CONAN: Copy number variation analysis software for genome-wide association studies

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Forer, Lukas ^a   Schönherr, Sebastian ^a,b   Weissensteiner, Hansi ^a   Haider, Florian ^a   Kluckner, Thomas ^a   Gieger, Christian ^c   Wichmann, Heinz Erich ^c,d,e   Specht, Günther ^b   Kronenberg, Florian ^a   Kloss Brandstätter, Anita ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

^b UNIVERSITY OF INNSBRUCK   (Austria)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d UNIVERSITY OF MUNICH   (Germany)

^e LUDWIG MAXIMILIANS UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CLIENT-SERVER SOFTWARE; COPY NUMBER VARIATIONS; FREELY AVAILABLE SOFTWARE; GENETIC REGULATION; GENOME-WIDE ASSOCIATION STUDIES; RAPID IDENTIFICATION; SINGLE NUCLEOTIDE POLYMORPHISMS; STATISTICAL INFERENCE;

GENE EXPRESSION;

GRAPHICAL USER INTERFACES;

ARTICLE; COMPUTER PROGRAM; COPY NUMBER VARIATION; GENETIC ASSOCIATION; GENOME; GENOMICS; METHODOLOGY; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA COPY NUMBER VARIATIONS; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 77953344765     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-318     Document Type: Article

References (26)

1. Johnson AD, O'Donnell CJ. An open access database of genome-wide association results. BMC Med Genet 2009, 10:6. 10.1186/1471-2350-10-6, 2639349, 19161620.
2. McCarroll SA. Extending genome-wide association studies to copy-number variation. Hum Mol Genet 2008, 17:R135-R142. 10.1093/hmg/ddn282, 18852202.
3. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876. 10.1038/nature06884, 18421352.
4. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature 2006, 444:444-454. 10.1038/nature05329, 2669898, 17122850.
5. McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 2008, 40:1107-1112. 10.1038/ng.215, 2731799, 19165925.
6. Willer CJ, Speliotes EK, Loos RJ, Li S, Lindgren CM, Heid IM, Berndt SI, Elliott AL, Jackson AU, Lamina C, et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat Genet 2009, 41:25-34. 10.1038/ng.287, 2695662, 19079261.
7. de CR, Riveira-Munoz E, Zeeuwen PL, Robarge J, Liao W, Dannhauser EN, Giardina E, Stuart PE, Nair R, Helms C, et al. Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat Genet 2009, 41:211-215. 10.1038/ng.313, 19169253.
8. Hollox EJ, Huffmeier U, Zeeuwen PL, Palla R, Lascorz J, Rodijk-Olthuis D, van de Kerkhof PC, Traupe H, de JG, den HM, et al. Psoriasis is associated with increased beta-defensin genomic copy number. Nat Genet 2008, 40:23-25. 10.1038/ng.2007.48, 2447885, 18059266.
9. Yang TL, Chen XD, Guo Y, Lei SF, Wang JT, Zhou Q, Pan F, Chen Y, Zhang ZX, Dong SS, et al. Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet 2008, 83:663-674. 10.1016/j.ajhg.2008.10.006, 2667994, 18992858.
10. Korn JM, Kuruvilla FG, McCarroll SA, Wysoker A, Nemesh J, Cawley S, Hubbell E, Veitch J, Collins PJ, Darvishi K, et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 2008, 40:1253-1260. 10.1038/ng.237, 2756534, 18776909.
11. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007, 35:2013-2025. 10.1093/nar/gkm076, 1874617, 17341461.
12. 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, 17:1665-1674. 10.1101/gr.6861907, 2045149, 17921354.
13. Yavas G, Koyuturk M, Ozsoyoglu M, Gould MP, Laframboise T. Cokgen: a software for the identification of rare copy number variation from SNP microarrays. Pac Symp Biocomput 2010, 371-382.
14. Gai X, Perin JC, Murphy K, O'Hara R, D'arcy M, Wenocur A, Xie HM, Rappaport EF, Shaikh TH, White PS. CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics. BMC Bioinformatics 2010, 11:-74. 10.1186/1471-2105-11-74, 2827374, 20132550.
15. Schönherr S, Weissensteiner H, Coassin S, Specht G, Kronenberg F, Brandstätter A. eCOMPAGT -- efficient combination and management of phenotypes and genotypes for genetic epidemiology. BMC Bioinformatics 2009, 10:139. 10.1186/1471-2105-10-139, 2685123, 19432954.
16. Weissensteiner H, Schönherr S, Specht G, Kronenberg F, Brandstätter A. eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. BMC Bioinformatics 2010, 11:122. 10.1186/1471-2105-11-122, 2841209, 20214782.
17. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
18. Sha BY, Yang TL, Zhao LJ, Chen XD, Guo Y, Chen Y, Pan F, Zhang ZX, Dong SS, Xu XH, et al. Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population. J Hum Genet 2009, 54:199-202. 10.1038/jhg.2009.10, 2733232, 19229253.
19. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 186604, 12045153.
20. Thorisson GA, Smith AV, Krishnan L, Stein LD. The International HapMap Project Web site. Genome Res 2005, 15:1592-1593. 10.1101/gr.4413105, 1310647, 16251469.
21. Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, et al. Ensembl 2008. Nucleic Acids Res 2008, 36:D707-D714. 10.1093/nar/gkm988, 2238821, 18000006.
22. R Development Core Team R: A language and environment for statistical computing 2008, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.
23. Deng FY, Zhao LJ, Pei YF, Sha BY, Liu XG, Yan H, Wang L, Yang TL, Recker RR, Papasian CJ, et al. Genome-wide copy number variation association study suggested VPS13B gene for osteoporosis in Caucasians. Osteoporos Int 2010, 21:579-87. 10.1007/s00198-009-0998-7, 19680589.
24. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
25. Wichmann HE, Gieger C, Illig T. KORA-gen--resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen 2005, 67(Suppl 1):S26-S30. 10.1055/s-2005-858226, 16032514.
26. Zerr T, Cooper GM, Eichler EE, Nickerson DA. Targeted interrogation of copy number variation using SCIMMkit. Bioinformatics 2010, 26:120-122. 10.1093/bioinformatics/btp606, 2796813, 19846438.