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ReMixT: clone-specific genomic structure estimation in cancer McPherson, Andrew W.; Roth, Andrew J. L.; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P.; Eirew, Peter; Bouchard-Côté, Alexandre; Aparicio, Samuel, 1963-; Sahinalp, S. Cenk; et al.

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 .

Item Metadata

Title
ReMixT: clone-specific genomic structure estimation in cancer
Creator
McPherson, Andrew W.; Roth, Andrew J. L.; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P.; Eirew, Peter; Bouchard-Côté, Alexandre; Aparicio, Samuel, 1963-; Sahinalp, S. Cenk; Shah, Sohrab P.
Publisher
BioMed Central
Date Issued
2017-07-27
Description
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 .
Subject
Cancer genomics; DNA sequencing; Tumour heterogeneity; Genomic rearrangement; Copy number variation
Genre
Article
Type
Text
Language
eng
Date Available
2017-07-27
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0349092
URI
http://hdl.handle.net/2429/62439
Affiliation
Medicine, Faculty of; Science, Faculty of; Non UBC; Pathology and Laboratory Medicine, Department of; Statistics, Department of
Citation
Genome Biology. 2017 Jul 27;18(1):140
Publisher DOI
10.1186/s13059-017-1267-2
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s)
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Rights

Attribution 4.0 International (CC BY 4.0)