{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:29:24Z","timestamp":1792794564213,"version":"4.5.0"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2022,12,5]],"date-time":"2022-12-05T00:00:00Z","timestamp":1670198400000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Academy of Medical Sciences Professorship","award":["AMSPR1\\1014"],"award-info":[{"award-number":["AMSPR1\\1014"]}],"id":[{"id":"https:\/\/ror.org\/00c489v88","id-type":"ROR","asserted-by":"crossref"}]},{"name":"UK Medical Research Council, Alzheimer\u2019s Society and Alzheimer\u2019s Research UK","id":[{"id":"https:\/\/ror.org\/02ymzm013","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Cardiff University School of Medicine Studentship","id":[{"id":"https:\/\/ror.org\/03kk7td41","id-type":"ROR","asserted-by":"crossref"}]},{"name":"MRC Centre","award":["MR\/L010305\/1"],"award-info":[{"award-number":["MR\/L010305\/1"]}]},{"DOI":"10.13039\/100005725","name":"CHDI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Welsh Clinical Academic Track Fellowship"},{"name":"MRC Clinical Research Training Fellowship","award":["MR\/P001629\/1"],"award-info":[{"award-number":["MR\/P001629\/1"]}]},{"name":"Patrick Berthoud Charitable Trust Fellowship","id":[{"id":"https:\/\/ror.org\/00nc7q809","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000368","name":"Brain Research Trust","doi-asserted-by":"publisher","award":["201617\u201306"],"award-info":[{"award-number":["201617\u201306"]}],"id":[{"id":"10.13039\/501100000368","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UKRI Future Leader Fellowship","award":["MR\/S031820\/1"],"award-info":[{"award-number":["MR\/S031820\/1"]}]},{"name":"Moorfields Eye Charity PhD studentship","id":[{"id":"https:\/\/ror.org\/017hm5p20","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and preclinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. Interrupted alleles are sometimes present within repeats and can alter disease manifestation. Determining repeat size mosaicism and identifying interruptions in targeted sequencing datasets remains a major challenge. This is in part because standard alignment tools are ill-suited for repetitive and unstable sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington\u2019s disease and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 blood-derived samples from Huntington\u2019s disease individuals and did not require prior knowledge of the flanking sequences. Furthermore, RD can be used to identify alleles with interruptions and provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and in the development of novel therapies.<\/jats:p>","DOI":"10.1093\/nargab\/lqac089","type":"journal-article","created":{"date-parts":[[2022,12,4]],"date-time":"2022-12-04T19:13:52Z","timestamp":1670181232000},"source":"Crossref","is-referenced-by-count":18,"title":["Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing"],"prefix":"10.1093","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5074-6618","authenticated-orcid":false,"given":"Alysha\u00a0S","family":"Taylor","sequence":"first","affiliation":[{"name":"UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building , Maindy Road, Cardiff , CF24 4HQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dinis","family":"Barros","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genomics, University of Lausanne, B\u00e2timent G\u00e9nopode , 1015 Lausanne , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6305-0844","authenticated-orcid":false,"given":"Nastassia","family":"Gobet","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genomics, University of Lausanne, B\u00e2timent G\u00e9nopode , 1015 Lausanne , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2472-4607","authenticated-orcid":false,"given":"Thierry","family":"Schuepbach","sequence":"additional","affiliation":[{"name":"Vital-IT Group, Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland"},{"name":"Newbiologix, Ch. De la corniche 6-8 , 1066 Epalinges , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6308-2136","authenticated-orcid":false,"given":"Branduff","family":"McAllister","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University , Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK"},{"name":"Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital , Boston , MA 02114, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorene","family":"Aeschbach","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genomics, University of Lausanne, B\u00e2timent G\u00e9nopode , 1015 Lausanne , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2112-7751","authenticated-orcid":false,"given":"Emma\u00a0L","family":"Randall","sequence":"additional","affiliation":[{"name":"UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building , Maindy Road, Cardiff , CF24 4HQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4910-5324","authenticated-orcid":false,"given":"Evgeniya","family":"Trofimenko","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genomics, University of Lausanne, B\u00e2timent G\u00e9nopode , 1015 Lausanne , Switzerland"},{"name":"Sorbonne Universit\u00e9, \u00c9cole normale sup\u00e9rieure, PSL University, CNRS, Laboratoire des biomol\u00e9cules , LBM, 75005 Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7629-0070","authenticated-orcid":false,"given":"Eleanor\u00a0R","family":"Heuchan","sequence":"additional","affiliation":[{"name":"UK Dementia Research Institute, Cardiff University, Hadyn Ellis Building , Maindy Road, Cardiff , CF24 4HQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paula","family":"Barszcz","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genomics, University of Lausanne, B\u00e2timent G\u00e9nopode , 1015 Lausanne , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7663-4080","authenticated-orcid":false,"given":"Marc","family":"Ciosi","sequence":"additional","affiliation":[{"name":"School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Davidson Building, University of Glasgow , Glasgow , G12 8QQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3091-0040","authenticated-orcid":false,"given":"Joanne","family":"Morgan","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University , Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8564-5198","authenticated-orcid":false,"given":"Nathaniel\u00a0J","family":"Hafford-Tear","sequence":"additional","affiliation":[{"name":"UCL Institute of Ophthalmology , 11-43 Bath Street, London , EC1V 9EL UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1816-6151","authenticated-orcid":false,"given":"Alice\u00a0E","family":"Davidson","sequence":"additional","affiliation":[{"name":"UCL Institute of Ophthalmology , 11-43 Bath Street, London , EC1V 9EL 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Genomics, Cardiff University , Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"REGISTRY\u00a0Investigators\u00a0of\u00a0the\u00a0European Huntington\u2019s\u00a0disease","family":"network","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3413-6841","authenticated-orcid":false,"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genomics, University of Lausanne, B\u00e2timent G\u00e9nopode , 1015 Lausanne , Switzerland"},{"name":"Health2030 Genome Center , Ch des Mines 14, 1202 Gen\u00e8ve , Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4953-7637","authenticated-orcid":false,"given":"Vincent","family":"Dion","sequence":"additional","affiliation":[{"name":"UK Dementia Research Institute, Cardiff University, Hadyn 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