Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

ABSTRACT:

Background

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed.

Results

We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds

SUBMITTER: Kuhn A 

PROVIDER: S-EPMC4494700 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature