Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue

Genome Biol. 2013 Mar 25;14(3):R24. doi: 10.1186/gb-2013-14-3-r24.

Abstract

Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell content is required. Patchwork is freely available as an R package, installable via R-Forge (http://patchwork.r-forge.r-project.org/).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Cell Line, Tumor
  • Computational Biology / methods*
  • DNA Copy Number Variations / genetics*
  • Female
  • Genome, Human / genetics*
  • Humans
  • Neoplasm Metastasis
  • Neoplasms / genetics*
  • Neoplasms / pathology
  • Reproducibility of Results
  • Sequence Analysis, DNA*
  • Software*