{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T03:41:46Z","timestamp":1770435706903,"version":"3.49.0"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Recent advances in sequencing technologies have enabled generation of large-scale genome sequencing data. These data can be used to characterize a variety of genomic features, including the DNA copy number profile of a cancer genome. A robust and reliable method for screening chromosomal alterations would allow a detailed characterization of the cancer genome with unprecedented accuracy.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We develop a method for identification of copy number alterations in a tumor genome compared to its matched control, based on application of Smith-Waterman algorithm to single-end sequencing data. In a performance test with simulated data, our algorithm shows &gt;90% sensitivity and &gt;90% precision in detecting a single copy number change that contains approximately 500 reads for the normal sample. With 100-bp reads, this corresponds to a ~50 kb region for 1X genome coverage of the human genome. We further refine the algorithm to develop rSW-seq, (recursive Smith-Waterman-seq) to identify alterations in a complex configuration, which are commonly observed in the human cancer genome. To validate our approach, we compare our algorithm with an existing algorithm using simulated and publicly available datasets. We also compare the sequencing-based profiles to microarray-based results.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We propose rSW-seq as an efficient method for detecting copy number changes in the tumor genome.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-432","type":"journal-article","created":{"date-parts":[[2010,8,19]],"date-time":"2010-08-19T06:13:47Z","timestamp":1282198427000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data"],"prefix":"10.1186","volume":"11","author":[{"given":"Tae-Min","family":"Kim","sequence":"first","affiliation":[]},{"given":"Lovelace J","family":"Luquette","sequence":"additional","affiliation":[]},{"given":"Ruibin","family":"Xi","sequence":"additional","affiliation":[]},{"given":"Peter J","family":"Park","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,8,18]]},"reference":[{"key":"3889_CR1","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1056\/NEJMra0803109","volume":"359","author":"S Frohling","year":"2008","unstructured":"Frohling S, Dohner H: Chromosomal abnormalities in cancer. N Engl J Med 2008, 359: 722\u2013734. 10.1056\/NEJMra0803109","journal-title":"N Engl J Med"},{"key":"3889_CR2","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1038\/ng1215","volume":"34","author":"DG Albertson","year":"2003","unstructured":"Albertson DG, Collins C, McCormick F, Gray JW: Chromosome aberrations in solid tumors. Nat Genet 2003, 34: 369\u2013376. 10.1038\/ng1215","journal-title":"Nat Genet"},{"issue":"Suppl","key":"3889_CR3","doi-asserted-by":"publisher","first-page":"S11","DOI":"10.1038\/ng1569","volume":"37","author":"D Pinkel","year":"2005","unstructured":"Pinkel D, Albertson DG: Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005, 37(Suppl):S11-S17. 10.1038\/ng1569","journal-title":"Nat Genet"},{"issue":"Spec No 2","key":"3889_CR4","doi-asserted-by":"publisher","first-page":"R145","DOI":"10.1093\/hmg\/ddg261","volume":"12","author":"DG Albertson","year":"2003","unstructured":"Albertson DG, Pinkel D: Genomic microarrays in human genetic disease and cancer. Hum Mol Genet 2003, 12(Spec No 2):R145-R152. 10.1093\/hmg\/ddg261","journal-title":"Hum Mol Genet"},{"key":"3889_CR5","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/ng754","volume":"29","author":"AM Snijders","year":"2001","unstructured":"Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, et al.: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001, 29: 263\u2013264. 10.1038\/ng754","journal-title":"Nat Genet"},{"key":"3889_CR6","doi-asserted-by":"publisher","first-page":"16156","DOI":"10.1073\/pnas.202610899","volume":"99","author":"TL Wang","year":"2002","unstructured":"Wang TL, Maierhofer C, Speicher MR, Lengauer C, Vogelstein B, Kinzler KW, Velculescu VE: Digital karyotyping. Proc Natl Acad Sci USA 2002, 99: 16156\u201316161. 10.1073\/pnas.202610899","journal-title":"Proc Natl Acad Sci USA"},{"key":"3889_CR7","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.gde.2006.10.009","volume":"16","author":"DR Bentley","year":"2006","unstructured":"Bentley DR: Whole-genome re-sequencing. Curr Opin Genet Dev 2006, 16: 545\u2013552. 10.1016\/j.gde.2006.10.009","journal-title":"Curr Opin Genet Dev"},{"key":"3889_CR8","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","volume":"437","author":"M Margulies","year":"2005","unstructured":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437: 376\u2013380.","journal-title":"Nature"},{"key":"3889_CR9","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.tig.2007.12.007","volume":"24","author":"ER Mardis","year":"2008","unstructured":"Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24: 133\u2013141.","journal-title":"Trends Genet"},{"key":"3889_CR10","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.ygeno.2008.07.001","volume":"92","author":"O Morozova","year":"2008","unstructured":"Morozova O, Marra MA: Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92: 255\u2013264. 