Home LiteratureArticle Details
PMID: 24633410 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

PyClone: statistical inference of clonal population structure in cancer.

Nature methods ·Vol. 11 ·No. 4 ·2014-04-00 ·Pages 396-8

Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Côté A, Shah SP

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.

MeSH Terms
Algorithms Alleles Animals Bayes Theorem Cluster Analysis DNA Mutational Analysis/methods Gene Expression Regulation, Neoplastic Humans Models, Biological Models, Statistical Mutation Neoplasms/metabolism Reproducibility of Results Software
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Roth Andrew
1] Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada. [2] Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Khattra Jaswinder
Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Yap Damian
Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Wan Adrian
Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Laks Emma
Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Biele Justina
Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Ha Gavin
1] Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada. [2] Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
Aparicio Samuel
1] Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
Bouchard-Côté Alexandre
Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada.
Shah Sohrab P
1] Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
References (22)
22 references, click to expand
  1. Genomic landscape of non-small cell lung cancer in smokers and never-smokers.
    Cell. 2012 Sep 14;150(6):1121-34 PMID: 22980976
  2. Analysis of circulating tumor DNA to monitor metastatic breast cancer.
    N Engl J Med. 2013 Mar 28;368(13):1199-209 PMID: 23484797
  3. Allele-specific copy number analysis of tumors.
    Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5 PMID: 20837533
  4. Fast and accurate long-read alignment with Burrows-Wheeler transform.
    Bioinformatics. 2010 Mar 1;26(5):589-95 PMID: 20080505
  5. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
    N Engl J Med. 2012 Mar 8;366(10):883-892 PMID: 22397650
  6. Primer3--new capabilities and interfaces.
    Nucleic Acids Res. 2012 Aug;40(15):e115 PMID: 22730293
  7. Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.
    Genome Biol. 2011 Dec 20;12(12):R124 PMID: 22185227
  8. The clonal evolution of tumor cell populations.
    Science. 1976 Oct 1;194(4260):23-8 PMID: 959840
  9. The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
    Nature. 2012 Apr 04;486(7403):395-9 PMID: 22495314
  10. Targeted capture and massively parallel sequencing of 12 human exomes.
    Nature. 2009 Sep 10;461(7261):272-6 PMID: 19684571
  11. A map of human genome variation from population-scale sequencing.
    Nature. 2010 Oct 28;467(7319):1061-73 PMID: 20981092
  12. Absolute quantification of somatic DNA alterations in human cancer.
    Nat Biotechnol. 2012 May;30(5):413-21 PMID: 22544022
  13. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data.
    Biostatistics. 2010 Jan;11(1):164-75 PMID: 19837654
  14. Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.
    Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):4009-14 PMID: 23412337
  15. The implications of clonal genome evolution for cancer medicine.
    N Engl J Med. 2013 Feb 28;368(9):842-51 PMID: 23445095
  16. Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.
    J Pathol. 2013 Sep;231(1):21-34 PMID: 23780408
  17. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
    Nature. 2009 Oct 8;461(7265):809-13 PMID: 19812674
  18. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.
    Sci Transl Med. 2012 May 30;4(136):136ra68 PMID: 22649089
  19. The life history of 21 breast cancers.
    Cell. 2012 May 25;149(5):994-1007 PMID: 22608083
  20. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data.
    Genome Biol. 2010;11(9):R92 PMID: 20858232
  21. Clonal evolution in cancer.
    Nature. 2012 Jan 18;481(7381):306-13 PMID: 22258609
  22. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.
    Nature. 2012 Jan 11;481(7382):506-10 PMID: 22237025
Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.2883
Published
2014-04-00
Epub
2014-00-16
Pages
396-8
Language
English
Region
United States
NLM ID
101215604
PMCID
PMC4864026
Subset
IM
Grants
Canadian Institutes of Health Research · 115170-1 · Canada
Canadian Institutes of Health Research · 126119-1 · Canada
Canadian Institutes of Health Research · 130831-1 · Canada
Canadian Institutes of Health Research · 131620-1 · Canada
External Links
PubMed source DOI: 10.1038/nmeth.2883 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2