RT Journal Article
SR Electronic
T1 TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 791665
DO 10.1101/791665
A1 Clement Goubert
A1 Jainy Thomas
A1 Lindsay M. Payer
A1 Jeffrey M. Kidd
A1 Julie Feusier
A1 W. Scott Watkins
A1 Kathleen H. Burns
A1 Lynn B. Jorde
A1 Cedric Feschotte
YR 2019
UL http://biorxiv.org/content/early/2019/10/03/791665.abstract
AB 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 Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu 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 ‘gold standard’ 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.