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

## TL;DR

This paper introduces a cost-effective and accurate method for genotyping transposable elements and structural variants using read count-based analysis of PCR products.

## Contribution

A novel high-throughput genotyping method for transposable elements and structural variants using next-generation sequencing and read counts.

## Key findings

- The method is flexible, efficient, and does not require rounds of optimization.
- It is cost-effective and highly accurate for genotyping structural variants.
- Applicable to genotyping in animal, plant, and human populations.

## Abstract

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.

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 of optimization), cost-effective and highly accurate.

This method 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.

The online version of this article (doi:10.1186/s12864-015-1700-4) contains supplementary material, which is available to authorized users.