Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006, 7: 85-97.
Article
CAS
PubMed
Google Scholar
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, González JR, Gratacòs 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: 444-454. 10.1038/nature05329.
Article
PubMed Central
CAS
PubMed
Google Scholar
McCarroll SA, Altshuler DM: Copy-number variation and association studies of human disease. Nat Genet. 2007, 39: S37-S42. 10.1038/ng2080.
Article
CAS
PubMed
Google Scholar
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE: Fine-scale structural variation of the human genome. Nat Genet. 2005, 37: 727-732. 10.1038/ng1562.
Article
CAS
PubMed
Google Scholar
Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Bradley BHRW, Clark RA, Anderson SA, O’Connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK: The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science. 2005, 307 (5714): 1434-1440. 10.1126/science.1101160.
Article
CAS
PubMed
Google Scholar
Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SCL, de Smith A, Blakemore AIF, Froguel P, Owen CJ, Pearce SHS, Teixeira L, Guillevin L, Graham DSC, Pusey CD, Cook HT, Vyse TJ, Aitman TJ: FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet. 2007, 39: 721-723. 10.1038/ng2046.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ionita-Laza I, Rogers A, Lange C, Raby B, Lee C: Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. Genomics. 2009, 93: 22-26. 10.1016/j.ygeno.2008.08.012.
Article
PubMed Central
CAS
PubMed
Google Scholar
Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet. 2007, 39: S16-S21. 10.1038/ng2028.
Article
PubMed Central
CAS
PubMed
Google Scholar
Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostat. 2005, 5: 557-572.
Article
Google Scholar
Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J: Quanti SNP: an objective bayes Hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucl Acids Res. 2007, 35 (6): 2013-2025. 10.1093/nar/gkm076.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M: Penn CNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007, 17: 1665-1674. 10.1101/gr.6861907.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rueda OM, Díaz-Uriarte R: Flexible and accurate detection of genomic copy-number changes from a CGH. PLos Comput Biol. 2007, 3 (6): e122-10.1371/journal.pcbi.0030122.
Article
PubMed Central
PubMed
Google Scholar
Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME: A robust statistical method for case-control association testing with copy number variation. Nat Genet. 2009, 40 (10): 1245-1252.
Article
Google Scholar
The Wellcome Trust Case Control Consortium: Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 2009, 464 (7289): 713-720.
Google Scholar
Winchester L, Yau C, Ragoussis J: Comparing CNV detection methods for SNP arrays. Brief Funct Genomics Proteomic. 2009, 8 (5): 353-366. 10.1093/bfgp/elp017.
Article
CAS
Google Scholar
Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapduram B, MacDonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L: Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011, 29: 512-520. 10.1038/nbt.1852.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fraley C, Raftery AE: Bayesian Regularization for normal mixture estimation and model-based clustering. J Classif. 2007, 24: 155-181. 10.1007/s00357-007-0004-5.
Article
Google Scholar
Ionita-Laza I, Perry GH, Raby BA, Klanderman B, Lee C, Laird NM, Weiss ST, Lange C: On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test. Genet Epidemiol. 2008, 32 (3): 273-284. 10.1002/gepi.20302.
Article
PubMed
Google Scholar
Eleftherohorinou H, Andersson-Assarsson JC, Walters RG, Moustafa JSES, Coin L, Jacobson P, Carlsson LM, Blakemore AI, Froguel P, Walley AJ, Falchi M: famCNV: copy number variant association for quantitative traits in families. Bioinformatics. 2011, 27 (13): 1873-1875. 10.1093/bioinformatics/btr264.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fraley C, Raftery AE: Model-based clustering, discriminant analysis, and density estimation. J Am Stat Ass. 2002, 97 (458): 611-631. 10.1198/016214502760047131.
Article
Google Scholar
Wang K, Chen Z, Tadesse MG, Glessner J, Grant SFA, Hakonarson H, Bucan M, Li M: Modeling genetic inheritance of copy number variations. Nucleic Acids Res. 2008, 36 (21): e138-10.1093/nar/gkn641.
Article
PubMed Central
PubMed
Google Scholar
The Childhood AsthmaManagementProgramResearchGroup: The Childhood Asthma Management Program (CAMP): design, rationale, and methods. Control Clin Trials. 1999, 20: 91-120.
Article
Google Scholar
The Childhood AsthmaManagementProgramResearchGroup: Long-term effects of budesonide or nedocromil in children with asthma. New Engl J Med. 2000, 343 (15): 1054-1063.
Article
Google Scholar
Rogers AJ, Chu JH, Darvishi K, Ionita-Laza I, Lehmann H, Mills R, Lee C, Raby BA: Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility. Clin Exp Allergy. 2012, [http://dx.doi.org/10.1111/cea.12060]
Google Scholar
Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, MacArthur DG, MacDonald JR, Onyiah I, Pang AWC, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, The Wellcome TrustCaseControlConsortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME: Origins and functional impact of copy number variation in the human genome. Nature. 2009, 464: 704-712.
Article
PubMed Central
PubMed
Google Scholar
The 1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038/nature09534.
Article
PubMed Central
Google Scholar
Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS: A highly annotated whole-genome sequence of a Korean individual. Nature. 2009, 460: 1011-1015.
PubMed Central
CAS
PubMed
Google Scholar
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE: Recent segmental duplications in the human genome. Science. 2002, 297 (5583): 1003-1007. 10.1126/science.1072047.
Article
CAS
PubMed
Google Scholar
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.
Article
PubMed Central
PubMed
Google Scholar
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: 949-951. 10.1038/ng1416.
Article
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25 (4): 402-408. 10.1006/meth.2001.1262.
Article
CAS
PubMed
Google Scholar
Ober C, Hoffjan S: Asthma genetics 2006: the long and winding road to gene discovery. Genes Immun. 2006, 7 (2): 95-100. 10.1038/sj.gene.6364284.
Article
CAS
PubMed
Google Scholar
Rogers AJ, Raby BA, Lasky-Su JA, Murphy A, Lazarus R, Klanderman BJ, Sylvia JS, Ziniti JP, Lange C, Celedon JC, Silverman EK, Weiss ST: Assessing the reproducibility of asthma candidate gene associations using genome-wide data. Am J Respir Crit Care Med. 2009, 179 (12): 1084-1090. 10.1164/rccm.200812-1860OC.
Article
PubMed Central
CAS
PubMed
Google Scholar
Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, von Mutius E, Farrall M, Lathrop M, Cookson WO, for the GABRIEL Consortium: A large-scale, consortium-based genomewide association study of asthma. New Engl J Med. 2010, 363: 1211-1221. 10.1056/NEJMoa0906312.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimäki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M: Strong association of de novo copy number mutations with autism. Science. 2007, 316 (5823): 445-449. 10.1126/science.1138659.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M: Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet. 2008, 40: 885-888.
Article
Google Scholar
Itsara A, Wu H, Smith JD, Nickerson DA, Romieu I, London SJ, Eichler EE: De novo rates and selection of large copy number variation. Genome Res. 2010, 20: 1469-1481. 10.1101/gr.107680.110.
Article
PubMed Central
CAS
PubMed
Google Scholar