SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing DataReport as inadecuate




SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data - Download this document for free, or read online. Document in PDF available to download.

Whole genome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. However, analysis of somatic copy-number changes from sequencing data is still challenging because of insufficient sequencing coverage, unknown tumor sample purity and subclonal heterogeneity. Here we describe a computational framework, named SomatiCA, which explicitly accounts for tumor purity and subclonality in the analysis of somatic copy-number profiles. Taking read depths RD and lesser allele frequencies LAF as input, SomatiCA will output 1 admixture rate for each tumor sample, 2 somatic allelic copy-number for each genomic segment, 3 fraction of tumor cells with subclonal change in each somatic copy number aberration SCNA, and 4 a list of substantial genomic aberration events including gain, loss and LOH. SomatiCA is available as a Bioconductor R package at http:-www.bioconductor.org-packages-2.13-bioc-html-SomatiCA.html.



Author: Mengjie Chen, Murat Gunel, Hongyu Zhao

Source: http://plos.srce.hr/



DOWNLOAD PDF




Related documents