ReMixT: clone-specific genomic structure estimation in cancer

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 aberr...

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Autores principales: McPherson, Andrew W., Roth, Andrew, Ha, Gavin, Chauve, Cedric, Steif, Adi, de Souza, Camila P. E., Eirew, Peter, Bouchard-Côté, Alexandre, Aparicio, Sam, Sahinalp, S. Cenk, Shah, Sohrab P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5530528/
https://www.ncbi.nlm.nih.gov/pubmed/28750660
http://dx.doi.org/10.1186/s13059-017-1267-2
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author McPherson, Andrew W.
Roth, Andrew
Ha, Gavin
Chauve, Cedric
Steif, Adi
de Souza, Camila P. E.
Eirew, Peter
Bouchard-Côté, Alexandre
Aparicio, Sam
Sahinalp, S. Cenk
Shah, Sohrab P.
author_facet McPherson, Andrew W.
Roth, Andrew
Ha, Gavin
Chauve, Cedric
Steif, Adi
de Souza, Camila P. E.
Eirew, Peter
Bouchard-Côté, Alexandre
Aparicio, Sam
Sahinalp, S. Cenk
Shah, Sohrab P.
author_sort McPherson, Andrew W.
collection PubMed
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1267-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-55305282017-08-02 ReMixT: clone-specific genomic structure estimation in cancer McPherson, Andrew W. Roth, Andrew Ha, Gavin Chauve, Cedric Steif, Adi de Souza, Camila P. E. Eirew, Peter Bouchard-Côté, Alexandre Aparicio, Sam Sahinalp, S. Cenk Shah, Sohrab P. Genome Biol Method 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-017-1267-2) contains supplementary material, which is available to authorized users. BioMed Central 2017-07-27 /pmc/articles/PMC5530528/ /pubmed/28750660 http://dx.doi.org/10.1186/s13059-017-1267-2 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
McPherson, Andrew W.
Roth, Andrew
Ha, Gavin
Chauve, Cedric
Steif, Adi
de Souza, Camila P. E.
Eirew, Peter
Bouchard-Côté, Alexandre
Aparicio, Sam
Sahinalp, S. Cenk
Shah, Sohrab P.
ReMixT: clone-specific genomic structure estimation in cancer
title 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_short ReMixT: clone-specific genomic structure estimation in cancer
title_sort remixt: clone-specific genomic structure estimation in cancer
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5530528/
https://www.ncbi.nlm.nih.gov/pubmed/28750660
http://dx.doi.org/10.1186/s13059-017-1267-2
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