TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Clément Goubert, Jainy Thomas, Lindsay M. Payer, Jeffrey M. Kidd, Julie Feusier, W. Scott Watkins, Kathleen H. Burns, Lynn B. Jorde, Cédric Feschotte

Research output: Contribution to journalArticle

Abstract

Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alus are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alus and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline - TypeTE - which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a high-quality set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.

Original languageEnglish (US)
Pages (from-to)e36
JournalNucleic acids research
Volume48
Issue number6
DOIs
StatePublished - Apr 6 2020

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data'. Together they form a unique fingerprint.

  • Cite this

    Goubert, C., Thomas, J., Payer, L. M., Kidd, J. M., Feusier, J., Watkins, W. S., Burns, K. H., Jorde, L. B., & Feschotte, C. (2020). TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic acids research, 48(6), e36. https://doi.org/10.1093/nar/gkaa074