Analyze multivariate phenotypes in genetic association studies by combining univariate association tests

Genetic Epidemiology

Volumn 34, Issue 5, 2010, Pages 444-454

  Yang, Qiong ^a,b   Wu, Hongsheng ^a,c   Guo, Chao Yu ^d,e   Fox, Caroline S ^b,f  

^a BOSTON UNIVERSITY SCHOOL OF PUBLIC HEALTH   (United States)

^b FRAMINGHAM HEART STUDY   (United States)

^c WENTWORTH INSTITUTE OF TECHNOLOGY   (United States)

^d BOSTON CHILDREN S HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Categorical data; Genetic association study; Genome wide association study; Multivariate phenotype; O'Brien's statistic

Indexed keywords

ARTICLE; GENETIC ASSOCIATION; GOUT; INTERMETHOD COMPARISON; MULTIVARIATE ANALYSIS; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM; UNIVARIATE ANALYSIS; URIC ACID BLOOD LEVEL;

ANALYSIS OF VARIANCE; GENETIC LINKAGE; GENETIC VARIATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GOUT; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; URIC ACID;

EID: 77954187595     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20497     Document Type: Article

References (38)

1. Abecasis GR, Cardon LR, Cookson WO, Sham PC, Cherny SS. 2001. Association analysis in a variance components framework. Genet Epidemiol 21:S341-S346.
2. Almasy L, Blangero J. 1998. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62: 1198-1211. (Pubitemid 28199022)
3. Choi HK, Mount DB, Reginato AM, American College of Physicians, American Physiological Society. 2005. Pathogenesis of gout. Ann Intern Med 143:499-516.
4. Crowley LV. 1964. Determination of uric acid: an automated analysis based on a carbonate method. Clin Chem 10:838-844.
5. Dawber TR, Kannel WB, Lyell LP. 1963. An approach to longitudinal studies in a community: the Framingham Study. Ann N Y Acad Sci 107:539-556.
6. Dehghan A, Kottgen A, Yang Q, Hwang SJ, Kao WL, Rivadeneira F, Boerwinkle E, Levy D, Hofman A, Astor BC, Benjamin EJ, van Duijn CM, Witteman JC, Coresh J, Fox CS. 2008. Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study. Lancet 372:1953-1961.
7. Devlin B, Roeder K. 1999. Genomic control for association studies. Biometrics 55:997-1004.
8. Feig DI, Kang DH, Johnson RJ. 2008. Uric acid and cardiovascular risk. N Engl J Med 359:1811-1821.
9. Feinleib M, Kannel WB, Garrison RJ, McNamara PM, Castelli WP. 1975. The Framingham Offspring Study. Design and preliminary data. Prev Med 4:518-525.
10. Fitzmaurice GM, Laird NM. 1993. A likelihood-based method for analysing longitudinal binary responses. Biometrika 80:141-151.
11. Fitzmaurice GM, Laird NM. 1997. Regression models for mixed discrete and continuous responses with potentially missing values. Biometrics 53:110-122.
12. Gordon A, Glazko G, Qiu X, Yakovlev A. 2007. Control of the mean number of false discoveries, bonferroni and stability of multiple testing. Ann Appl Stat 1:179-190.
13. Hastie T, Tibshirani R, Friedman JH. 2003. Cross-Validation in the Elements of Statistical Learning. New York: Springer. p 214-217.
14. International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallee C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archeveque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
15. Klei L, Luca D, Devlin B, Roeder K. 2008. Pleiotropy and principal components of heritability combine to increase power for association analysis. Genet Epidemiol 32:9-19.
16. Kolz M, Johnson T, Sanna S, Teumer A, Vitart V, Perola M, Mangino M, Albrecht E, Wallace C, Farrall M, Johansson A, Nyholt DR, Aulchenko Y, Beckmann JS, Bergmann S, Bochud M, Brown M, Campbell H, EUROSPAN Consortium, Connell J, Dominiczak A, Homuth G, Lamina C, McCarthy MI, ENGAGE Consortium, Meitinger T, Mooser V, Munroe P, Nauck M, Peden J, Prokisch H, Salo P, Salomaa V, Samani NJ, Schlessinger D, Uda M, Volker U, Waeber G, Waterworth D, Wang-Sattler R, Wright AF, Adamski J, Whitfield JB, Gyllensten U, Wilson JF, Rudan I, Pramstaller P, Watkins H, PROCARDIS Consortium, Doering A, Wichmann HE, KORA Study, Spector TD, Peltonen L, Volzke H, Nagaraja R, Vollenweider P, Caulfield M, WTCCC, Illig T, Gieger C. 2009. Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. PLoS Genet 5:e1000504.
17. Laird NM, Ware JH. 1982. Random-effects models for longitudinal data. Biometrics 38:963-974.
18. Lange C, van Steen K, Andrew T, Lyon H, DeMeo DL, Raby B, Murphy A, Silverman EK, MacGregor A, Weiss ST, Laird NM. 2004. A family-based association test for repeatedly measured quantitative traits adjusting for unknown environmental and/or polygenic effects. Stat Appl Genet Mol Biol 3:Article17.
