SomaticSignatures: inferring mutational signatures from single-nucleotide variants

被引：232

作者：

Gehring, Julian S. ^{[1
,2
]}

Fischer, Bernd ^{[1
,3
]}

Lawrence, Michael ^{[2
]}

Huber, Wolfgang ^{[1
]}

机构：

[1] European Mol Biol Lab, Genome Biol Unit, D-69117 Heidelberg, Germany

[2] Genentech Inc, Dept Bioinformat & Computat Biol, San Francisco, CA 94080 USA

[3] German Canc Res Ctr, Computat Genome Biol, D-69120 Heidelberg, Germany

来源：

BIOINFORMATICS | 2015年 / 31卷 / 22期

基金：

美国国家科学基金会;

关键词：

BIOCONDUCTOR;

D O I：

10.1093/bioinformatics/btv408

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements existing methods for pattern decomposition, supports extension through user-defined approaches and integrates with existing Bioconductor workflows.

引用

页码：3673 / 3675

页数：3

共 11 条

[1] Signatures of mutational processes in human cancer [J].

Alexandrov, Ludmil B. ;

Nik-Zainal, Serena ;

Wedge, David C. ;

Aparicio, Samuel A. J. R. ;

Behjati, Sam ;

Biankin, Andrew V. ;

Bignell, Graham R. ;

Bolli, Niccolo ;

Borg, Ake ;

Borresen-Dale, Anne-Lise ;

Boyault, Sandrine ;

Burkhardt, Birgit ;

Butler, Adam P. ;

Caldas, Carlos ;

Davies, Helen R. ;

Desmedt, Christine ;

Eils, Roland ;

Eyfjord, Jorunn Erla ;

Foekens, John A. ;

Greaves, Mel ;

Hosoda, Fumie ;

Hutter, Barbara ;

Ilicic, Tomislav ;

Imbeaud, Sandrine ;

Imielinsk, Marcin ;

Jaeger, Natalie ;

Jones, David T. W. ;

Jones, David ;

Knappskog, Stian ;

Kool, Marcel ;

Lakhani, Sunil R. ;

Lopez-Otin, Carlos ;

Martin, Sancha ;

Munshi, Nikhil C. ;

Nakamura, Hiromi ;

Northcott, Paul A. ;

Pajic, Marina ;

Papaemmanuil, Elli ;

Paradiso, Angelo ;

Pearson, John V. ;

Puente, Xose S. ;

Raine, Keiran ;

Ramakrishna, Manasa ;

Richardson, Andrea L. ;

Richter, Julia ;

Rosenstiel, Philip ;

Schlesner, Matthias ;

Schumacher, Ton N. ;

Span, Paul N. ;

Teague, Jon W. .

NATURE, 2013, 500 (7463) :415-+

[2] Deciphering Signatures of Mutational Processes Operative in Human Cancer [J].

Alexandrov, Ludmil B. ;

Nik-Zainal, Serena ;

Wedge, David C. ;

Campbell, Peter J. ;

Stratton, Michael R. .

CELL REPORTS, 2013, 3 (01) :246-259

[3] Metagenes and molecular pattern discovery using matrix factorization [J].

Brunet, JP ;

Tamayo, P ;

Golub, TR ;

Mesirov, JP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (12) :4164-4169

[4] Spectrum of diverse genomic alterations define non-clear cell renal carcinoma [J].

Durinck, Steffen ;

Stawiski, Eric W. ;

Pavia-Jimenez, Andrea ;

Modrusan, Zora ;

Kapur, Payal ;

Jaiswal, Bijay S. ;

Zhang, Na ;

Toffessi-Tcheuyap, Vanina ;

Nguyen, Thong T. ;

Pahuja, Kanika Bajaj ;

Chen, Ying-Jiun ;

Saleem, Sadia ;

Chaudhuri, Subhra ;

Heldens, Sherry ;

Jackson, Marlena ;

Pena-Llopis, Samuel ;

Guillory, Joseph ;

Toy, Karen ;

Ha, Connie ;

