{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,24]],"date-time":"2024-08-24T07:07:50Z","timestamp":1724483270158},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Dispersed duplications (DDs) such as transposon element insertions and copy number variations are ubiquitous in the human genome. They have attracted the interest of biologists as well as medical researchers due to their role in both evolution and disease. The efforts of discovering DDs in high-throughput sequencing data are currently dominated by database-oriented approaches that require pre-existing knowledge of the DD elements to be detected.<\/jats:p>\n               <jats:p>Results: We present dd_detection, a database-free approach to finding DD events in high-throughput sequencing data. dd_detection is able to detect DDs purely from paired-end read alignments. We show in a comparative study that this method is able to compete with database-oriented approaches in recovering validated transposon insertion events. We also experimentally validate the predictions of dd_detection on a human DNA sample, showing that it can find not only duplicated elements present in common databases but also DDs of novel type.<\/jats:p>\n               <jats:p>Availability and implementation: The software presented in this article is open source and available from https:\/\/bitbucket.org\/mkroon\/dd_detection<\/jats:p>\n               <jats:p>Contact: \u00a0kye@genome.wustl.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv621","type":"journal-article","created":{"date-parts":[[2015,10,28]],"date-time":"2015-10-28T02:38:45Z","timestamp":1445999925000},"page":"505-510","source":"Crossref","is-referenced-by-count":14,"title":["Detecting dispersed duplications in high-throughput sequencing data using a database-free approach"],"prefix":"10.1093","volume":"32","author":[{"given":"M.","family":"Kroon","sequence":"first","affiliation":[{"name":"1 Department of Molecular Epidemiology, Leiden University Medical Center, Leiden,"}]},{"given":"E.W.","family":"Lameijer","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Epidemiology, Leiden University Medical Center, Leiden,"}]},{"given":"N.","family":"Lakenberg","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Epidemiology, Leiden University Medical Center, Leiden,"}]},{"given":"J.Y.","family":"Hehir-Kwa","sequence":"additional","affiliation":[{"name":"2 Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Center, Nijmegen,"},{"name":"3 Donders Centre for Neuroscience, Nijmegen, The Netherlands and"}]},{"given":"D.T.","family":"Thung","sequence":"additional","affiliation":[{"name":"2 Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Center, Nijmegen,"}]},{"given":"P.E.","family":"Slagboom","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Epidemiology, Leiden University Medical Center, Leiden,"}]},{"given":"J.N.","family":"Kok","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Epidemiology, Leiden University Medical Center, Leiden,"}]},{"given":"K.","family":"Ye","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Epidemiology, Leiden University Medical Center, Leiden,"},{"name":"4 The Genome Institute, Washington University, St Louis, MO 63108, USA"}]}],"member":"286","published-online":{"date-parts":[[2015,10,27]]},"reference":[{"key":"2023020110315982500_btv621-B1","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res."},{"key":"2023020110315982500_btv621-B2","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation","volume":"6","author":"Chen","year":"2009","journal-title":"Nat. Methods"},{"key":"2023020110315982500_btv621-B3","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/ng.768","article-title":"Discovery and genotyping of genome structural polymorphism by sequencing on a population scale","volume":"43","author":"Handsaker","year":"2011","journal-title":"Nat. Genet."},{"key":"2023020110315982500_btv621-B4","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1101\/gr.115956.110","article-title":"Alu repeat discovery and characterization within human genomes","volume":"21","author":"Hormozdiari","year":"2011","journal-title":"Genome Res."},{"key":"2023020110315982500_btv621-B5","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1159\/000084979","article-title":"Repbase update, a database of eukaryotic repetitive elements","volume":"110","author":"Jurka","year":"2005","journal-title":"Cytogenet. Genome Res."