{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:26:12Z","timestamp":1790778372122,"version":"4.1.0"},"reference-count":35,"publisher":"Cold Spring Harbor Laboratory","issue":"11","funder":[{"name":"SURF Cooperative"},{"name":"NIH\/NINDS","award":["P01 NS084974"],"award-info":[{"award-number":["P01 NS084974"]}]},{"name":"NIH\/NINDS","award":["R01 NS080882"],"award-info":[{"award-number":["R01 NS080882"]}]},{"name":"Thierry Latran Foundation"},{"DOI":"10.13039\/501100001826","name":"Netherlands Organization for Health Research and Development","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001826","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100014076","name":"ALS Foundation Netherlands","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100014076","id-type":"DOI","asserted-by":"crossref"}]},{"name":"MND Association (UK)"},{"DOI":"10.13039\/100000888","name":"W.M. 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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\n                    <jats:italic>C9orf72<\/jats:italic>\n                    repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212\/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786\/2789, 95% CI [0.997, 1.00]) of the wild-type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associated with fragile X syndrome, Friedreich's ataxia, and Huntington's disease, and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.\n                  <\/jats:p>","DOI":"10.1101\/gr.225672.117","type":"journal-article","created":{"date-parts":[[2017,9,8]],"date-time":"2017-09-08T20:30:23Z","timestamp":1504902623000},"page":"1895-1903","source":"Crossref","is-referenced-by-count":386,"title":["Detection of long repeat expansions from PCR-free whole-genome sequence data"],"prefix":"10.1101","volume":"27","author":[{"given":"Egor","family":"Dolzhenko","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joke J.F.A.","family":"van Vugt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard J.","family":"Shaw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitchell 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