{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T07:08:25Z","timestamp":1778828905930,"version":"3.51.4"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1059,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2\u20136 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads.<\/jats:p>\n               <jats:p>Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRTTM sequencing (Pacific Biosciences), determined 2.3\u20133.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads.<\/jats:p>\n               <jats:p>Availability and implementation: Our TRhist software is available at http:\/\/trhist.gi.k.u-tokyo.ac.jp\/.<\/jats:p>\n               <jats:p>Contact: \u00a0moris@cb.k.u-tokyo.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt647","type":"journal-article","created":{"date-parts":[[2013,11,10]],"date-time":"2013-11-10T01:09:20Z","timestamp":1384045760000},"page":"815-822","source":"Crossref","is-referenced-by-count":61,"title":["Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing"],"prefix":"10.1093","volume":"30","author":[{"given":"Koichiro","family":"Doi","sequence":"first","affiliation":[{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, 2Department of Information and Communication Engineering, Faculty of Engineering and 3Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taku","family":"Monjo","sequence":"additional","affiliation":[{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, 2Department of Information and Communication Engineering, Faculty of Engineering and 3Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan"},{"name":"1 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, 2Department of Information and Communication Engineering, Faculty of Engineering and 3Department of Neurology, Graduate School of Medicine, The University of Tokyo, 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