Global optimization of somatic variant identification in cancer genomes with a global community challenge

被引:38
作者
Boutros, Paul C. [1 ,2 ,3 ]
Ewing, Adam D. [4 ]
Ellrott, Kyle [4 ]
Norman, Thea C. [5 ]
Dang, Kristen K. [5 ]
Hu, Yin [5 ]
Kellen, Michael R. [5 ]
Suver, Christine [5 ]
Bare, J. Christopher [5 ]
Stein, Lincoln D. [1 ,6 ]
Spellman, Paul T. [7 ]
Stolovitzky, Gustavo [8 ]
Friend, Stephen H. [5 ]
Margolin, Adam A. [5 ]
Stuart, Joshua M. [4 ]
机构
[1] Ontario Inst Canc Res, Informat & Biocomp Program, Toronto, ON, Canada
[2] Univ Toronto, Dept Med Biophys, Toronto, ON, Canada
[3] Univ Toronto, Dept Pharmacol & Toxicol, Toronto, ON, Canada
[4] Univ Calif Santa Cruz, Dept Biomol Engn, Santa Cruz, CA 95064 USA
[5] Sage Bionetworks, Seattle, WA USA
[6] Univ Toronto, Dept Mol Genet, Toronto, ON, Canada
[7] Oregon Hlth & Sci Univ, Knight Canc Inst, Dept Mol & Med Genet, Portland, OR 97201 USA
[8] TJ Watson Res Ctr, IBM Computat Biol Ctr, Yorktown Hts, NY USA
关键词
D O I
10.1038/ng.2932
中图分类号
Q3 [遗传学];
学科分类号
071007 [遗传学];
摘要
引用
收藏
页码:318 / 319
页数:2
相关论文
共 10 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]
APPLICATIONS OF NEXT-GENERATION SEQUENCING Genome structural variation discovery and genotyping [J].
Alkan, Can ;
Coe, Bradley P. ;
Eichler, Evan E. .
NATURE REVIEWS GENETICS, 2011, 12 (05) :363-375
[3]
[Anonymous], 2013, NAT GENET, V45, P1263
[4]
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing [J].
Ding, Li ;
Ley, Timothy J. ;
Larson, David E. ;
Miller, Christopher A. ;
Koboldt, Daniel C. ;
Welch, John S. ;
Ritchey, Julie K. ;
Young, Margaret A. ;
Lamprecht, Tamara ;
McLellan, Michael D. ;
McMichael, Joshua F. ;
Wallis, John W. ;
Lu, Charles ;
Shen, Dong ;
Harris, Christopher C. ;
Dooling, David J. ;
Fulton, Robert S. ;
Fulton, Lucinda L. ;
Chen, Ken ;
Schmidt, Heather ;
Kalicki-Veizer, Joelle ;
Magrini, Vincent J. ;
Cook, Lisa ;
McGrath, Sean D. ;
Vickery, Tammi L. ;
Wendl, Michael C. ;
Heath, Sharon ;
Watson, Mark A. ;
Link, Daniel C. ;
Tomasson, Michael H. ;
Shannon, William D. ;
Payton, Jacqueline E. ;
Kulkarni, Shashikant ;
Westervelt, Peter ;
Walter, Matthew J. ;
Graubert, Timothy A. ;
Mardis, Elaine R. ;
Wilson, Richard K. ;
DiPersio, John F. .
NATURE, 2012, 481 (7382) :506-510
[5]
Comparing somatic mutation-callers: beyond Venn diagrams [J].
Kim, Su Yeon ;
Speed, Terence P. .
BMC BIOINFORMATICS, 2013, 14
[6]
Mutational heterogeneity in cancer and the search for new cancer-associated genes [J].
