ProbABEL package for genome-wide association analysis of imputed data

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Aulchenko, Yurii S ^a,b   Struchalin, Maksim V ^a   van Duijn, Cornelia M ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX TRAITS; COX PROPORTIONAL HAZARDS MODELS; DATA CALL; GENOME-WIDE ASSOCIATION; QUANTITATIVE TRAITS; SCORE TEST; SINGLE-NUCLEOTIDE POLYMORPHISMS;

GENES; POPULATION STATISTICS;

UNCERTAINTY ANALYSIS;

ANIMALIA;

ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; GENETIC ASSOCIATION; GENOTYPE; HUMAN; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SOFTWARE;

EID: 77951152163     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-134     Document Type: Article

References (30)

1. 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(23):9362-9367. 10.1073/pnas.0903103106, 2687147,2687147, 19474294.
2. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81(3):559-575. 10.1086/519795, 1950838, 17701901.
3. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics 2007, 23(10):1294-1296. 10.1093/bioinformatics/btm108, 17384015.
4. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007, 39(7):906-913. 10.1038/ng2088, 17572673.
5. Clayton D, Leung HT. An R package for analysis of whole-genome association studies. Hum Hered 2007, 64:45-51. 10.1159/000101422, 17483596.
6. Li Y, Abecasis G. Mach 1.0: Rapid Haplotype Reconstruction and Missing Genotype Inference. American Journal of Human Genetics 2006, S79:2290.
7. Li Y, Willer C, Sanna S, Abecasis G. Genotype imputation. Annu Rev Genomics Hum Genet 2009, 10:387-406. 10.1146/annurev.genom.9.081307.164242, 19715440.
8. Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 2007, 3(7):e114. 10.1371/journal.pgen.0030114, 1934390, 17676998.
9. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009, 5(6):e1000529. 10.1371/journal.pgen.1000529, 2689936, 19543373.
10. Devlin B, Roeder K. Genomic control for association studies. Biometrics 1999, 55(4):997-1004. 10.1111/j.0006-341X.1999.00997.x, 11315092.
11. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006, 38(8):904-909. 10.1038/ng1847, 16862161.
12. Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 2006, 38(2):203-208. 10.1038/ng1702, 16380716.
13. Aulchenko YS, de Koning DJ, Haley C. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 2007, 177:577-585. 10.1534/genetics.107.075614, 2013682, 17660554.
14. Chen WM, Abecasis GR. Family-based association tests for genomewide association scans. Am J Hum Genet 2007, 81(5):913-926. 10.1086/521580, 2265659, 17924335.
15. Amin N, van Duijn CM, Aulchenko YS. A genomic background based method for association analysis in related individuals. PLoS One 2007, 2(12):e1274. 10.1371/journal.pone.0001274, 2093991, 18060068.
16. McCulloch CE, Searle SR. Generalized, Linear, and Mixed Models 2001, John Wiley & Sons, Inc.
17. White H. A Heteroskedasticity-Consistent Covariance Matrix and a Direct Test for Heteroskedasticity. Econometrica 1980, 48:817-838.
18. Zeileis A. Econometric Computing with HC and HAC Covariance Matrix Estimators. Journal of Statistical Software 2004, 11:1-17.
19. Astle W, Balding DJ. Population structure and cryptic relatedness in genetic association studies. Statistical Science
20. Pardo LM, MacKay I, Oostra B, van Duijn CM, Aulchenko YS. The effect of genetic drift in a young genetically isolated population. Ann Hum Genet 2005, 69(Pt 3):288-295. 10.1046/J.1469-1809.2005.00162.x, 15845033.
