ReMixT: clone-specific genomic structure estimation in cancer.

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, Genome biology 18, 140 (2017)
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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 .