ArticleGenome research2017
Detection of long repeat expansions from PCR-free whole-genome sequence data.
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Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 259 papers, 3 of them syntheses that pooled it.
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259citing papers in PubMed, 3 pooled it
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259 citing papers in PubMed, 3 syntheses or guidelines pooled it, 425 citations in OpenAlex.
- 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
- Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology.Nature genetics · 2021Pooled it
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- GWAS on short tandem repeats identifies genetic mechanisms in Alzheimer's disease.Nature communications · 2026Article
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- Computational Short Tandem Repeat Genotyping Reveals Clinically Relevant Expansions in a Large Turkish Neurodegeneration Disease Cohort.International journal of molecular sciences · 2026Article
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- Unraveling the genetic architecture of non-Huntington chorea: a biobank-scale study of rare variants and repeat expansions.NPJ genomic medicine · 2026Article
- Genetic analysis of neurodegenerative diseases.The Journal of clinical investigation · 2026Review
- Clinical and genetic diagnostic challenges in presumed hereditary ataxia.Journal of neurology · 2026Article
- Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit.Genome research · 2026Article
- Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications.Genome research · 2026Article
199 more citing papers are in PubMed but not listed here.
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Authors and funding
45 authors at 13 institutions in 4 countries.
Egor DolzhenkoIllumina Incorporated, San Diego, California 92122, USA.
Joke J F A van VugtDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
Richard J ShawIllumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom.
Mitchell A BekritskyIllumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom.
Marka van BlitterswijkDepartment of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224, USA.
Giuseppe NarzisiNew York Genome Center, New York, New York 10013, USA.
Subramanian S AjayIllumina Incorporated, San Diego, California 92122, USA.
Vani RajanIllumina Incorporated, San Diego, California 92122, USA.
Bryan R LajoieIllumina Incorporated, San Diego, California 92122, USA.
Nathan H JohnsonIllumina Incorporated, San Diego, California 92122, USA.
Zoya KingsburyIllumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom.
Sean J HumphrayIllumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom.
Raymond D SchellevisDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
William J BrandsDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
Matt BakerDepartment of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224, USA.
Rosa RademakersDepartment of Neuroscience, Mayo Clinic, Jacksonville, Florida 32224, USA.
Maarten KooymanSURFsara, 1098 XG Amsterdam, The Netherlands.
Gijs H P TazelaarDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
Michael A van EsDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
Russell McLaughlinAcademic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Republic of Ireland.
William SprovieroDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Aleksey ShatunovDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Ashley JonesDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Ahmad Al KhleifatDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Alan PittmanDepartment of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3BG, United Kingdom.
Sarah MorganDepartment of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3BG, United Kingdom.
Orla HardimanAcademic Unit of Neurology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin 2, Republic of Ireland.
Ammar Al-ChalabiDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Chris ShawDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Bradley SmithDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Edmund J NeoDepartment of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RX, United Kingdom.
Karen MorrisonUniversity of Southampton, Southampton SO17 1BJ, United Kingdom.
Pamela J ShawSheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom.
Catherine ReevesNew York Genome Center, New York, New York 10013, USA.
Lara WinterkornNew York Genome Center, New York, New York 10013, USA.
Nancy S WexlerColumbia University, New York, New York 10032, USA.
US–Venezuela Collaborative Research Group
David E HousmanDepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Christopher W NgDepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Alina L LiDepartment of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Ryan J TaftIllumina Incorporated, San Diego, California 92122, USA.
Leonard H van den BergDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
David R BentleyIllumina Limited, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, CB10 1XL, United Kingdom.
Jan H VeldinkDepartment of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands.
Michael A EberleIllumina Incorporated, San Diego, California 92122, USA.
King's College London · GBIllumina (United States) · USUtrecht University · NLIllumina (United Kingdom) · GBJacksonville College · USMassachusetts Institute of Technology · USNew York Genome Center · USTrinity College Dublin · IEUniversity College London · GBHereditary Disease Foundation · USSURFsara (Netherlands) · NLUniversity of Sheffield · GBUniversity of Southampton · GB
Funding
Project 3: Neuropathology of the multi-proteinopathy of c9FTD/ALS.P01NS084974 · NINDS · MAYO CLINIC JACKSONVILLE · PI PETRUCELLI, LEONARD · 2014 to 2024
$17.6MGenetic Discovery and Pathobiology of Frontotemporal Lobar Degeneration and Related TDP-43 ProteinopathiesR35NS097261 · NINDS · MAYO CLINIC JACKSONVILLE · PI RADEMAKERS, ROSA · 2017 to 2019
$2.9MGGGGCC hexanucleotide repeat expansions in neurodegenerative diseaseR01NS080882 · NINDS · MAYO CLINIC JACKSONVILLE · PI RADEMAKERS, ROSA · 2012 to 2016
$1.6MMedical Research Council ES/L008238/1Medical Research Council MR/L501529/1Motor Neurone Disease Association ALCHALABI-DOBSON/APR14/829-791Motor Neurone Disease Association JONES/OCT15/958-799Motor Neurone Disease Association MCLAUGHLIN/OCT15/957-799Motor Neurone Disease Association SMITH/APR16/847-791MRF_ MRF-060-0003-RG-SMITHNINDS NIH HHS P01 NS084974NINDS NIH HHS R01 NS080882NINDS NIH HHS R35 NS097261Wellcome Trust
Abstract
Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence of the
Indexed as
DNA Repeat ExpansionAlgorithmsAmyotrophic Lateral SclerosisC9orf72 ProteinDatabases, GeneticHumansPrecision MedicineSensitivity and SpecificitySoftwareWhole Genome SequencingC9orf72 ProteinC9orf72 protein, human
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