Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.

ABSTRACT:

Motivation

Next-generation sequencing (NGS) has revolutionized the study of cancer genomes. However, the reads obtained from NGS of tumor samples often consist of a mixture of normal and tumor cells, which themselves can be of multiple clonal types. A prominent problem in the analysis of cancer genome sequencing data is deconvolving the mixture to identify the reads associated with tumor cells or a particular subclone of tumor cells. Solving the problem is, however, challenging because of the so-called 'identifiability problem', where different combinations of tumor purity and ploidy often explain the sequencing data equally well.

Results

We propose a new model to resolve the identifiability problem by integrating two types of sequencing information-somatic copy number alter

SUBMITTER: Li Y 

PROVIDER: S-EPMC4103592 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature