{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T02:27:08Z","timestamp":1768444028441,"version":"3.49.0"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Somatically-acquired translocations may serve as important markers for assessing the cause and nature of diseases like cancer. Algorithms to locate translocations may use next-generation sequencing (NGS) platform data. However, paired-end strategies do not accurately predict precise translocation breakpoints, and \"split-read\" methods may lose sensitivity if a translocation boundary is not captured by many sequenced reads. To address these challenges, we have developed \"Bellerophon\", a method that uses discordant read pairs to identify potential translocations, and subsequently uses \"soft-clipped\" reads to predict the location of the precise breakpoints. Furthermore, for each chimeric breakpoint, our method attempts to classify it as a participant in an unbalanced translocation, balanced translocation, or interchromosomal insertion.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We compared Bellerophon to four previously published algorithms for detecting structural variation (SV). Using two simulated datasets and two prostate cancer datasets, Bellerophon had overall better performance than the other methods. Furthermore, our method accurately predicted the presence of the interchromosomal insertions placed in our simulated dataset, which is an ability that the other SV prediction programs lack.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The combined use of paired reads and soft-clipped reads allows Bellerophon to detect interchromosomal breakpoints with high sensitivity, while also mitigating losses in specificity. This trend is seen across all datasets examined. Because it does not perform assembly on soft-clipped subreads, Bellerophon may be limited in experiments where sequence read lengths are short.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Availability<\/jats:title>\n            <jats:p>The program can be downloaded from <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/cbc.case.edu\/Bellerophon\" ext-link-type=\"uri\">http:\/\/cbc.case.edu\/Bellerophon<\/jats:ext-link>\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-s5-s6","type":"journal-article","created":{"date-parts":[[2013,4,10]],"date-time":"2013-04-10T18:15:17Z","timestamp":1365617717000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data"],"prefix":"10.1186","volume":"14","author":[{"given":"Matthew","family":"Hayes","sequence":"first","affiliation":[]},{"given":"Jing","family":"Li","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,4,10]]},"reference":[{"key":"5774_CR1","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1038\/nature05329","volume":"444","author":"R Redon","year":"2006","unstructured":"Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marhshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal R, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME: Global variation in copy number in the human genome. Nature. 2006, 444: 444-454. 10.1038\/nature05329.","journal-title":"Nature"},{"key":"5774_CR2","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1126\/science.1098918","volume":"305","author":"J Sebat","year":"2004","unstructured":"Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M: Large-Scale Copy Number Polymorphism in the Human Genome. Science. 2004, 305: 525-528. 10.1126\/science.1098918.","journal-title":"Science"},{"key":"5774_CR3","volume-title":"Nat Educ","author":"C O'Connor","year":"2008","unstructured":"O'Connor C: Human chromosome translocations and cancer. Nat Educ. 2008, 1:"},{"key":"5774_CR4","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/nrc2091","volume":"7","author":"F Mitelman","year":"2007","unstructured":"Mitelman F, Johansson B, Mertens F: The impace of translocations and gene fusions in cancer causation. Nature Reviews Cancer. 2007, 7: 233-245. 10.1038\/nrc2091.","journal-title":"Nature Reviews Cancer"},{"key":"5774_CR5","first-page":"1497","volume":"132","author":"P Nowell","year":"1960","unstructured":"Nowell P, Hungerford D: A minute chromosome in chronic granulocytic leukemia. Science. 1960, 132: 1497-","journal-title":"Science"},{"key":"5774_CR6","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1038\/nature08645","volume":"462","author":"P Stephens","year":"2009","unstructured":"Stephens P, McBride D, Lin M, Varela I, Pleasance E, Simpson J, Stebbings L, Leroy C, Edkins S, Mudie L, Greenman C, Jia M, Latimer C, Teague J, Lau K, Burton J, Quail M, Swerdlow H, Churcher C, Natrajan R, Sieuwerts A, Martens J, Silver D, Langerod A, Russnes H, Foekens J, Reis-Filho J, van't VeerL, Richardson A, Borresen-Dale A, Campbell P, Futreal PA, Stratton MR: Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009, 462: 1005-1010. 10.1038\/nature08645.","journal-title":"Nature"},{"key":"5774_CR7","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","volume":"24","author":"E Mardis","year":"2009","unstructured":"Mardis E: The impact of next-generation sequence technology on genetics. Trends Genet. 2009, 24: 133-141.","journal-title":"Trends Genet"},{"key":"5774_CR8","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.tig.2007.12.006","volume":"24","author":"M Pop","year":"2008","unstructured":"Pop M, Salzberg SL: Bioinformatics challenges of new sequencing technology. Trends Genet. 