ArticleNucleic acids research2015
Discovery and characterization of Alu repeat sequences via precise local read assembly.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 35 citations in OpenAlex.
- Reflections on the Human Genome Diversity Project: a conversation with Marcus W. Feldman, Henry T. Greely, and Mary-Claire King.Genetics · 2026Article
- Review
- Telomere Position Effect-Over Long Distances Acts as a Genome-Wide Epigenetic Regulator Through a Common Alu Element.Aging cell · 2025Article
- Sequence-Selective Recognition of the d(GGCGCC)ACS omega · 2024Article
- Genome graphs detect human polymorphisms in active epigenomic state during influenza infection.Cell genomics · 2023Article
- Retrotransposon insertions associated with risk of neurologic and psychiatric diseases.EMBO reports · 2023Article
- 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
- Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder.Mobile DNA · 2021Article
- A single mutation in the ACTR8 gene associated with lineage-specific expression in primates.BMC evolutionary biology · 2020Article
- TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.Nucleic acids research · 2020Article
- LINE-1-Mediated AluYa5 Insertion Underlying Complete Autosomal Recessive IFN-γR1 Deficiency.Journal of clinical immunology · 2019Article
- Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids.Retrovirology · 2019Article
- AluMine: alignment-free method for the discovery of polymorphic Alu element insertions.Mobile DNA · 2019Article
- Spliced integrated retrotransposed element (SpIRE) formation in the human genome.PLoS biology · 2018Article
- Is mitochondrial DNA quantitation in blastocyst trophectoderm cells predictive of developmental competence and outcome in clinical IVF?Journal of assisted reproduction and genetics · 2017Review
- Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease.Ophthalmology · 2017Article
- Age-Associated ALU Element Instability in White Blood Cells Is Linked to Lower Survival in Elderly Adults: A Preliminary Cohort Study.PloS one · 2017Article
- Discovery of rare, diagnosticMobile DNA · 2017Article
- Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Alu insertions have contributed to >11% of the human genome and ∼30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project (HGDP) panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1010 fully assembled insertions, obtaining >99% agreement with genotypes obtained by PCR. In our assembled sequences, we find evidence of premature insertion mechanisms and observe 5' truncation in 16% of AluYa5 and AluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5' truncations. Additionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotransposition mechanisms.
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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.