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Mob DNA. 2019 Mar 8;10:8. doi: 10.1186/s13100-019-0148-5. eCollection 2019.

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.

Author information

1
1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.
2
2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.
3
3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.
4
4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA.
5
5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.
6
Departamento de Bioquímica, Instituto de Química, Universidade de São Paul, São Paulo, Brazil.
7
7Genome Technology Center, Division of Advanced Research Technologies, NYU Langone Health, New York, NY USA.

Abstract

Background:

Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA.

Results:

Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient's constitutional make-up.

Conclusions:

TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes.

KEYWORDS:

LINE-1; Next generation sequencing; Targeted PCR

Conflict of interest statement

Not applicable.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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