RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing.

ABSTRACT: With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we compared the observed coverage with the expected normal coverage. Thresholds for determ

SUBMITTER: Chang LC 

PROVIDER: S-EPMC4849420 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature