LINE-1 genotyping of human samples

Like other structural variants, transposable element insertions can be highly polymorphic across individuals of the same population. Despite their abundance in most genomes, their functional impact and evolutionary dynamics remain poorly understood. Recently, genome resequencing methods have yielded large catalogs of polymorphic insertions but these methods are impractical for many genotyping applications as they remain expensive and can have insufficient accuracy. We describe a large scale genotyping method for transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. It relies on high-throughput sequencing of multiplex, site-specific PCR amplification products. Sequencing reads are used to ensure specificity of the amplification products and to make robust, read count-based genotype calls. We used our approach to perform allelic genotyping of LINE-1 retrotransposon insertions in humans and showed that its accuracy is comparable to standard individual PCR assays visualized by gel electrophoresis. It does not require lengthy optimization rounds and it is cheaper than standard genotyping for medium scale experiments (e.g. 1000 genotype calls) and larger. High-throughput and accurate read count-based genotyping can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.