10.1016\/j.ygeno.2008.07.001","journal-title":"Genomics"},{"key":"3889_CR11","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/ng.437","volume":"41","author":"C Alkan","year":"2009","unstructured":"Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, et al.: Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 2009, 41: 1061\u20131067. 10.1038\/ng.437","journal-title":"Nat Genet"},{"key":"3889_CR12","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1101\/gr.092981.109","volume":"19","author":"S Yoon","year":"2009","unstructured":"Yoon S, Xuan Z, Makarov V, Ye K, Sebat J: Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 2009, 19: 1586\u20131592. 10.1101\/gr.092981.109","journal-title":"Genome Res"},{"key":"3889_CR13","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"TF Smith","year":"1981","unstructured":"Smith TF, Waterman MS: Identification of common molecular subsequences. J Mol Biol 1981, 147: 195\u2013197. 10.1016\/0022-2836(81)90087-5","journal-title":"J Mol Biol"},{"key":"3889_CR14","doi-asserted-by":"publisher","first-page":"3455","DOI":"10.1093\/nar\/gki643","volume":"33","author":"TS Price","year":"2005","unstructured":"Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ, Smith L, Greenfield A, Tiganescu A, Buckle V, et al.: SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res 2005, 33: 3455\u20133464. 10.1093\/nar\/gki643","journal-title":"Nucleic Acids Res"},{"key":"3889_CR15","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nmeth.1276","volume":"6","author":"DY Chiang","year":"2009","unstructured":"Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES: High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 2009, 6: 99\u2013103. 10.1038\/nmeth.1276","journal-title":"Nat Methods"},{"key":"3889_CR16","doi-asserted-by":"publisher","first-page":"3763","DOI":"10.1093\/bioinformatics\/bti611","volume":"21","author":"WR Lai","year":"2005","unstructured":"Lai WR, Johnson MD, Kucherlapati R, Park PJ: Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005, 21: 3763\u20133770. 10.1093\/bioinformatics\/bti611","journal-title":"Bioinformatics"},{"key":"3889_CR17","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","volume":"5","author":"AB Olshen","year":"2004","unstructured":"Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5: 557\u2013572. 10.1093\/biostatistics\/kxh008","journal-title":"Biostatistics"},{"key":"3889_CR18","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1186\/1471-2105-10-80","volume":"10","author":"C Xie","year":"2009","unstructured":"Xie C, Tammi MT: CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 2009, 10: 80. 10.1186\/1471-2105-10-80","journal-title":"BMC Bioinformatics"},{"key":"3889_CR19","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1101\/gr.7.10.986","volume":"7","author":"S Audic","year":"1997","unstructured":"Audic S, Claverie JM: The significance of digital gene expression profiles. Genome Res 1997, 7: 986\u2013995.","journal-title":"Genome Res"},{"key":"3889_CR20","first-page":"2475","volume":"7","author":"MJ Zinda","year":"2001","unstructured":"Zinda MJ, Johnson MA, Paul JD, Horn C, Konicek BW, Lu ZH, Sandusky G, Thomas JE, Neubauer BL, Lai MT, et al.: AKT-1, -2, and -3 are expressed in both normal and tumor tissues of the lung, breast, prostate, and colon. Clin Cancer Res 2001, 7: 2475\u20132479.","journal-title":"Clin Cancer Res"},{"key":"3889_CR21","doi-asserted-by":"publisher","first-page":"1270","DOI":"10.1101\/gr.088633.108","volume":"19","author":"F Hormozdiari","year":"2009","unstructured":"Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC: Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 2009, 19: 1270\u20131278. 10.1101\/gr.088633.108","journal-title":"Genome Res"},{"key":"3889_CR22","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/nmeth.f.256","volume":"6","author":"S Lee","year":"2009","unstructured":"Lee S, Hormozdiari F, Alkan C, Brudno M: MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat Methods 2009, 6: 473\u2013474. 10.1038\/nmeth.f.256","journal-title":"Nat Methods"},{"key":"3889_CR23","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10: R25. 10.1186\/gb-2009-10-3-r25","journal-title":"Genome Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-432.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T05:28:52Z","timestamp":1630474132000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-432"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,18]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3889"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-432","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,8,18]]},"assertion":[{"value":"31 December 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 August 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 August 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"432"}}