Harris, Corissa J. ;

Holloman, Eboni ;

Hill, Haley M. ;

Stinson, Jeremy ;

Rivers, Celina Sanchez ;

Janakiraman, Vasantharajan ;

Wang, Weiru ;

Kinch, Lisa N. ;

Grishin, Nick V. ;

Haverty, Peter M. ;

Chow, Bernard ;

Gehring, Julian S. ;

Reeder, Jens ;

Pau, Gregoire ;

Wu, Thomas D. ;

Margulis, Vitaly ;

Lotan, Yair ;

Sagalowsky, Arthur ;

Pedrosa, Ivan ;

de Sauvage, Frederic J. ;

Brugarolas, James ;

Seshagiri, Somasekar .

NATURE GENETICS, 2015, 47 (01) :13-+

[5] EMu: probabilistic inference of mutational processes and their localization in the cancer genome [J].

Fischer, Andrej ;

Illingworth, Christopher J. R. ;

Campbell, Peter J. ;

Mustonen, Ville .

GENOME BIOLOGY, 2013, 14 (04)

[6]

Gehring J.S., 2014, SOMATICCANCERALTERAT

[7] Bioconductor: open software development for computational biology and bioinformatics [J].

Gentleman, RC ;

Carey, VJ ;

Bates, DM ;

Bolstad, B ;

Dettling, M ;

Dudoit, S ;

Ellis, B ;

Gautier, L ;

Ge, YC ;

Gentry, J ;

Hornik, K ;

Hothorn, T ;

Huber, W ;

Iacus, S ;

Irizarry, R ;

Leisch, F ;

Li, C ;

Maechler, M ;

Rossini, AJ ;

Sawitzki, G ;

Smith, C ;

Smyth, G ;

Tierney, L ;

Yang, JYH ;

Zhang, JH .

GENOME BIOLOGY, 2004, 5 (10)

[8] Mutational Processes Molding the Genomes of 21 Breast Cancers [J].

Nik-Zainal, Serena ;

Alexandrov, Ludmil B. ;

Wedge, David C. ;

Van Loo, Peter ;

Greenman, Christopher D. ;

Raine, Keiran ;

Jones, David ;

Hinton, Jonathan ;

Marshall, John ;

Stebbings, Lucy A. ;

Menzies, Andrew ;

Martin, Sancha ;

Leung, Kenric ;

Chen, Lina ;

Leroy, Catherine ;

Ramakrishna, Manasa ;

Rance, Richard ;

Lau, King Wai ;

Mudie, Laura J. ;

Varela, Ignacio ;

McBride, David J. ;

Bignell, Graham R. ;

Cooke, Susanna L. ;

Shlien, Adam ;

Gamble, John ;

Whitmore, Ian ;

Maddison, Mark ;

Tarpey, Patrick S. ;

Davies, Helen R. ;

Papaemmanuil, Elli ;

Stephens, Philip J. ;

McLaren, Stuart ;

Butler, Adam P. ;

Teague, Jon W. ;

Jonsson, Goran ;

Garber, Judy E. ;

Silver, Daniel ;

Miron, Penelope ;

Fatima, Aquila ;

Boyault, Sandrine ;

Langerod, Anita ;

Tutt, Andrew ;

Martens, John W. M. ;

Aparicio, Samuel A. J. R. ;

Borg, Ake ;

Salomon, Anne Vincent ;

Thomas, Gilles ;

Borresen-Dale, Anne-Lise ;

Richardson, Andrea L. ;

Neuberger, Michael S. .

CELL, 2012, 149 (05) :979-993

[9] VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants [J].

Obenchain, Valerie ;

Lawrence, Michael ;

Carey, Vincent ;

Gogarten, Stephanie ;

Shannon, Paul ;

Morgan, Martin .

BIOINFORMATICS, 2014, 30 (14) :2076-2078

[10]

Pournelle G. H., 1953, Journal of Mammalogy, V34, P133, DOI 10.1890/0012-9658(2002)083[1421:SDEOLC]2.0.CO

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