Determining multiallelic complex copy number and sequence variation from high coverage exome sequencing data.

ABSTRACT:

Background

Copy number variation (CNV) is a major component of genomic variation, yet methods to accurately type genomic CNV lag behind methods that type single nucleotide variation. High-throughput sequencing can contribute to these methods by using sequence read depth, which takes the number of reads that map to a given part of the reference genome as a proxy for copy number of that region, and compares across samples. Furthermore, high-throughput sequencing also provides information on the sequence differences between copies within and between individuals.

Methods

In this study we use high-coverage phase 3 exome sequences of the 1000 Genomes project to infer diploid copy number of the beta-defensin genomic region, a well-studied CNV that carries several beta-defensin gene

SUBMITTER: Forni D 

PROVIDER: S-EPMC4630827 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature