{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T18:14:01Z","timestamp":1784052841218,"version":"3.55.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,3,6]],"date-time":"2009-03-06T00:00:00Z","timestamp":1236297600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1471-2105-10-80","type":"journal-article","created":{"date-parts":[[2009,3,6]],"date-time":"2009-03-06T19:14:02Z","timestamp":1236366842000},"source":"Crossref","is-referenced-by-count":487,"title":["CNV-seq, a new method to detect copy number variation using high-throughput sequencing"],"prefix":"10.1186","volume":"10","author":[{"given":"Chao","family":"Xie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martti T","family":"Tammi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2009,3,6]]},"reference":[{"issue":"5683","key":"2810_CR1","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, M\u00e5n\u00e9r 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(5683):525\u2013528. 10.1126\/science.1098918","journal-title":"Science"},{"issue":"9","key":"2810_CR2","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1038\/ng1416","volume":"36","author":"AJ Iafrate","year":"2004","unstructured":"Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet 2004, 36(9):949\u2013951. 10.1038\/ng1416","journal-title":"Nat Genet"},{"issue":"7118","key":"2810_CR3","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, Gonz\u00e1lez JR, Gratac\u00f2s M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, 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(7118):444\u2013454. 10.1038\/nature05329","journal-title":"Nature"},{"issue":"7 Suppl","key":"2810_CR4","doi-asserted-by":"publisher","first-page":"S16","DOI":"10.1038\/ng2028","volume":"39","author":"NP Carter","year":"2007","unstructured":"Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 2007, 39(7 Suppl):S16-S21. 10.1038\/ng2028","journal-title":"Nat Genet"},{"issue":"4","key":"2810_CR5","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1002\/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I","volume":"20","author":"S Solinas-Toldo","year":"1997","unstructured":"Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, D\u00f6hner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997, 20(4):399\u2013407. 10.1002\/(SICI)1098-2264(199712)20:4<399::AID-GCC12>3.0.CO;2-I","journal-title":"Genes Chromosomes Cancer"},{"issue":"2","key":"2810_CR6","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/2524","volume":"20","author":"D Pinkel","year":"1998","unstructured":"Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20(2):207\u2013211. 10.1038\/2524","journal-title":"Nat Genet"},{"key":"2810_CR7","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1038\/nmeth1156","volume":"5","author":"SC Schuster","year":"2008","unstructured":"Schuster SC: Next-generation sequencing transforms today's biology. Nat Methods 2008, 5: 16\u201318. 10.1038\/nmeth1156","journal-title":"Nat Methods"},{"issue":"7057","key":"2810_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, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376\u2013380.","journal-title":"Nature"},{"issue":"6","key":"2810_CR9","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(6):545\u2013552. 10.1016\/j.gde.2006.10.009","journal-title":"Curr Opin Genet Dev"},{"issue":"7","key":"2810_CR10","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1101\/gr.076463.108","volume":"18","author":"A Valouev","year":"2008","unstructured":"Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM: A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008, 18(7):1051\u20131063. 10.1101\/gr.076463.108","journal-title":"Genome Res"},{"issue":"7","key":"2810_CR11","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/nmeth0708-585","volume":"5","author":"J Shendure","year":"2008","unstructured":"Shendure J: The beginning of the end for microarrays? Nat Methods 2008, 5(7):585\u2013587. 10.1038\/nmeth0708-585","journal-title":"Nat Methods"},{"issue":"5830","key":"2810_CR12","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1126\/science.1141319","volume":"316","author":"DS Johnson","year":"2007","unstructured":"Johnson DS, Mortazavi A, Myers RM, Wold B: Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316(5830):1497\u20131502. 10.1126\/science.1141319","journal-title":"Science"},{"issue":"7184","key":"2810_CR13","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nature06745","volume":"452","author":"SJ Cokus","year":"2008","unstructured":"Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452(7184):215\u2013219. 10.1038\/nature06745","journal-title":"Nature"},{"issue":"2","key":"2810_CR14","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1038\/nmeth.1179","volume":"5","author":"LW Hillier","year":"2008","unstructured":"Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER: Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 2008, 5(2):183\u2013188. 10.1038\/nmeth.1179","journal-title":"Nat Methods"},{"issue":"3","key":"2810_CR15","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/nmeth.1185","volume":"5","author":"CP Van Tassell","year":"2008","unstructured":"Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS: SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 2008, 5(3):247\u2013252. 10.1038\/nmeth.1185","journal-title":"Nat Methods"},{"issue":"7","key":"2810_CR16","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1101\/gr.076166.108","volume":"18","author":"W Chen","year":"2008","unstructured":"Chen W, Kalscheuer V, Tzschach A, Menzel C, Ullmann R, Schulz MH, Erdogan F, Li N, Kijas Z, Arkesteijn G, Pajares IL, Goetz-Sothmann M, Heinrich U, Rost I, Dufke A, Grasshoff U, Glaeser B, Vingron M, Ropers HH: Mapping translocation breakpoints by next-generation sequencing. Genome Res 2008, 18(7):1143\u20131149. 