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

Xun Chen; Guillaume Bourque; Clément Goubert

doi:10.1007/978-1-0716-2883-6_4

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

Methods Mol Biol. 2023:2607:63-83. doi: 10.1007/978-1-0716-2883-6_4.

Authors

Xun Chen¹, Guillaume Bourque^{2

3

4

5}, Clément Goubert^{6

7

8}

Affiliations

¹ Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan. xunchen85@gmail.com.
² Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
³ Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
⁴ McGill Genome Centre, Montreal, QC, Canada.
⁵ Human Genetics, McGill University, Montreal, QC, Canada.
⁶ Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada. goubert.clement@gmail.com.
⁷ McGill Genome Centre, Montreal, QC, Canada. goubert.clement@gmail.com.
⁸ Human Genetics, McGill University, Montreal, QC, Canada. goubert.clement@gmail.com.

PMID: 36449158
DOI: 10.1007/978-1-0716-2883-6_4

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.

Keywords: High-throughput sequencing; Polymorphism; Reference-based genotyping; Transposable element.

MeSH terms

Computational Biology*
DNA Transposable Elements* / genetics
Genome, Human
Genotype
Humans
Polymorphism, Genetic

Substances

DNA Transposable Elements