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

BMC Genomics. 2015 Jul 8;16(1):508. doi: 10.1186/s12864-015-1700-4.

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 of optimization), cost-effective and highly accurate.

Conclusions: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • DNA Transposable Elements / genetics*
  • Genotype
  • Genotyping Techniques / methods
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Polymorphism, Genetic / genetics*
  • Sequence Analysis, DNA / methods

Substances

  • DNA Transposable Elements

Associated data

  • BioProject/PRJNA271692
  • SRA/SRP051735