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PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

2015; Springer Science+Business Media; Volume: 16; Issue: 1 Linguagem: Inglês

10.1186/s13059-015-0602-8

1465-6914

Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris,

Genetic factors in colorectal cancer

Abstract Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods. PhyloWGS is free, open-source software, available at https://github.com/morrislab/phylowgs .