Mar 19, 2015

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

Genome Biology
Amit G DeshwarQuaid Morris

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.

  • References38
  • Citations58

References

Mentioned in this Paper

Computer Software
Somatic Mutation
Reconstructive Surgical Procedures
Neoplasms
Tumor Cells, Malignant
Structure
Subclone
Alleles
Genome Sequencing
Whole Genome Sequencing

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