Journal
GENOME BIOLOGY
Volume 18, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-017-1267-2
Keywords
Cancer genomics; DNA sequencing; Tumour heterogeneity; Genomic rearrangement; Copy number variation
Funding
- Discovery Frontiers project grant
- Cancer Genome Collaboratory - Natural Sciences and Engineering Research Council (NSERC)
- Cancer Genome Collaboratory - Genome Canada (GC)
- Cancer Genome Collaboratory - Canadian Institutes of Health Research (CIHR)
- Cancer Genome Collaboratory - Canada Foundation for Innovation (CFI)
- BC Cancer Foundation
- Canadian Breast Cancer Foundation
- Canadian Cancer Society Research Institute [701584]
- Terry Fox Research Institute
- CIHR [MOP-115170]
- CIHR Foundation [FDN-143246]
- Canada Research Chairs
- NIH [GM108348]
- Indiana University Precision Health Grand Challenge Initiative
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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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