Tica, JelenaLee, EunjungUntergasser, AndreasMeiers, SaschaGarfield, David A.Gokcumen, OmerFurlong, Eileen E.M.Park, PeterStütz, Adrian M.Korbel, Jan O.2016-06-142016Tica, Jelena, Eunjung Lee, Andreas Untergasser, Sascha Meiers, David A. Garfield, Omer Gokcumen, Eileen E.M. Furlong, Peter J. Park, Adrian M. Stütz, and Jan O. Korbel. 2016. “Next-generation sequencing-based detection of germline L1-mediated transductions.” BMC Genomics 17 (1): 342. doi:10.1186/s12864-016-2670-x. http://dx.doi.org/10.1186/s12864-016-2670-x.1471-2164http://nrs.harvard.edu/urn-3:HUL.InstRepos:27320352Background: 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2670-x) contains supplementary material, which is available to authorized users.en-USRetrotransposonL1TransductionsNGSBioinformaticsGenomeGeneticsPrimatesSingle-molecule sequencingNext-generation sequencing-based detection of germline L1-mediated transductionsJournal Article2016-06-1410.1186/s12864-016-2670-x