},{"key":"2023020110315982500_btv621-B6","doi-asserted-by":"crossref","DOI":"10.1038\/332164a0","article-title":"Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man","volume":"332","author":"Kazazian","year":"1988","journal-title":"Nature"},{"key":"2023020110315982500_btv621-B7","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1093\/bioinformatics\/bts697","article-title":"RetroSeq: transposable element discovery from next-generation sequencing data","volume":"29","author":"Keane","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020110315982500_btv621-B8","first-page":"656","article-title":"BLAT-the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023020110315982500_btv621-B9","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2023020110315982500_btv621-B10","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023020110315982500_btv621-B11","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1126\/science.1222077","article-title":"Landscape of somatic retrotransposition in human cancers","volume":"337","author":"Lee","year":"2012","journal-title":"Science"},{"key":"2023020110315982500_btv621-B12","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020110315982500_btv621-B13","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/ng0696-245","article-title":"Mutation analysis in the BRCA2 gene in primary breast cancers","volume":"13","author":"Miki","year":"1996","journal-title":"Nature Genet."},{"key":"2023020110315982500_btv621-B14","first-page":"215","article-title":"PrefixSpan: mining sequential patterns efficiently by prefix-projected pattern growth","author":"Pei","year":"2001"},{"key":"2023020110315982500_btv621-B15","doi-asserted-by":"crossref","first-page":"395","DOI":"10.3390\/biology1020395","article-title":"TE-Locate: a tool to locate and group transposable element occurrences using paired-end next-generation sequencing data","volume":"1","author":"Platzer","year":"2012","journal-title":"Biology"},{"key":"2023020110315982500_btv621-B16","author":"Smit","year":"1996"},{"key":"2023020110315982500_btv621-B17","doi-asserted-by":"crossref","first-page":"e1002236","DOI":"10.1371\/journal.pgen.1002236","article-title":"A comprehensive map of mobile element insertion polymorphisms in humans","volume":"7","author":"Stewart","year":"2011","journal-title":"PLoS Genet."},{"key":"2023020110315982500_btv621-B18","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1\u2009092 human genomes","volume":"491","author":"The 1000 Genomes Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2023020110315982500_btv621-B19","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1186\/s13059-014-0488-x","article-title":"Mobster: accurate detection of mobile element insertions in next generation sequencing data","volume":"15","author":"Thung","year":"2014","journal-title":"Genome Biol."},{"key":"2023020110315982500_btv621-B20","doi-asserted-by":"crossref","first-page":"3484","DOI":"10.1093\/bioinformatics\/btu431","article-title":"Gustaf: detecting and correctly classifying SVs in the NGS twilight zone","volume":"30","author":"Trappe","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020110315982500_btv621-B21","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1002\/humu.20307","article-title":"dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans","volume":"27","author":"Wang","year":"2006","journal-title":"Hum. Mutat."},{"key":"2023020110315982500_btv621-B22","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1186\/1471-2164-15-795","article-title":"Tangram: a comprehensive toolbox for mobile element insertion detection","volume":"15","author":"Wu","year":"2014","journal-title":"BMC Genomics"},{"key":"2023020110315982500_btv621-B23","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1093\/bioinformatics\/btl665","article-title":"An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences","volume":"23","author":"Ye","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020110315982500_btv621-B24","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","article-title":"Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads","volume":"25","author":"Ye","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020110315982500_btv621-B25","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1017\/thg.2013.73","article-title":"Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs","volume":"16","author":"Ye","year":"2013","journal-title":"Twin Res. Hum. Genet."},{"key":"2023020110315982500_btv621-B26","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/bioinformatics\/btr712","article-title":"PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data","volume":"28","author":"Zhang","year":"2012","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/4\/505\/49017449\/bioinformatics_32_4_505.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/4\/505\/49017449\/bioinformatics_32_4_505.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T21:53:33Z","timestamp":1675288413000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/4\/505\/1744181"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,10,27]]},"references-count":26,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2016,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv621","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,2,15]]},"published":{"date-parts":[[2015,10,27]]}}}