PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. 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.
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References in zbMATH (referenced in 4 articles )
Showing results 1 to 4 of 4.
- Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
- Zeng, Li; Warren, Joshua L.; Zhao, Hongyu: Phylogeny-based tumor subclone identification using a Bayesian feature allocation model (2019)
- Zhou, Tianjian; Sengupta, Subhajit; Müller, Peter; Ji, Yuan: TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data (2019)
- Xie, Fangzheng; Zhou, Mingyuan; Xu, Yanxun: Baycount: a Bayesian decomposition method for inferring tumor heterogeneity using RNA-seq counts (2018)