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Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments

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Transposable Elements

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2607))

Abstract

Transposable element (TE) insertions are a major source of structural variation in the human genome. Due to the repetitive nature and biological importance of TEs, many bioinformatic tools have been developed to identify and genotype TE insertion polymorphisms using high-throughput short-reads. In this chapter, we outline recently developed methods to characterize TE insertion polymorphisms in human populations. We also provide detailed protocols to tackle this question primarily using three software: MELT2, ERVcaller, and TypeREF.

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Author information

Authors and Affiliations

  1. Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan

    Xun Chen & Guillaume Bourque

  2. Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada

    Guillaume Bourque & Clément Goubert

  3. McGill Genome Centre, Montreal, QC, Canada

    Guillaume Bourque & Clément Goubert

  4. Human Genetics, McGill University, Montreal, QC, Canada

    Guillaume Bourque & Clément Goubert

Authors
  1. Xun Chen
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  2. Guillaume Bourque
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  3. Clément Goubert
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Editor information

Editors and Affiliations

  1. Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK

    Miguel R. Branco

  2. School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK

    Alexandre de Mendoza Soler

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Chen, X., Bourque, G., Goubert, C. (2023). Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2883-6_4

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

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