21. Anderson CA, Pettersson FH, Barrett JC, Zhuang JJ, Ragoussis J, Cardon LR, Morris AP. Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms. Am J Hum Genet 2008, 83:112-119. 10.1016/j.ajhg.2008.06.008, 2443836, 18589396.
22. Hao K, Chudin E, McElwee J, Schadt EE. Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies. BMC Genet 2009, 10:27. 10.1186/1471-2156-10-27, 2709633, 19531258.
23. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002, 30:97-101. 10.1038/ng786, 11731797.
24. Perez-Enciso M, Misztal I. Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics 2004, 20(16):2792-2798. 10.1093/bioinformatics/bth331, 15166025.
25. Kim W, Gordon D, Sebat J, Ye KQ, Finch SJ. Computing power and sample size for case-control association studies with copy number polymorphism: application of mixture-based likelihood ratio test. PLoS One 2008, 3(10):e3475. 10.1371/journal.pone.0003475, 2566806, 18941524.
26. Axenovich TI, Zorkoltseva IV, Belonogova NM, Struchalin MV, Kirichenko AV, Kayser M, Oostra BA, van Duijn CM, Aulchenko YS. Linkage analysis of adult height in a large pedigree from a Dutch genetically isolated population. Hum Genet 2009, 126(3):457-471. 10.1007/s00439-009-0686-x, 19466457.
27. Estrada K, Krawczak M, Schreiber S, van Duijn K, Stolk L, van Meurs JBJ, Liu F, Penninx BWJH, Smit JH, Vogelzangs N, Hottenga JJ, Willemsen G, de Geus EJC, Lorentzon M, von Eller-Eberstein H, Lips P, Schoor N, Pop V, de Keijzer J, Hofman A, Aulchenko YS, Oostra BA, Ohlsson C, Boomsma DI, Uitterlinden AG, van Duijn CM, Rivadeneira F, Kayser M. A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the etiology of human height variation. Hum Mol Genet 2009, 18(18):3516-3524. 10.1093/hmg/ddp296, 2729669, 19570815.
28. Woodward OM, Koettgen A, Coresh J, Boerwinkle E, Guggino WB, Koettgen M. Identification of a urate transporter, ABCG2, with a common functional polymorphism causing gout. Proc Natl Acad Sci USA 2009, 106(25):10338-10342. 10.1073/pnas.0901249106, 2700910, 19506252.
29. Heard-Costa NL, Zillikens MC, Monda KL, Johansson A, Harris TB, Fu M, Haritunians T, Feitosa MF, Aspelund T, Eiriksdottir G, Garcia M, Launer LJ, Smith AV, Mitchell BD, McArdle PF, Shuldiner AR, Bielinski SJ, Boerwinkle E, Brancati F, Demerath EW, Pankow JS, Arnold AM, Chen YDI, Glazer NL, McKnight B, Psaty BM, Rotter JI, Amin N, Campbell H, Gyllensten U, Pattaro C, Pramstaller PP, Rudan I, Struchalin M, Vitart V, Gao X, Kraja A, Province MA, Zhang Q, Atwood LD, Dupuis J, Hirschhorn JN, Jaquish CE, O'Donnell CJ, Vasan RS, White CC, Aulchenko YS, Estrada K, Hofman A, Rivadeneira F, Uitterlinden AG, Witteman JCM, Oostra BA, Kaplan RC, Gudnason V, O'Connell JR, Borecki IB, van Duijn CM, Cupples LA, Fox CS, North KE. NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. PLoS Genet 2009, 5(6):e1000539. 10.1371/journal.pgen.1000539, 2695005, 19557197.
30. Vink JM, Smit AB, de Geus EJC, Sullivan P, Willemsen G, Hottenga JJ, Smit JH, Hoogendijk WJ, Zitman FG, Peltonen L, Kaprio J, Pedersen NL, Magnusson PK, Spector TD, Kyvik KO, Morley KI, Heath AC, Martin NG, Westendorp RGJ, Slagboom PE, Tiemeier H, Hofman A, Uitterlinden AG, Aulchenko YS, Amin N, van Duijn C, Penninx BW, Boomsma DI. Genome-wide association study of smoking initiation and current smoking. Am J Hum Genet 2009, 84(3):367-379. 10.1016/j.ajhg.2009.02.001, 2667987, 19268276.