PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing.

ABSTRACT:

Background

Copy number variations (CNVs) represent an important type of genetic variation that deeply impact phenotypic polymorphisms and human diseases. The advent of high-throughput sequencing technologies provides an opportunity to revolutionize the discovery of CNVs and to explore their relationship with diseases. However, most of the existing methods depend on sequencing depth and show instability with low sequence coverage. In this study, using low coverage whole-genome sequencing (LCS) we have developed an effective population-scale CNV calling (PSCC) method.

Methodology/principal findings

In our novel method, two-step correction was used to remove biases caused by local GC content and complex genomic characteristics. We chose a binary segmentation method to locate CN

SUBMITTER: Li X 

PROVIDER: S-EPMC3897425 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature