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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; Shah, Sohrab P.
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
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Creator | |
Publisher |
BioMed Central
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Date Issued |
2017-07-27
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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
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Subject | |
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Type | |
Language |
eng
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Date Available |
2017-07-27
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Provider |
Vancouver : University of British Columbia Library
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Rights |
Attribution 4.0 International (CC BY 4.0)
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DOI |
10.14288/1.0349092
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URI | |
Affiliation | |
Citation |
Genome Biology. 2017 Jul 27;18(1):140
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Publisher DOI |
10.1186/s13059-017-1267-2
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Peer Review Status |
Reviewed
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Scholarly Level |
Faculty
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Copyright Holder |
The Author(s)
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DSpace
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Item Media
Item Citations and Data
Rights
Attribution 4.0 International (CC BY 4.0)