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BMC Genomics. 2016 May 10;17:342. doi: 10.1186/s12864-016-2670-x.

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

Author information

1
European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
2
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
3
Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA.
4
Center of Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 282, Heidelberg, 69120, Germany.
5
Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, 14260-1300, USA.
6
European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany. adrian.stuetz@embl.de.
7
European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany. jan.korbel@embl.de.
8
European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK. jan.korbel@embl.de.

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.

KEYWORDS:

Bioinformatics; Genetics; Genome; L1; NGS; Primates; Retrotransposon; Single-molecule sequencing; Transductions

PMID:
27161561
PMCID:
PMC4862182
DOI:
10.1186/s12864-016-2670-x
[Indexed for MEDLINE]
Free PMC Article

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