Next-generation sequencing-based detection of germline L1-mediated transductions
Garfield, David A.
Furlong, Eileen E.M.
Stütz, Adrian M.
Korbel, Jan O.
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CitationTica, 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.
AbstractBackground: 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.
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