch Med, Dept Med, Div Oncol, St Louis, MO 63110 USA

[20] Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA

[21] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[22] Univ Toronto, Dept Mol Genet, Toronto, ON, Canada

[23] Inst Catalana Recerca & Estudis Avancais, Barcelona, Spain

来源：

NATURE METHODS | 2013年 / 10卷 / 08期

关键词：

TERT PROMOTER MUTATIONS; SOMATIC MUTATIONS; PROTEIN FUNCTION; DATABASE; IMPACT; ANNOTATION; PREDICTION; SIFT; SNPS; HALLMARKS;

D O I：

10.1038/nmeth.2562

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：723 / 729

页数：7

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