{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,27]],"date-time":"2025-11-27T16:15:10Z","timestamp":1764260110455,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,8,26]],"date-time":"2020-08-26T00:00:00Z","timestamp":1598400000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["17\/CDA\/4737"],"award-info":[{"award-number":["17\/CDA\/4737"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Repeat expansions are an important class of genetic variation in neurological diseases. However, the identification of novel repeat expansions using conventional sequencing methods is a challenge due to their typical lengths relative to short sequence reads and difficulty in producing accurate and unique alignments for repetitive sequence. However, this latter property can be harnessed in paired-end sequencing data to infer the possible locations of repeat expansions and other structural variation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This article presents REscan, a command-line utility that infers repeat expansion loci from paired-end short read sequencing data by reporting the proportion of reads orientated towards a locus that do not have an adequately mapped mate. A high REscan statistic relative to a population of data suggests a repeat expansion locus for experimental follow-up. This approach is validated using genome sequence data for 259 cases of amyotrophic lateral sclerosis, of which 24 are positive for a large repeat expansion in C9orf72, showing that REscan statistics readily discriminate repeat expansion carriers from non-carriers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>C source code at https:\/\/github.com\/rlmcl\/rescan (GNU General Public Licence v3).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa753","type":"journal-article","created":{"date-parts":[[2020,8,19]],"date-time":"2020-08-19T11:45:25Z","timestamp":1597837525000},"page":"871-872","source":"Crossref","is-referenced-by-count":2,"title":["REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3915-2135","authenticated-orcid":false,"given":"Russell Lewis","family":"McLaughlin","sequence":"first","affiliation":[{"name":"Smurfit Institute of Genetics , Trinity College Dublin, Dublin D02 PN40, Ireland"}]}],"member":"286","published-online":{"date-parts":[[2020,8,26]]},"reference":[{"key":"2023051704120256400_btaa753-B1","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/S1474-4422(12)70014-5","article-title":"Cognitive and clinical characteristics of patients with amyotrophic lateral sclerosis carrying a C9orf72 repeat expansion: a population-based cohort study","volume":"11","author":"Byrne","year":"2012","journal-title":"Lancet Neurol"},{"key":"2023051704120256400_btaa753-B2","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s13059-018-1505-2","article-title":"STRetch: detecting and discovering pathogenic short tandem repeat expansions","volume":"19","author":"Dashnow","year":"2018","journal-title":"Genome Biol"},{"key":"2023051704120256400_btaa753-B3","first-page":"1895","article-title":"Detection of long repeat expansions from PCR-free whole-genome sequence data","volume":"27","author":"Dolzhenko","year":"2017","journal-title":"Am. J. Hum. Genet"},{"key":"2023051704120256400_btaa753-B4","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1093\/bioinformatics\/btt314","article-title":"Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms","volume":"29","author":"Raczy","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051704120256400_btaa753-B5","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1097\/WCO.0b013e32835a3efb","article-title":"How do C9ORF72 repeat expansions cause amyotrophic lateral sclerosis and frontotemporal dementia: can we learn from other noncoding repeat expansion disorders?","volume":"25","author":"van Blitterswijk","year":"2012","journal-title":"Curr. Opin. Neurol"},{"key":"2023051704120256400_btaa753-B6","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1038\/s41431-018-0177-4","article-title":"Project MinE: study design and pilot analyses of a large-scale whole-genome sequencing study in amyotrophic lateral sclerosis","volume":"26","author":"van Rheenen","year":"2018","journal-title":"Eur. J. Hum. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa753\/34691727\/btaa753.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/6\/871\/50357200\/btaa753.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/6\/871\/50357200\/btaa753.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T04:13:00Z","timestamp":1684296780000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/6\/871\/5897410"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,26]]},"references-count":6,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2021,5,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa753","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,3,15]]},"published":{"date-parts":[[2020,8,26]]}}}