PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

Genome Biology
Amit G DeshwarQuaid Morris

Abstract

Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods. PhyloWGS is free, open-source software, available at https://github.com/morrislab/phylowgs.

References

Oct 1, 1976·Science·P C Nowell
Apr 1, 1983·Theoretical Population Biology·R R Hudson
Jan 27, 2000·Cell·D Hanahan, R A Weinberg
Nov 29, 2008·Science·Charles G MullighanJames R Downing
Nov 26, 2009·Biochimica Et Biophysica Acta·Andriy Marusyk, Kornelia Polyak
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Jun 12, 2010·Molecular Oncology·Nicholas E Navin, James Hicks
Mar 8, 2011·Cell·Douglas Hanahan, Robert A Weinberg
Nov 9, 2011·Proceedings of the National Academy of Sciences of the United States of America·Ruibin XiPeter J Park
Mar 9, 2012·The New England Journal of Medicine·Marco GerlingerCharles Swanton
May 1, 2012·Nature Biotechnology·Scott L CarterGad Getz
May 15, 2012·Bioinformatics·Christopher T SaundersR Keira Cheetham
May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
Feb 12, 2013·Nature Biotechnology·Kristian CibulskisGad Getz
Mar 1, 2013·The New England Journal of Medicine·Samuel Aparicio, Carlos Caldas
Jun 12, 2013·Bioinformatics·Nicholas B Larson, Brooke L Fridley
Jul 31, 2013·Nucleic Acids Research·Francesco StrinoYuval Kluger
Jul 31, 2013·Genome Biology·Layla OesperBenjamin J Raphael
Sep 21, 2013·Nature·Rebecca A BurrellCharles Swanton
Sep 21, 2013·Nature·Philippe L BedardLillian L Siu
Sep 28, 2013·Nature Genetics·UNKNOWN Cancer Genome Atlas Research NetworkJoshua M Stuart
Nov 2, 2013·Bioinformatics·Noemi AndorClaudia Petritsch
Feb 4, 2014·BMC Bioinformatics·Wei JiaoQuaid Morris
Mar 19, 2014·Nature Methods·Andrew RothSohrab P Shah
Jun 3, 2014·Cell Reports·Andrej FischerVille Mustonen
Jul 11, 2014·PLoS Computational Biology·Habil ZareWilliam Stafford Noble
Jul 11, 2014·PLoS Genetics·Andrew E O HughesTimothy A Graubert

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Citations

Oct 2, 2015·BMC Bioinformatics·Erich A PetersonDonald J Johann
Apr 7, 2016·Nature Communications·Hamid NikbakhtJavad Nazarian
May 7, 2015·Genome Biology·Victoria PopicSerafim Batzoglou
May 7, 2016·Genome Biology·Katharina JahnNiko Beerenwinkel
Jul 29, 2016·Cell Systems·Mohammed El-KebirBenjamin J Raphael
Aug 31, 2016·Proceedings of the National Academy of Sciences of the United States of America·Yuchao JiangNancy R Zhang
Nov 9, 2016·BMC Genomics·Christopher A MillerRichard K Wilson
Jan 6, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nilgun DonmezS Cenk Sahinalp
Jan 10, 2017·Nature Communications·Renea A TaylorRobert G Bristow
Feb 14, 2017·Nature Reviews. Genetics·Russell Schwartz, Alejandro A Schäffer
Feb 22, 2017·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Stephanie LheureuxAmit M Oza
Jul 1, 2016·PloS One·E Michael GertzAlejandro A Schäffer
May 13, 2017·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·June-Koo LeeYoung Seok Ju
Feb 1, 2017·Nature Communications·Johannes G ReiterMartin A Nowak
Apr 17, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Simone ZaccariaBenjamin J Raphael
Dec 28, 2017·BioMed Research International·Ying LiangWen Zhu
Jun 23, 2018·Bioinformatics·Sayaka MiuraSudhir Kumar
Nov 30, 2018·PloS One·Marleen M NieboerJeroen de Ridder
Feb 11, 2018·Nature Communications·Melanie Werner-KleinChristoph A Klein
Jan 30, 2019·International Journal of Cancer. Journal International Du Cancer·Eszter NémethDávid Szüts
Aug 14, 2018·Bioinformatics·Edin HusićAlexandru I Tomescu
Apr 6, 2019·Bioinformatics·Alberto MagiAlessandro Maria Vannucchi
Mar 29, 2019·Nature Reviews. Genetics·Samra TurajlicCharles Swanton
Sep 13, 2019·Bioinformatics·Nuraini AguseMohammed El-Kebir
Oct 5, 2019·Bioinformatics·Camir RickettsIman Hajirasouliha
Feb 14, 2020·PLoS Computational Biology·Christoffer FlensburgIan J Majewski
Jan 11, 2020·Nature Biotechnology·Adriana SalcedoPaul C Boutros
Mar 18, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Haoyun LeiRussell Schwartz

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Software Mentioned

BWA
SciClone
Clomial
BIC
PhyloWGS
TrAp
MuTect
THetA
PhyloSub
CODA R

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