ArticleNucleic acids research2020
TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- Investigating mobile element variations by statistical genetics.Human genome variation · 2024Review
- Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Characterizing mobile element insertions in 5675 genomes.Nucleic acids research · 2022Article
- The Absence of Retroelement Activity Is Characteristic for Childhood Acute Leukemias and Adult Acute Lymphoblastic Leukemia.International journal of molecular sciences · 2022Article
- Single-Strand Annealing in Cancer.International journal of molecular sciences · 2021Review
- SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events.Mobile DNA · 2020Article
- Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data.Current protocols in human genetics · 2020Review
- The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity.Genome biology and evolution · 2020Article
- Contribution of unfixed transposable element insertions to human regulatory variation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data.Mobile DNA · 2020Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alus are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alus and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline - TypeTE - which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a high-quality set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.