2008, 24: 142-149. 10.1016\/j.tig.2007.12.006.","journal-title":"Trends Genet"},{"key":"5774_CR9","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/nmeth.1363","volume":"6","author":"K Chen","year":"2009","unstructured":"Chen K, Wallis JW, McLellan MD, Larson D, Kalicki J, Pohl C, McGrath S, Wendl M, Zhang Q, Locke D, Shi X, Fulton R, Ley T, Wilson R, Ding L, Mardis E: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009, 6: 677-681. 10.1038\/nmeth.1363.","journal-title":"Nat Methods"},{"key":"5774_CR10","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp208","volume":"25","author":"S Sindi","year":"2009","unstructured":"Sindi S, Helman E, Bashir A, Raphael B: A geometric approach for classification and comparison of structural variants. Bioinformatics. 2009, 25: 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"key":"5774_CR11","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1093\/bioinformatics\/btq293","volume":"26","author":"B Zeitouni","year":"2010","unstructured":"Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-ne P, Nicolas A, Delattre O, Barillot E: SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics. 2010, 26: 1895-1896. 10.1093\/bioinformatics\/btq293.","journal-title":"Bioinformatics"},{"key":"5774_CR12","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1038\/nmeth.1628","volume":"8","author":"J Wang","year":"2011","unstructured":"Wang J, Mullighan C, Easton J, Roberts S, Heatley S, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer J, Naeve C, Mardis E, Wilson R, Downing J, Zhang J: CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011, 8: 652-654. 10.1038\/nmeth.1628.","journal-title":"Nat Methods"},{"key":"5774_CR13","volume-title":"Bioinformatics","author":"TM Keane","year":"2013","unstructured":"Keane TM, Wong K, Adams DJ: RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics. 2013, 29:"},{"key":"5774_CR14","volume-title":"Bioinformatics","author":"T Rausch","year":"2012","unstructured":"Rausch T, Zichner T, Schalttl A, Stutz A, Benes Vladimir, Korbel J: DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012, 28:"},{"key":"5774_CR15","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1093\/bioinformatics\/btp208","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment\/Map format and SAMTools. Bioinformatics. 2009, 25: 222-230. 10.1093\/bioinformatics\/btp208.","journal-title":"Bioinformatics"},{"key":"5774_CR16","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093\/bioinformatics\/btp324.","journal-title":"Bioinformatics"},{"key":"5774_CR17","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"W Kent","year":"2002","unstructured":"Kent W: The BLAST-Like Alignment Tool. Genome Res. 2002, 12: 656-664.","journal-title":"Genome Res"},{"key":"5774_CR18","volume-title":"Chromosome Abnormalities and Genetic Counseling","author":"R Gardner","year":"1989","unstructured":"Gardner R, Sutherland G: Chromosome Abnormalities and Genetic Counseling. 1989, Oxford, UK: Oxford University Press"},{"key":"5774_CR19","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1016\/j.eururo.2009.04.036","volume":"56","author":"S Tomlins","year":"2009","unstructured":"Tomlins S, Bjartell A, Chinnaiyan A, Jenster G, Nam R, Rubin M, Schalken J: ETS gene fusions in prostate cancer: from discovery to daily clinical practice. Eur Urol. 2009, 56: 275-286. 10.1016\/j.eururo.2009.04.036.","journal-title":"Eur Urol"},{"key":"5774_CR20","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1101\/gr.114116.110","volume":"21","author":"K Howarth","year":"2011","unstructured":"Howarth K, Pole J, Beavis JC, Batty EM, Newman S, Bignell GR, Edwards PA: Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles. Genome Res. 2011, 21: 525-534. 10.1101\/gr.114116.110.","journal-title":"Genome Res"},{"key":"5774_CR21","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nature09744","volume":"470","author":"MM Berger","year":"2011","unstructured":"Berger MM, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esqueva R, Pueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger LA, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, Kantoff PW, Chin L, Gabriel SB, Gerstein MB, Golub TR, Meyerson M, Tewari A, Lander ES, Getz G, Rubin MA, Garraway LA: The genomic complexity of primary human prostate cancer. Nature. 2011, 470: 214-220. 10.1038\/nature09744.","journal-title":"Nature"},{"key":"5774_CR22","volume-title":"PLOS ONE","author":"M Hayes","year":"2012","unstructured":"Hayes M, Pyon YS, Li J: A Model-Based Clustering Method for Genomic Structural Variant Prediction and Genotyping Using Paired-End Sequencing Data. PLOS ONE. 2012, 7:"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S5-S6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T22:53:10Z","timestamp":1630536790000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S5-S6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4]]},"references-count":22,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2013,4]]}},"alternative-id":["5774"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s5-s6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,4]]},"assertion":[{"value":"10 April 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S6"}}