Literature DB >> 24633410

PyClone: statistical inference of clonal population structure in cancer.

Andrew Roth1, Jaswinder Khattra2, Damian Yap2, Adrian Wan2, Emma Laks2, Justina Biele2, Gavin Ha1, Samuel Aparicio3, Alexandre Bouchard-Côté4, Sohrab P Shah3.   

Abstract

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.

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Year:  2014        PMID： 24633410      PMCID： PMC4864026          DOI： 10.1038/nmeth.2883

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  22 in total

1.  Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.

Authors:  Tim Forshew; Muhammed Murtaza; Christine Parkinson; Davina Gale; Dana W Y Tsui; Fiona Kaper; Sarah-Jane Dawson; Anna M Piskorz; Mercedes Jimenez-Linan; David Bentley; James Hadfield; Andrew P May; Carlos Caldas; James D Brenton; Nitzan Rosenfeld
Journal:  Sci Transl Med       Date:  2012-05-30       Impact factor: 17.956

2.  The life history of 21 breast cancers.

Authors:  Serena Nik-Zainal; Peter Van Loo; David C Wedge; Ludmil B Alexandrov; Christopher D Greenman; King Wai Lau; Keiran Raine; David Jones; John Marshall; Manasa Ramakrishna; Adam Shlien; Susanna L Cooke; Jonathan Hinton; Andrew Menzies; Lucy A Stebbings; Catherine Leroy; Mingming Jia; Richard Rance; Laura J Mudie; Stephen J Gamble; Philip J Stephens; Stuart McLaren; Patrick S Tarpey; Elli Papaemmanuil; Helen R Davies; Ignacio Varela; David J McBride; Graham R Bignell; Kenric Leung; Adam P Butler; Jon W Teague; Sancha Martin; Goran Jönsson; Odette Mariani; Sandrine Boyault; Penelope Miron; Aquila Fatima; Anita Langerød; Samuel A J R Aparicio; Andrew Tutt; Anieta M Sieuwerts; Åke Borg; Gilles Thomas; Anne Vincent Salomon; Andrea L Richardson; Anne-Lise Børresen-Dale; P Andrew Futreal; Michael R Stratton; Peter J Campbell
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

3.  Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Authors:  Andrea Sottoriva; Inmaculada Spiteri; Sara G M Piccirillo; Anestis Touloumis; V Peter Collins; John C Marioni; Christina Curtis; Colin Watts; Simon Tavaré
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-14       Impact factor: 11.205

Review 4.  Clonal evolution in cancer.

Authors:  Mel Greaves; Carlo C Maley
Journal:  Nature       Date:  2012-01-18       Impact factor: 49.962

5.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

Authors:  Marco Gerlinger; Andrew J Rowan; Stuart Horswell; James Larkin; David Endesfelder; Eva Gronroos; Pierre Martinez; Nicholas Matthews; Aengus Stewart; Charles Swanton; M Math; Patrick Tarpey; Ignacio Varela; Benjamin Phillimore; Sharmin Begum; Neil Q McDonald; Adam Butler; David Jones; Keiran Raine; Calli Latimer; Claudio R Santos; Mahrokh Nohadani; Aron C Eklund; Bradley Spencer-Dene; Graham Clark; Lisa Pickering; Gordon Stamp; Martin Gore; Zoltan Szallasi; Julian Downward; P Andrew Futreal
Journal:  N Engl J Med       Date:  2012-03-08       Impact factor: 91.245

6.  Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.

Authors:  Li Ding; Timothy J Ley; David E Larson; Christopher A Miller; Daniel C Koboldt; John S Welch; Julie K Ritchey; Margaret A Young; Tamara Lamprecht; Michael D McLellan; Joshua F McMichael; John W Wallis; Charles Lu; Dong Shen; Christopher C Harris; David J Dooling; Robert S Fulton; Lucinda L Fulton; Ken Chen; Heather Schmidt; Joelle Kalicki-Veizer; Vincent J Magrini; Lisa Cook; Sean D McGrath; Tammi L Vickery; Michael C Wendl; Sharon Heath; Mark A Watson; Daniel C Link; Michael H Tomasson; William D Shannon; Jacqueline E Payton; Shashikant Kulkarni; Peter Westervelt; Matthew J Walter; Timothy A Graubert; Elaine R Mardis; Richard K Wilson; John F DiPersio
Journal:  Nature       Date:  2012-01-11       Impact factor: 49.962

7.  Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.

