title: Next-generation sequencing-based detection of germline L1-mediated transductions.
abstract: 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.
  
  
  
  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.
  
  
  
  By enabling detection of polymorphic transductions, TIGER makes this form of relevant structural variation amenable for population and personal genome analysis.
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
authors.forename: Jelena
authors.initials: J
authors.lastname: Tica
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.|Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: Eunjung
authors.initials: E
authors.lastname: Lee
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.|Center of Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 282, Heidelberg, 69120, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Untergasser
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
authors.forename: Sascha
authors.initials: S
authors.lastname: Meiers
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
authors.forename: David A
authors.initials: DA
authors.lastname: Garfield
authors.affiliation: Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, 14260-1300, USA.
authors.forename: Omer
authors.initials: O
authors.lastname: Gokcumen
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
authors.forename: Eileen E M
authors.initials: EE
authors.lastname: Furlong
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.|Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany. adrian.stuetz@embl.de.
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Stütz
authors.affiliation: European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany. jan.korbel@embl.de.|European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK. jan.korbel@embl.de.
authors.forename: Jan O
authors.initials: JO
authors.lastname: Korbel
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016678:Genome; D005854:Germ Cells / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D008253:Macaca mulatta / Q000235:genetics; D002679:Pan troglodytes / Q000235:genetics; D014161:Transduction, Genetic
keywords: Bioinformatics; Genetics; Genome; L1; NGS; Primates; Retrotransposon; Single-molecule sequencing; Transductions