PyClone: statistical inference of clonal population structure in cancer
作者： Andrew Roth , Jaswinder Khattra , Damian Yap , Adrian Wan , Emma Laks
DOI: 10.1038/NMETH.2883
关键词:
摘要: We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination. Single-cell sequencing validation demonstrates PyClone's accuracy.
nature.com
sci-hub.se 参考文章(24)
Ali Bashashati, Gavin Ha, Alicia Tone, Jiarui Ding, Leah M Prentice, Andrew Roth, Jamie Rosner, Karey Shumansky, Steve Kalloger, Janine Senz, Winnie Yang, Melissa McConechy, Nataliya Melnyk, Michael Anglesio, Margaret TY Luk, Kane Tse, Thomas Zeng, Richard Moore, Yongjun Zhao, Marco A Marra, Blake Gilks, Stephen Yip, David G Huntsman, Jessica N McAlpine, Sohrab P Shah, None, Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling The Journal of Pathology. ,vol. 231, pp. 21- 34 ,(2013) , 10.1002/PATH.4230
P. Nowell, The clonal evolution of tumor cell populations Science. ,vol. 194, pp. 23- 28 ,(1976) , 10.1126/SCIENCE.959840
Sarah B. Ng, Emily H. Turner, Peggy D. Robertson, Steven D. Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E. Eichler, Michael Bamshad, Deborah A. Nickerson, Jay Shendure, Targeted capture and massively parallel sequencing of 12 human exomes Nature. ,vol. 461, pp. 272- 276 ,(2009) , 10.1038/NATURE08250
Samuel Aparicio, Carlos Caldas, None, The Implications of Clonal Genome Evolution for Cancer Medicine The New England Journal of Medicine. ,vol. 368, pp. 842- 851 ,(2013) , 10.1056/NEJMRA1204892
Sohrab P Shah, Ryan D Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh, Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Guliany, Janine Senz, Christian Steidl, Robert A Holt, Steven Jones, Mark Sun, Gillian Leung, Richard Moore, Tesa Severson, Greg A Taylor, Andrew E Teschendorff, Kane Tse, Gulisa Turashvili, Richard Varhol, René L Warren, Peter Watson, Yongjun Zhao, Carlos Caldas, David Huntsman, Martin Hirst, Marco A Marra, Samuel Aparicio, None, Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution Nature. ,vol. 461, pp. 809- 813 ,(2009) , 10.1038/NATURE08489
P. Van Loo, S. H. Nordgard, O. C. Lingjaerde, H. G. Russnes, I. H. Rye, W. Sun, V. J. Weigman, P. Marynen, A. Zetterberg, B. Naume, C. M. Perou, A.-L. Borresen-Dale, V. N. Kristensen, Allele-specific copy number analysis of tumors Proceedings of the National Academy of Sciences of the United States of America. ,vol. 107, pp. 16910- 16915 ,(2010) , 10.1073/PNAS.1009843107
Mel Greaves, Carlo C. Maley, Clonal evolution in cancer Nature. ,vol. 481, pp. 306- 313 ,(2012) , 10.1038/NATURE10762
A. Sottoriva, I. Spiteri, S. G. M. Piccirillo, A. Touloumis, V. P. Collins, J. C. Marioni, C. Curtis, C. Watts, S. Tavare, Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 4009- 4014 ,(2013) , 10.1073/PNAS.1219747110
Arno Fritsch, Katja Ickstadt, Improved criteria for clustering based on the posterior similarity matrix Bayesian Analysis. ,vol. 4, pp. 367- 391 ,(2009) , 10.1214/09-BA414
Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer, Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Genome Biology. ,vol. 12, pp. R124- 13 ,(2011) , 10.1186/GB-2011-12-12-R124