Lawrence, Michael S. ;
Stojanov, Petar ;
Polak, Paz ;
Kryukov, Gregory V. ;
Cibulskis, Kristian ;
Sivachenko, Andrey ;
Carter, Scott L. ;
Stewart, Chip ;
Mermel, Craig H. ;
Roberts, Steven A. ;
Kiezun, Adam ;
Hammerman, Peter S. ;
McKenna, Aaron ;
Drier, Yotam ;
Zou, Lihua ;
Ramos, Alex H. ;
Pugh, Trevor J. ;
Stransky, Nicolas ;
Helman, Elena ;
Kim, Jaegil ;
Sougnez, Carrie ;
Ambrogio, Lauren ;
Nickerson, Elizabeth ;
Shefler, Erica ;
Cortes, Maria L. ;
Auclair, Daniel ;
Saksena, Gordon ;
Voet, Douglas ;
Noble, Michael ;
DiCara, Daniel ;
Lin, Pei ;
Lichtenstein, Lee ;
Heiman, David I. ;
Fennell, Timothy ;
Imielinski, Marcin ;
Hernandez, Bryan ;
Hodis, Eran ;
Baca, Sylvan ;
Dulak, Austin M. ;
Lohr, Jens ;
Landau, Dan-Avi ;
Wu, Catherine J. ;
Melendez-Zajgla, Jorge ;
Hidalgo-Miranda, Alfredo ;
Koren, Amnon ;
McCarroll, Steven A. ;
Mora, Jaume ;
Lee, Ryan S. ;
Crompton, Brian ;
Onofrio, Robert .
NATURE, 2013, 499 (7457) :214-218
[7]
Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer [J].
Margolin, Adam A. ;
Bilal, Erhan ;
Huang, Erich ;
Norman, Thea C. ;
Ottestad, Lars ;
Mecham, Brigham H. ;
Sauerwine, Ben ;
Kellen, Michael R. ;
Mangravite, Lara M. ;
Furia, Matthew D. ;
Vollan, Hans Kristian Moen ;
Rueda, Oscar M. ;
Guinney, Justin ;
Deflaux, Nicole A. ;
Hoff, Bruce ;
Schildwachter, Xavier ;
Russnes, Hege G. ;
Park, Daehoon ;
Vang, Veronica O. ;
Pirtle, Tyler ;
Youseff, Lamia ;
Citro, Craig ;
Curtis, Christina ;
Kristensen, Vessela N. ;
Hellerstein, Joseph ;
Friend, Stephen H. ;
Stolovitzky, Gustavo ;
Aparicio, Samuel ;
Caldas, Carlos ;
Borresen-Dale, Anne-Lise .
SCIENCE TRANSLATIONAL MEDICINE, 2013, 5 (181)
[8]
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing [J].
O'Rawe, Jason ;
Jiang, Tao ;
Sun, Guangqing ;
Wu, Yiyang ;
Wang, Wei ;
Hu, Jingchu ;
Bodily, Paul ;
Tian, Lifeng ;
Hakonarson, Hakon ;
Johnson, W. Evan ;
Wei, Zhi ;
Wang, Kai ;
Lyon, Gholson J. .
GENOME MEDICINE, 2013, 5
[9]
Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges [J].
Prill, Robert J. ;
Marbach, Daniel ;
Saez-Rodriguez, Julio ;
Sorger, Peter K. ;
Alexopoulos, Leonidas G. ;
Xue, Xiaowei ;
Clarke, Neil D. ;
Altan-Bonnet, Gregoire ;
Stolovitzky, Gustavo .
PLOS ONE, 2010, 5 (02)
[10]
The Cancer Genome Atlas Pan-Cancer analysis project [J].
Weinstein, John N. ;
Collisson, Eric A. ;
Mills, Gordon B. ;
Shaw, Kenna R. Mills ;
Ozenberger, Brad A. ;
Ellrott, Kyle ;
Shmulevich, Ilya ;
Sander, Chris ;
Stuart, Joshua M. .
NATURE GENETICS, 2013, 45 (10) :1113-1120