{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T08:52:34Z","timestamp":1775638354227,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Recent years have witnessed an increase in research activity for the detection of structural variants (SVs) and their association to human disease. The advent of next-generation sequencing technologies make it possible to extend the scope of structural variation studies to a point previously unimaginable as exemplified by the 1000 Genomes Project. Although various computational methods have been described for the detection of SVs, no such algorithm is yet fully capable of discovering transposon insertions, a very important class of SVs to the study of human evolution and disease. In this article, we provide a complete and novel formulation to discover both loci and classes of transposons inserted into genomes sequenced with high-throughput sequencing technologies. In addition, we also present \u2018conflict resolution\u2019 improvements to our earlier combinatorial SV detection algorithm (VariationHunter) by taking the diploid nature of the human genome into consideration. We test our algorithms with simulated data from the Venter genome (HuRef) and are able to discover &amp;gt;85% of transposon insertion events with precision of &amp;gt;90%. We also demonstrate that our conflict resolution algorithm (denoted as VariationHunter-CR) outperforms current state of the art (such as original VariationHunter, BreakDancer and MoDIL) algorithms when tested on the genome of the Yoruba African individual (NA18507).<\/jats:p>\n               <jats:p>Availability: The implementation of algorithm is available at http:\/\/compbio.cs.sfu.ca\/strvar.htm.<\/jats:p>\n               <jats:p>Contact: \u00a0eee@gs.washington.edu; cenk@cs.sfu.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq216","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i350-i357","source":"Crossref","is-referenced-by-count":180,"title":["Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery"],"prefix":"10.1093","volume":"26","author":[{"given":"Fereydoun","family":"Hormozdiari","sequence":"first","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Iman","family":"Hajirasouliha","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phuong","family":"Dao","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faraz","family":"Hach","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deniz","family":"Yorukoglu","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"},{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Evan E.","family":"Eichler","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"},{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S. Cenk","family":"Sahinalp","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 2 Department of Genome Sciences, University of Washington and 3 Howard Hughes Medical Institute, Seattle, WA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"key":"2023012508073383400_B1","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/ng.437","article-title":"Personalized copy number and segmental duplication maps using next-generation sequencing:","volume":"41","author":"Alkan","year":"2009","journal-title":"Nat. Genet."},{"key":"2023012508073383400_B2","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1086\/378594","article-title":"An Alu transposition model for the origin and expansion of human segmental duplications","volume":"73","author":"Bailey","year":"2003","journal-title":"Am. J. Hum. Genet."},{"key":"2023012508073383400_B3","doi-asserted-by":"crossref","first-page":"e1000051","DOI":"10.1371\/journal.pcbi.1000051","article-title":"Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer","volume":"4","author":"Bashir","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2023012508073383400_B4","doi-asserted-by":"crossref","first-page":"e1000403","DOI":"10.1371\/journal.pgen.1000403","article-title":"Death and resurrection of the human IRGM gene","volume":"5","author":"Bekpen","year":"2009","journal-title":"PLoS Genet."},{"key":"2023012508073383400_B5","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/nature07517","article-title":"Accurate whole human genome sequencing using reversible terminator chemistry","volume":"456","author":"Bentley","year":"2008","journal-title":"Nature"},{"key":"2023012508073383400_B6","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":"2023012508073383400_B7","doi-asserted-by":"crossref","first-page":"e1000432","DOI":"10.1371\/journal.pcbi.1000432","article-title":"Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants","volume":"5","author":"Du","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012508073383400_B8","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","article-title":"Base-calling of automated sequencer traces using phred. II. error probabilities","volume":"8","author":"Ewing","year":"1998","journal-title":"Genome Res."},{"key":"2023012508073383400_B9","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrg1767","article-title":"Structural variation in the human genome","volume":"7","author":"Feuk","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"2023012508073383400_B10","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1002\/net.3230120410","article-title":"Efficient algorithms for interval graphs and circular-arc graphs","volume":"12","author":"Gupta","year":"1982","journal-title":"Networks"},{"key":"2023012508073383400_B11","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1101\/gr.093153.109","article-title":"Exon-trapping mediated by the human retrotransposon SVA","volume":"19","author":"Hancks","year":"2009","journal-title":"Genome Res."