{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T21:23:23Z","timestamp":1788989003103,"version":"build-2803163510"},"reference-count":15,"publisher":"Springer Science and Business Media LLC","issue":"S11","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,10]]},"DOI":"10.1186\/s12859-017-1802-x","type":"journal-article","created":{"date-parts":[[2017,10,3]],"date-time":"2017-10-03T03:10:49Z","timestamp":1507000249000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["PennCNV in whole-genome sequencing data"],"prefix":"10.1186","volume":"18","author":[{"given":"Leandro","family":"de Ara\u00fajo Lima","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,10,3]]},"reference":[{"key":"1802_CR1","doi-asserted-by":"crossref","first-page":"138","DOI":"10.3389\/fgene.2015.00138","volume":"6","author":"M Pirooznia","year":"2015","unstructured":"Pirooznia M, Goes FS, Zandi PP. Whole-genome CNV analysis: advances in computational approaches. Front Genet. 2015; 6:138.","journal-title":"Front Genet"},{"issue":"11","key":"1802_CR2","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1101\/gr.6861907","volume":"17","author":"K Wang","year":"2007","unstructured":"Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007; 17(11):1665\u201374.","journal-title":"Genome Res"},{"issue":"7304","key":"1802_CR3","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/nature09146","volume":"466","author":"D Pinto","year":"2010","unstructured":"Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C. Functional impact of global rare copy number variation in autism spectrum disorders. Nature. 2010; 466(7304):368\u201372.","journal-title":"Nature"},{"issue":"7246","key":"1802_CR4","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/nature07953","volume":"459","author":"JT Glessner","year":"2009","unstructured":"Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, Zhang H, Estes A, Brune CW, Bradfield JP, Imielinski M, Frackelton EC, Reichert J, Crawford EL, Munson J, Sleiman PM, Chiavacci R, Annaiah K, Thomas K, Hou C, Glaberson W, Flory J, Otieno F, Garris M, Soorya L, Klei L, Piven J, Meyer KJ, Anagnostou E, Sakurai T, Game RM, Rudd DS, Zurawiecki D, McDougle CJ, Davis LK, Miller J, Posey DJ, Michaels S, Kolevzon A, Silverman JM, Bernier R, Levy SE, Schultz RT, Dawson G, Owley T, McMahon WM, Wassink TH, Sweeney JA, Nurnberger JI, Coon H, Sutcliffe JS, Minshew NJ, Grant SF, Bucan M, Cook EH, Buxbaum JD, Devlin B, Schellenberg GD, Hakonarson H. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature. 2009; 459(7246):569\u201373.","journal-title":"Nature"},{"issue":"7246","key":"1802_CR5","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1038\/nature07999","volume":"459","author":"K Wang","year":"2009","unstructured":"Wang K, Zhang H, Ma D, Bucan M, Glessner JT, Abrahams BS, Salyakina D, Imielinski M, Bradfield JP, Sleiman PM, Kim CE, Hou C, Frackelton E, Chiavacci R, Takahashi N, Sakurai T, Rappaport E, Lajonchere CM, Munson J, Estes A, Korvatska O, Piven J, Sonnenblick LI, Alvarez Retuerto AI, Herman EI, Dong H, Hutman T, Sigman M, Ozonoff S, Klin A, Owley T, Sweeney JA, Brune CW, Cantor RM, Bernier R, Gilbert JR, Cuccaro ML, McMahon WM, Miller J, State MW, Wassink TH, Coon H, Levy SE, Schultz RT, Nurnberger JI, Haines JL, Sutcliffe JS, Cook EH, Minshew NJ, Buxbaum JD, Dawson G, Grant SF, Geschwind DH, Pericak-Vance MA, Schellenberg GD, Hakonarson H. Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature. 2009; 459(7246):528\u201333.","journal-title":"Nature"},{"issue":"7181","key":"1802_CR6","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1038\/nature06742","volume":"451","author":"M Jakobsson","year":"2008","unstructured":"Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Genotype, haplotype and copy-number variation in worldwide human populations. Nature. 2008; 451(7181):998\u20131003.","journal-title":"Nature"},{"issue":"1","key":"1802_CR7","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/2040-2392-4-8","volume":"4","author":"L Shi","year":"2013","unstructured":"Shi L, Zhang X, Golhar R, Otieno FG, He M, Hou C, Kim C, Keating B, Lyon GJ, Wang K, Hakonarson H. Whole-genome sequencing in an autism multiplex family. Mol Autism. 