10.1101\/gr.076166.108","journal-title":"Genome Res"},{"issue":"7","key":"2810_CR17","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621\u2013628. 10.1038\/nmeth.1226","journal-title":"Nat Methods"},{"key":"2810_CR18","volume-title":"Genome Res","author":"J Marioni","year":"2008","unstructured":"Marioni J, Mason C, Mane S, Stephens M, Gilad Y: RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008."},{"issue":"5881","key":"2810_CR19","doi-asserted-by":"publisher","first-page":"1344","DOI":"10.1126\/science.1158441","volume":"320","author":"U Nagalakshmi","year":"2008","unstructured":"Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320(5881):1344\u20131349. 10.1126\/science.1158441","journal-title":"Science"},{"issue":"7199","key":"2810_CR20","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1038\/nature07002","volume":"453","author":"BT Wilhelm","year":"2008","unstructured":"Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, B\u00e4hler J: Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453(7199):1239\u20131243. 10.1038\/nature07002","journal-title":"Nature"},{"issue":"7189","key":"2810_CR21","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/nature06884","volume":"452","author":"DA Wheeler","year":"2008","unstructured":"Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song Xz, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM: The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452(7189):872\u2013876. 10.1038\/nature06884","journal-title":"Nature"},{"key":"2810_CR22","volume-title":"PhD thesis","author":"E Sherwood","year":"2007","unstructured":"Sherwood E: Methods and applications in DNA sequence alignments. PhD thesis. Karolinska Institutet; 2007."},{"issue":"15","key":"2810_CR23","doi-asserted-by":"publisher","first-page":"4663","DOI":"10.1093\/nar\/gkg653;","volume":"31","author":"MT Tammi","year":"2003","unstructured":"Tammi MT, Arner E, Kindlund E, Andersson B: Correcting errors in shotgun sequences. Nucleic Acids Res 2003, 31(15):4663\u20134672. 10.1093\/nar\/gkg653;","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"2810_CR24","doi-asserted-by":"publisher","first-page":"e254","DOI":"10.1371\/journal.pbio.0050254","volume":"5","author":"S Levy","year":"2007","unstructured":"Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AWC, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC: The diploid genome sequence of an individual human. PLoS Biol 2007, 5(10):e254. 10.1371\/journal.pbio.0050254","journal-title":"PLoS Biol"},{"issue":"3","key":"2810_CR25","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1093\/biomet\/56.3.635","volume":"56","author":"DV Hinkley","year":"1969","unstructured":"Hinkley DV: On the ratio of two correlated normal random variables. Biometrika 1969, 56(3):635\u2013639. 10.1093\/biomet\/56.3.635","journal-title":"Biometrika"},{"issue":"11","key":"2810_CR26","doi-asserted-by":"publisher","first-page":"1338","DOI":"10.1287\/mnsc.21.11.1338","volume":"21","author":"J Hayya","year":"1975","unstructured":"Hayya J, Armstrong D, Gressis N: A note on the ratio of two normally distributed variables. Manage Sci 1975, 21(11):1338\u20131341. 10.1287\/mnsc.21.11.1338","journal-title":"Manage Sci"},{"issue":"3","key":"2810_CR27","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/0022-2836(75)90213-2","volume":"94","author":"F Sanger","year":"1975","unstructured":"Sanger F, Coulson AR: A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975, 94(3):441\u2013448. 10.1016\/0022-2836(75)90213-2","journal-title":"J Mol Biol"},{"issue":"12","key":"2810_CR28","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1038\/nmeth.1270","volume":"5","author":"MA Quail","year":"2008","unstructured":"Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ: A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5(12):1005\u20131010. 10.1038\/nmeth.1270","journal-title":"Nat Methods"},{"key":"2810_CR29","doi-asserted-by":"crossref","unstructured":"Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, (36 Database):D13-D21.","DOI":"10.1093\/nar\/gkm1000"},{"issue":"3","key":"2810_CR30","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1101\/gr.8.3.186","volume":"8","author":"B Ewing","year":"1998","unstructured":"Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186\u2013194.","journal-title":"Genome Res"},{"issue":"5","key":"2810_CR31","doi-asserted-by":"publisher","first-page":"925","DOI":"10.1101\/gr.1860604","volume":"14","author":"E Birney","year":"2004","unstructured":"Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M: An overview of Ensembl. Genome Res 2004, 14(5):925\u2013928. 10.1101\/gr.1860604","journal-title":"Genome Res"},{"key":"2810_CR32","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2008","unstructured":"R Development Core Team:R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria; 2008. [ http:\/\/www.R-project.org ]"},{"issue":"4","key":"2810_CR33","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ: BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656\u2013664.","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-80.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-10-80\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-10-80.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,18]],"date-time":"2019-05-18T13:54:40Z","timestamp":1558187680000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-10-80"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,3,6]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["2810"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-10-80","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,3,6]]},"article-number":"80"}}