Next-generation sequencing-based detection of germline L1-mediated transductions

Citation:

Tica J*, Lee E*, Untergasser A, Meiers S, Garfield DA, Gokcumen O, Furlong EEM, Park PJ, Stütz AM**, Korbel JO**. Next-generation sequencing-based detection of germline L1-mediated transductions. BMC Genomics 2016;17:342.

Date Published:

2016 05 10

Abstract:

BACKGROUND: While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for detecting polymorphic germline non-reference transductions in massively-parallel sequencing data has been lacking. RESULTS: Here we present the computational approach TIGER (Transduction Inference in GERmline genomes), enabling the discovery of non-reference L1-mediated transductions by combining L1 discovery with detection of unique insertion sequences and detailed characterization of insertion sites. We employed TIGER to characterize polymorphic transductions in fifteen genomes from non-human primate species (chimpanzee, orangutan and rhesus macaque), as well as in a human genome. We achieved high accuracy as confirmed by PCR and two single molecule DNA sequencing techniques, and uncovered differences in relative rates of transduction between primate species. CONCLUSIONS: By enabling detection of polymorphic transductions, TIGER makes this form of relevant structural variation amenable for population and personal genome analysis.

Last updated on 11/28/2017