2013; 4(1):8.","journal-title":"Mol Autism"},{"key":"1802_CR8","doi-asserted-by":"crossref","first-page":"160025","DOI":"10.1038\/sdata.2016.25","volume":"3","author":"JM Zook","year":"2016","unstructured":"Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data. 2016; 3:160025.","journal-title":"Sci Data"},{"issue":"16","key":"1802_CR9","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","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(16):2078\u20139.","journal-title":"Bioinformatics"},{"key":"1802_CR10","unstructured":"Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, Altshuler DM, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A, Clark AG, Donnelly P, Eichler EE, Flicek P, Gabriel SB, Gibbs RA, Green ED, Hurles ME, Knoppers BM, Korbel JO, Lander ES, Lee C, Lehrach H, Mardis ER, Marth GT, McVean GA, Nickerson DA, Schmidt JP, Sherry ST, Wang J, Wilson RK, Gibbs RA, Dinh H, Kovar C, Lee S, Lewis L, Muzny D, Reid J, Wang M, Wang J, Fang X, Guo X, Jian M, Jiang H, Jin X, Li G, Li J, Li Y, Li Z, Liu X, Lu Y, Ma X, Su Z, Tai S, Tang M, Wang B, Wang G, Wu H, Wu R, Yin Y, Zhang W, Zhao J, Zhao M, Zheng X, Zhou Y, Lander ES, Altshuler DM, Gabriel SB, Gupta N, Flicek P, Clarke L, Leinonen R, Smith RE, Zheng-Bradley X, Bentley DR, Grocock R, Humphray S, James T, Kingsbury Z, Lehrach H, Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML, Sherry ST, McVean GA, Mardis ER, Wilson RK, Fulton L, Fulton R, Weinstock GM, Durbin RM, Balasubramaniam S, Burton J, Danecek P, Keane TM, Kolb-Kokocinski A, McCarthy S, Stalker J, Quail M, Schmidt JP, Davies CJ, Gollub J, Webster T, Wong B, Zhan Y, Auton A, Gibbs RA, Yu F, Bainbridge M, Challis D, Evani US, Lu J, Muzny D, Nagaswamy U, Reid J, Sabo A, Wang Y, Yu J, Wang J, Coin LJ, Fang L, Guo X, Jin X, Li G, Li Q, Li Y, Li Z, Lin H, Liu B, Luo R, Qin N, Shao H, Wang B, Xie Y, Ye C, Yu C, Zhang F, Zheng H, Zhu H, Marth GT, Garrison EP, Kural D, Lee WP, Leong WF, Ward AN, Wu J, Zhang M, Lee C, Griffin L, Hsieh CH, Mills RE, Shi X, von Grotthuss M, Zhang C, Daly MJ, DePristo MA, Altshuler DM, Banks E, Bhatia G, Carneiro MO, del Angel G, Gabriel SB, Genovese G, Gupta N, Handsaker RE, Hartl C, Lander ES, McCarroll SA, Nemesh JC, Poplin RE, Schaffner SF, Shakir K, Yoon SC, Lihm J, Makarov V, Jin H, Kim W, Kim KC, Korbel JO, Rausch T, Flicek P, Beal K, Clarke L, Cunningham F, Herrero J, McLaren WM, Ritchie GR, Smith RE, Zheng-Bradley X, Clark AG, Gottipati S, Keinan A, Rodriguez-Flores JL, Sabeti PC, Grossman SR, Tabrizi S, Tariyal R, Cooper DN, Ball EV, Stenson PD, Bentley DR, Barnes B, Bauer M, Cheetham R, Cox T, Eberle M, Humphray S, Kahn S, Murray L, Peden J, Shaw R, Ye K, Batzer MA, Konkel MK, Walker JA, MacArthur DG, Lek M, Sudbrak R, Amstislavskiy VS, Herwig R, Shriver MD, Bustamante CD, Byrnes JK, De La Vega FM, Gravel S, Kenny EE, Kidd JM, Lacroute P, Maples BK, Moreno-Estrada A, Zakharia F, Halperin E, Baran Y, Craig DW, Christoforides A, Homer N, Izatt T, Kurdoglu AA, Sinari SA, Squire K, Sherry ST, Xiao C, Sebat J, Bafna V, Ye, K, Burchard, EG, Hernandez, RD, Gignoux, CR, Haussler, D, Katzman, SJ, Kent, WJ, Howie, B, Ruiz-Linares, A, Dermitzakis, ET, Lappalainen, T, Devine, SE, Liu, X, Maroo, A, Tallon, LJ, Rosenfeld, JA, Michelson, LP, Abecasis, GR, Kang, HM, Anderson, P, Angius, A, Bigham, A, Blackwell, T, Busonero, F, Cucca, F, Fuchsberger, C, Jones, C, Jun, G, Li, Y, Lyons, R, Maschio, A, Porcu, E. An integrated map of genetic variation from 1092 human genomes. Nature. 2012; 491(7422):56\u201365."},{"issue":"16","key":"1802_CR11","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1093\/nar\/gkq603","volume":"38","author":"K Wang","year":"2010","unstructured":"Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38(16):164.","journal-title":"Nucleic Acids Res"},{"key":"1802_CR12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/0471250953.bi1112s47","volume":"47","author":"AR Quinlan","year":"2014","unstructured":"Quinlan AR. BEDTools: The Swiss-Army tool for genome feature analysis. Curr Protoc Bioinforma. 2014; 47:1\u201334.","journal-title":"Curr Protoc Bioinforma"},{"issue":"14","key":"1802_CR13","doi-asserted-by":"crossref","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(14):1754\u201360.","journal-title":"Bioinformatics"},{"issue":"6","key":"1802_CR14","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011; 21(6):974\u201384.","journal-title":"Genome Res"},{"issue":"6","key":"1802_CR15","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/gb-2014-15-6-r84","volume":"15","author":"RM Layer","year":"2014","unstructured":"Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 2014; 15(6):84.","journal-title":"Genome Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1802-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,4]],"date-time":"2019-10-04T01:33:58Z","timestamp":1570152838000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1802-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10]]},"references-count":15,"journal-issue":{"issue":"S11","published-print":{"date-parts":[[2017,10]]}},"alternative-id":["1802"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1802-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10]]},"article-number":"383"}}