{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T05:22:37Z","timestamp":1674883357865},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation : Chromosome rearrangement events are triggered by atypical breaking and rejoining of DNA molecules, which are observed in many cancer-related diseases. The detection of rearrangement is typically done by using short reads generated by next-generation sequencing (NGS) and combining the reads with knowledge of a reference genome. Because structural variations and genomes differ from one person to another, intermediate comparison via a reference genome may lead to loss of information.<\/jats:p>\n               <jats:p>Results : In this article, we propose a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements. This is done by directly comparing a set of NGS normal reads with another set that may be rearranged. Our method SlideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100\u00d7, it finds \u223c88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.<\/jats:p>\n               <jats:p>Availability and implementation : The source code of SlideSort-BPR can be freely downloaded from https:\/\/code.google.com\/p\/slidesort-bpr\/ .<\/jats:p>\n               <jats:p>Contact : ewijaya@ifrec.osaka-u.ac.jp or mhamada@waseda.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu360","type":"journal-article","created":{"date-parts":[[2014,5,30]],"date-time":"2014-05-30T02:31:57Z","timestamp":1401417117000},"page":"2559-2567","source":"Crossref","is-referenced-by-count":3,"title":["Reference-free prediction of rearrangement breakpoint reads"],"prefix":"10.1093","volume":"30","author":[{"given":"Edward","family":"Wijaya","sequence":"first","affiliation":[{"name":"1 Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, 3 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and 4 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo 169\u20138555, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kana","family":"Shimizu","sequence":"additional","affiliation":[{"name":"1 Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, 3 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and 4 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo 169\u20138555, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"1 Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, 3 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and 4 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo 169\u20138555, Japan"},{"name":"1 Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, 3 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and 4 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo 169\u20138555, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michiaki","family":"Hamada","sequence":"additional","affiliation":[{"name":"1 Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, 3 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and 4 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo 169\u20138555, Japan"},{"name":"1 Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, 2 Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, 3 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and 4 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N\u201306\u201310, 3\u20134\u20131, Okubo Shinjuku-ku, Tokyo 169\u20138555, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,5,29]]},"reference":[{"key":"2023012711554367100_btu360-B1","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/ng1215","article-title":"Chromosome aberrations in solid tumors","volume":"34","author":"Albertson","year":"2003","journal-title":"Nat. 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