},{"key":"2023012508073383400_B12","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/ng.2007.48","article-title":"Psoriasis is associated with increased bold beta-defensin genomic copy number","volume":"40","author":"Hollox","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012508073383400_B13","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1101\/gr.088633.108","article-title":"Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes","volume":"19","author":"Hormozdiari","year":"2009","journal-title":"Genome Res."},{"key":"2023012508073383400_B14","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":"2023012508073383400_B15","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature06862","article-title":"Mapping and sequencing of structural variation from eight human genomes","volume":"453","author":"Kidd","year":"2008","journal-title":"Nature"},{"key":"2023012508073383400_B16","doi-asserted-by":"crossref","first-page":"R23","DOI":"10.1186\/gb-2009-10-2-r23","article-title":"PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data","volume":"10","author":"Korbel","year":"2009","journal-title":"Genome Biol."},{"key":"2023012508073383400_B17","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1126\/science.1149504","article-title":"Paired-end mapping reveals extensive structural variation in the human genome","volume":"318","author":"Korbel","year":"2007","journal-title":"Science"},{"key":"2023012508073383400_B18","doi-asserted-by":"crossref","first-page":"i59","DOI":"10.1093\/bioinformatics\/btn176","article-title":"A robust framework for detecting structural variations in a genome","volume":"24","author":"Lee","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508073383400_B19","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/nmeth.f.256","article-title":"Modil: detecting small indels from clone-end sequencing with mixtures of distributions","volume":"6","author":"Lee","year":"2009","journal-title":"Nat. Methods"},{"key":"2023012508073383400_B20","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1038\/ng.215","article-title":"Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease","volume":"40","author":"McCarroll","year":"2008","journal-title":"Nat. Genet."},{"key":"2023012508073383400_B21","doi-asserted-by":"crossref","first-page":"e254","DOI":"10.1371\/journal.pbio.0050254","article-title":"The diploid genome sequence of an individual human","volume":"5","author":"Levy","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012508073383400_B22","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/nmeth.1374","article-title":"Computational methods for discovering structural variation with next-generation sequencing","volume":"6","author":"Medvedev","year":"2009","journal-title":"Nat. Methods"},{"key":"2023012508073383400_B23","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.tig.2007.02.006","article-title":"Which transposable elements are active in the human genome?","volume":"23","author":"Mills","year":"2007","journal-title":"Trends Genet."},{"key":"2023012508073383400_B24","doi-asserted-by":"crossref","DOI":"10.1101\/gr.102970.109","article-title":"Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome","author":"Quinlan","year":"2010","journal-title":"Genome Res."},{"key":"2023012508073383400_B25","doi-asserted-by":"crossref","first-page":"i222","DOI":"10.1093\/bioinformatics\/btp208","article-title":"A geometric approach for classification and comparison of structural variants","volume":"25","author":"Sindi","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508073383400_B26","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/ng1562","article-title":"Fine-scale structural variation of the human genome","volume":"37","author":"Tuzun","year":"2005","journal-title":"Nat. Genet."},{"key":"2023012508073383400_B27","doi-asserted-by":"crossref","first-page":"7696","DOI":"10.1073\/pnas.1232418100","article-title":"End-sequence profiling: sequence-based analysis of aberrant genomes","volume":"100","author":"Volik","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508073383400_B28","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1101\/gr.091827.109","article-title":"Mobile elements create structural variation: analysis of a complete human genome","volume":"19","author":"Xing","year":"2009","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/12\/i350\/48855182\/bioinformatics_26_12_i350.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/12\/i350\/48855182\/bioinformatics_26_12_i350.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:11:14Z","timestamp":1674634274000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/12\/i350\/286093"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,1]]},"references-count":28,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2010,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq216","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,6,15]]},"published":{"date-parts":[[2010,6,1]]}}}