Authors:  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
Journal:  Genome Biol       Date:  2011-12-20       Impact factor: 13.583

8.  Targeted capture and massively parallel sequencing of 12 human exomes.

Authors:  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
Journal:  Nature       Date:  2009-08-16       Impact factor: 49.962

9.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937

10.  Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.

Authors:  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 T Y 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
Journal:  J Pathol       Date:  2013-09       Impact factor: 7.996
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  402 in total

1.  Tumor Heterogeneity Correlates with Less Immune Response and Worse Survival in Breast Cancer Patients.

Authors:  Kerry-Ann McDonald; Tsutomu Kawaguchi; Qianya Qi; Xuan Peng; Mariko Asaoka; Jessica Young; Mateusz Opyrchal; Li Yan; Santosh Patnaik; Eigo Otsuji; Kazuaki Takabe
Journal:  Ann Surg Oncol       Date:  2019-04-08       Impact factor: 5.344

2.  Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes.

Authors:  Ruidong Xue; Lu Chen; Chong Zhang; Masashi Fujita; Ruoyan Li; Shu-Mei Yan; Choon Kiat Ong; Xiwen Liao; Qiang Gao; Shota Sasagawa; Yanmeng Li; Jincheng Wang; Hua Guo; Qi-Tao Huang; Qian Zhong; Jing Tan; Lisha Qi; Wenchen Gong; Zhixian Hong; Meng Li; Jingmin Zhao; Tao Peng; Yinying Lu; Kiat Hon Tony Lim; Arnoud Boot; Atushi Ono; Kazuaki Chayama; Zemin Zhang; Steve George Rozen; Bin Tean Teh; Xin Wei Wang; Hidewaki Nakagawa; Mu-Sheng Zeng; Fan Bai; Ning Zhang
Journal:  Cancer Cell       Date:  2019-05-23       Impact factor: 31.743

3.  SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors:  Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal:  J Immunother Cancer       Date:  2020-12       Impact factor: 13.751

4.  CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples.

Authors:  Matthew A Myers; Gryte Satas; Benjamin J Raphael
Journal:  Cell Syst       Date:  2019-06-19       Impact factor: 10.304

5.  Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma.

Authors:  Jozefina Casuscelli; Nils Weinhold; Gunes Gundem; Lu Wang; Emily C Zabor; Esther Drill; Patricia I Wang; Gouri J Nanjangud; Almedina Redzematovic; Amrita M Nargund; Brandon J Manley; Maria E Arcila; Nicholas M Donin; John C Cheville; R Houston Thompson; Allan J Pantuck; Paul Russo; Emily H Cheng; William Lee; Satish K Tickoo; Irina Ostrovnaya; Chad J Creighton; Elli Papaemmanuil; Venkatraman E Seshan; A Ari Hakimi; James J Hsieh
Journal:  JCI Insight       Date:  2017-06-15

6.  Single Cell Genomics for Tumor Heterogeneity.

Authors:  Hae-Ock Lee; Woong-Yang Park
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

7.  Algorithmic methods to infer the evolutionary trajectories in cancer progression.

Authors:  Giulio Caravagna; Alex Graudenzi; Daniele Ramazzotti; Rebeca Sanz-Pamplona; Luca De Sano; Giancarlo Mauri; Victor Moreno; Marco Antoniotti; Bud Mishra
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-28       Impact factor: 11.205

8.  Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing.

Authors:  Yuchao Jiang; Yu Qiu; Andy J Minn; Nancy R Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-29       Impact factor: 11.205

9.  Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.

Authors:  Srinivas R Viswanathan; Gavin Ha; Andreas M Hoff; Jeremiah A Wala; Jian Carrot-Zhang; Christopher W Whelan; Nicholas J Haradhvala; Samuel S Freeman; Sarah C Reed; Justin Rhoades; Paz Polak; Michelle Cipicchio; Stephanie A Wankowicz; Alicia Wong; Tushar Kamath; Zhenwei Zhang; Gregory J Gydush; Denisse Rotem; J Christopher Love; Gad Getz; Stacey Gabriel; Cheng-Zhong Zhang; Scott M Dehm; Peter S Nelson; Eliezer M Van Allen; Atish D Choudhury; Viktor A Adalsteinsson; Rameen Beroukhim; Mary-Ellen Taplin; Matthew Meyerson
Journal:  Cell       Date:  2018-06-18       Impact factor: 41.582

Review 10.  Harnessing Tumor Evolution to Circumvent Resistance.

Authors:  Katherine L Pogrebniak; Christina Curtis
Journal:  Trends Genet       Date:  2018-06-11       Impact factor: 11.639
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