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

Markus Mayrhofer, Sebastian DiLorenzo and Anders Isaksson*

Author affiliations

Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden

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Citation and License

Genome Biology 2013, 14:R24  doi:10.1186/gb-2013-14-3-r24

Published: 25 March 2013

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/ webcite).

Keywords:
Cancer; allele-specific copy number analysis; whole-genome sequencing; aneuploidy; tumor heterogeneity; chromothripsis