ArticleBioinformatics (Oxford, England)2019
ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 256 papers, 3 of them syntheses that pooled it.
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The trial behind it
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
256 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Genome-Wide Association Study of Corneal Dystrophy Uncovers Novel Risk Loci and Enables Improved Polygenic Prediction of Fuchs Endothelial Corneal Dystrophy.Investigative ophthalmology & visual science · 2026Pooled it
- Detection of repeat expansion variants using next generation sequencing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG).Genetics in medicine : official journal of the American College of Medical Genetics · 2026Guideline
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- Genome-wide analysis of common structural variants in Alzheimer's disease identifies a risk-associated regulatory CCG repeat in FAM193B.Nature neuroscience · 2026Article
- Juvenile Huntington Disease With Cerebellar-Predominant Atrophy Identified by Genome Sequencing.Annals of clinical and translational neurology · 2026Article
- Characterising the motif composition and allele length distribution of ZFHX3 GGC repeat expansions in amyotrophic lateral sclerosis.Journal of human genetics · 2026Article
- Genome-wide tandem repeat expansions modify schizophrenia risk in the presence of a 22q11.2 deletion.Molecular psychiatry · 2026Article
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Optimized Cas9-Enriched Nanopore Sequencing and Analysis Workflow for Clinical Diagnosis of Repeat Expansion Disorders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Childhood-onset ataxia with dystonia: expanding the spectrum of VWA3B-related disorders.Journal of human genetics · 2026Article
- Multiomic approaches identify a rare CCG repeat expansion in BCLAF3 in neurodevelopmental disorders.Genome medicine · 2026Article
- Dissecting the relationship between haplotypes around ATXN2 CAG repeats and the number of CAA interruptions by long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
- Tandem repeat polymorphisms are associated with brain structure: results of two large population-based studies.Genome medicine · 2026Article
- Characterisation of the SMN1/2 locus using a highly specific variant caller on whole-genome sequence data from 500,000 individuals.European journal of human genetics : EJHG · 2026Article
- Repeat expansions in Parkinson's disease and parkinsonism across ancestries: insights from a global genetic cohort.medRxiv : the preprint server for health sciences · 2026Article
- Short-read genome sequencing at population scale: diagnostic insights from 2317 patients.European journal of human genetics : EJHG · 2026Article
- Tandem repeats in human brain evolution and disease susceptibility.Molecules and cells · 2026Review
- Large-scale analysis of FMR1 CGG repeat length and risk of premature ovarian insufficiency in over 92 000 women.Human reproduction (Oxford, England) · 2026Article
- Population-scale genomic medicine with the Hong Kong Genome Project.Nature medicine · 2026Article
196 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
Abstract
summaryWe describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION: ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.