Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection.

ABSTRACT: Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high-depth whole-genome sequencing data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population o

SUBMITTER: Yu Q 

PROVIDER: S-EPMC5603766 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature