ReMixT: clone-specific genomic structure estimation in cancer

Abstract Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-speci...

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Main Authors:	Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah
Format:	Article
Language:	English
Published:	BMC 2017-07-01
Series:	Genome Biology
Subjects:	Cancer genomics DNA sequencing Tumour heterogeneity Genomic rearrangement Copy number variation
Online Access:	http://link.springer.com/article/10.1186/s13059-017-1267-2

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spelling	doaj-99c30900a9c74f33a721484d36c747f62020-11-24T21:03:01ZengBMCGenome Biology1474-760X2017-07-0118111410.1186/s13059-017-1267-2ReMixT: clone-specific genomic structure estimation in cancerAndrew W. McPherson0Andrew Roth1Gavin Ha2Cedric Chauve3Adi Steif4Camila P. E. de Souza5Peter Eirew6Alexandre Bouchard-Côté7Sam Aparicio8S. Cenk Sahinalp9Sohrab P. Shah10Department of Molecular Oncology, BC Cancer AgencyDepartment of Statistics, Oxford UniversityDana-Farber Cancer InstituteDepartment of Mathematics, Simon Fraser UniversityDepartment of Molecular Oncology, BC Cancer AgencyDepartment of Molecular Oncology, BC Cancer AgencyDepartment of Molecular Oncology, BC Cancer AgencyDepartment of Statistics, University of British ColumbiaDepartment of Molecular Oncology, BC Cancer AgencyVancouver Prostate CentreDepartment of Molecular Oncology, BC Cancer AgencyAbstract Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt .http://link.springer.com/article/10.1186/s13059-017-1267-2Cancer genomicsDNA sequencingTumour heterogeneityGenomic rearrangementCopy number variation
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Andrew W. McPherson Andrew Roth Gavin Ha Cedric Chauve Adi Steif Camila P. E. de Souza Peter Eirew Alexandre Bouchard-Côté Sam Aparicio S. Cenk Sahinalp Sohrab P. Shah
spellingShingle	Andrew W. McPherson Andrew Roth Gavin Ha Cedric Chauve Adi Steif Camila P. E. de Souza Peter Eirew Alexandre Bouchard-Côté Sam Aparicio S. Cenk Sahinalp Sohrab P. Shah ReMixT: clone-specific genomic structure estimation in cancer Genome Biology Cancer genomics DNA sequencing Tumour heterogeneity Genomic rearrangement Copy number variation
author_facet	Andrew W. McPherson Andrew Roth Gavin Ha Cedric Chauve Adi Steif Camila P. E. de Souza Peter Eirew Alexandre Bouchard-Côté Sam Aparicio S. Cenk Sahinalp Sohrab P. Shah
author_sort	Andrew W. McPherson
title	ReMixT: clone-specific genomic structure estimation in cancer
title_short	ReMixT: clone-specific genomic structure estimation in cancer
title_full	ReMixT: clone-specific genomic structure estimation in cancer
title_fullStr	ReMixT: clone-specific genomic structure estimation in cancer
title_full_unstemmed	ReMixT: clone-specific genomic structure estimation in cancer
title_sort	remixt: clone-specific genomic structure estimation in cancer
publisher	BMC
series	Genome Biology
issn	1474-760X
publishDate	2017-07-01
description	Abstract Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt .
topic	Cancer genomics DNA sequencing Tumour heterogeneity Genomic rearrangement Copy number variation
url	http://link.springer.com/article/10.1186/s13059-017-1267-2
work_keys_str_mv	AT andrewwmcpherson remixtclonespecificgenomicstructureestimationincancer AT andrewroth remixtclonespecificgenomicstructureestimationincancer AT gavinha remixtclonespecificgenomicstructureestimationincancer AT cedricchauve remixtclonespecificgenomicstructureestimationincancer AT adisteif remixtclonespecificgenomicstructureestimationincancer AT camilapedesouza remixtclonespecificgenomicstructureestimationincancer AT petereirew remixtclonespecificgenomicstructureestimationincancer AT alexandrebouchardcote remixtclonespecificgenomicstructureestimationincancer AT samaparicio remixtclonespecificgenomicstructureestimationincancer AT scenksahinalp remixtclonespecificgenomicstructureestimationincancer AT sohrabpshah remixtclonespecificgenomicstructureestimationincancer
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ReMixT: clone-specific genomic structure estimation in cancer

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