19. Lawrence RC, Felson DT, Helmick CG, Arnold LM, Choi H, Deyo RA, Gabriel S, Hirsch R, Hochberg MC, Hunder GG, Jordan JM, Katz JN, Kremers HM, Wolfe F, National Arthritis Data Workgroup. 2008. Estimates of the prevalence of arthritis and other rheumatic conditions in the United States. Part II. Arthritis Rheum 58:26-35.
20. Li S, Sanna S, Maschio A, Busonero F, Usala G, Mulas A, Lai S, Dei M, Orru M, Albai G, Bandinelli S, Schlessinger D, Lakatta E, Scuteri A, Najjar SS, Guralnik J, Naitza S, Crisponi L, Cao A, Abecasis G, Ferrucci L, Uda M, Chen WM, Nagaraja R. 2007. The GLUT9 gene is associated with serum uric acid levels in Sardinia and Chianti cohorts. PLoS Genet 3:e194.
21. Liang K, Zeger SL. 1986. Longitudinal data analysis using generalized linear models. Biometrika 73:13-22.
22. Liang S, Gong F, Zhao X, Wang X, Shen G, Xu Y, Yang H, Ruan X, Wei Y. 2009. Prokaryotic expression, purification of a new tumor-relative protein FAM92A1-289 and its characterization in renal cell carcinoma. Cancer Lett 276:81-87.
23. Liu J, Pei Y, Papasian CJ, Deng HW. 2009. Bivariate association analyses for the mixture of continuous and binary traits with the use of extended generalized estimating equations. Genet Epidemiol 33:217-227.
24. Lynch KJ, Touma E, Niforatos W, Kage KL, Burgard EC, van Biesen T, Kowaluk EA, Jarvis MF. 1999. Molecular and functional characterization of human P2X(2) receptors. Mol Pharmacol 56:1171-1181.
25. Manolio TA, Brooks LD, Collins FS. 2008. A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118:1590-1605. (Pubitemid 351632361)
26. O'Brien PC. 1984. Procedures for comparing samples with multiple endpoints. Biometrics 40:1079-1087.
27. Orho-Melander M, Melander O, Guiducci C, Perez-Martinez P, Corella D, Roos C, Tewhey R, Rieder MJ, Hall J, Abecasis G, Tai ES, Welch C, Arnett DK, Lyssenko V, Lindholm E, Saxena R, de Bakker PI, Burtt N, Voight BF, Hirschhorn JN, Tucker KL, Hedner T, Tuomi T, Isomaa B, Eriksson KF, Taskinen MR, Wahlstrand B, Hughes TE, Parnell LD, Lai CQ, Berglund G, Peltonen L, Vartiainen E, Jousilahti P, Havulinna AS, Salomaa V, Nilsson P, Groop L, Altshuler D, Ordovas JM, Kathiresan S. 2008. Common missense variant in the glucokinase regulatory protein gene is associated with increased plasma triglyceride and C-reactive protein but lower fasting glucose concentrations. Diabetes 57:3112-3121.
28. Rifai N, Ridker PM. 2002. Inflammatory markers and coronary heart disease. Curr Opin Lipidol 13:383-389. (Pubitemid 34831941)
29. Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science 273:1516-1517. (Pubitemid 26301653)
30. Schwarcz R. 2004. The kynurenine pathway of tryptophan degradation as a drug target. Curr Opin Pharmacol 4:12-17. (Pubitemid 38145832)
31. Splansky GL, Corey D, Yang Q, Atwood LD, Cupples LA, Benjamin EJ, D'Agostino RBS, Fox CS, Larson MG, Murabito JM, O'Donnell CJ, Vasan RS, Wolf PA, Levy D. 2007. The Third Generation Cohort of the National Heart, Lung, and Blood Institute's Framingham Heart Study: design, recruitment, and initial examination. Am J Epidemiol 165:1328-1335. (Pubitemid 47234329)
32. Wallace C, Newhouse SJ, Braund P, Zhang F, Tobin M, Falchi M, Ahmadi K, Dobson RJ, Marcano AC, Hajat C, Burton P, Deloukas P, Brown M, Connell JM, Dominiczak A, Lathrop GM, Webster J, Farrall M, Spector T, Samani NJ, Caulfield MJ, Munroe PB. 2008. Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. Am J Hum Genet 82:139-149.
33. Wei LJ, Johnson WE. 1985. Combining dependent tests with incomplete repeated measurements. Biometrika 72:359-364.
34. Woodward OM, Kottgen A, Coresh J, Boerwinkle E, Guggino WB, Kottgen M. 2009. Identification of a urate transporter, ABCG2, with a common functional polymorphism causing gout. Proc Natl Acad Sci USA 106:10338-10342.
35. Xu X, Tian L, Wei LJ. 2003. Combining dependent tests for linkage or association across multiple phenotypic traits. Biostatistics 4:223-229.
36. Yang Q, Guo CY, Cupples LA, Levy D, Wilson PW, Fox CS. 2005. Genome-wide search for genes affecting serum uric acid levels: the Framingham Heart Study. Metabolism 54:1435-1441. (Pubitemid 41527011)
37. Yudkin JS, Kumari M, Humphries SE, Mohamed-Ali V. 2000. Inflammation, obesity, stress and coronary heart disease: is interleukin-6 the link? Atherosclerosis 148:209-214.
38. Zhang Y, Zhang KX, He X, Yuan WT, Wang GL, Mao SY, Gao PJ, Huang W, Zhu DL. 2005. A polymorphism of kynureninase gene in a hypertensive candidate chromosomal region is associated with essential hypertension. Zhonghua Xin Xue Guan Bing Za Zhi 33:588-591. (Pubitemid 41371801)