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

Genome Biol. 2015 Feb 13;16(1):35. doi: 10.1186/s13059-015-0602-8.


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Clone Cells
  • Cluster Analysis
  • Computer Simulation
  • DNA Copy Number Variations
  • Gene Frequency
  • Genetic Heterogeneity
  • Genome, Human*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mutation
  • Neoplasms / genetics*
  • Phylogeny*
  • Reference Standards