CoNVEX: copy number variation estimation in exome sequencing data using HMM.

ABSTRACT:

Background

One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequencing (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic variations. However, finding CNV in Cancer samples using WES data has not been fully explored.

Results

We present a new method, called CoNVEX, to estimate copy number variation in whole exome sequencing data. It uses ratio of tumour and matched normal average read depths at each exonic region, to predict the copy gain or loss. The useful signal produced by WES data will be hindered by the intrinsic noise present in the data itself. This limits its capacity to be used as a highly reliable CNV detection source. Here, we propose a method that consists of discrete

SUBMITTER: Amarasinghe KC 

PROVIDER: S-EPMC3549847 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature