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

被引：53

作者：

Mayrhofer, Markus ^{[1
]}

DiLorenzo, Sebastian ^{[1
]}

Isaksson, Anders ^{[1
]}

机构：

[1] Uppsala Univ, Dept Med Sci, Sci Life Lab, SE-75185 Uppsala, Sweden

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 03期

关键词：

Cancer; allele-specific copy number analysis; whole-genome sequencing; aneuploidy; tumor heterogeneity; chromothripsis; SOMATIC MUTATION; CANCER;

D O I：

10.1186/gb-2013-14-3-r24

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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/).

引用

页数：10

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