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

Amit G Deshwar, Shankar Vembu, Christina K Yung, Gun Jang, Lincoln Stein, Quaid Morris
2015 Genome Biology  
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
more » ... 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.
doi:10.1186/s13059-015-0602-8 pmid:25786235 fatcat:7qr2yg2rebeabeerwemid6zpuq