A comparison of strategies for analyzing dichotomous outcomes in genome-wide association studies with general pedigrees

Genetic Epidemiology

Volumn 35, Issue 7, 2011, Pages 650-657

  Chen, Ming Huei ^a,b,c   Liu, Xuan ^b   Wei, Fengrong ^d   Larson, Martin G ^b,c,e   Fox, Caroline S ^c,f   Vasan, Ramachandran S ^a,c   Yang, Qiong ^b,c  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

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

^c FRAMINGHAM HEART STUDY   (United States)

^d UNIVERSITY OF WEST GEORGIA   (United States)

^e Boston University   (United States)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Dichotomous phenotypes; Familial relatedness; Genetic association

Indexed keywords

ARTICLE; CORRELATION ANALYSIS; GENETIC ASSOCIATION; GENETIC MODEL; GENETIC VARIABILITY; MULTIPLE REGRESSION; PHENOTYPE; TASK PERFORMANCE;

COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; GOUT; HUMANS; LINEAR MODELS; MODELS, GENETIC; PEDIGREE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SAMPLE SIZE;

EID: 80054731679     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20614     Document Type: Article

References (18)

1. Almasy L, Blangero J. 1998. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
2. Atkinson B, Therneau T, Zhao JH. 2009. Kinship: mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees. Available at:.
3. Bates DM, DebRoy S. 2004. Linear mixed models and penalized least squares. J Multivariate Anal 91:1-17.
4. Breslow NE, Clayton DG. 1993. Approximate inference in generalized linear mixed models. J Am Stat Assoc 88:9-25.
5. Browning SR, Briley JD, Briley LP, Chandra G, Charnecki JH, Ehm MG, Johansson KA, Jones BJ, Karter AJ, Yarnall DP, Wagner MJ. 2005. Case-control single-marker and haplotypic association analysis of pedigree data. Genet Epidemiol 28:110-122.
6. Chen MH, Yang Q. 2010. GWAF: an R package for genome-wide association analyses with family data. Bioinformatics 26:580-581.
7. Hauck Jr WW, Donner A. 1977. Wald's test as applied to hypotheses in logit analysis. J Am Stat Assoc 72:851-853.
8. Kang, HM, Sul JH, Service SK, Zaitlen NA, Kong S, Freimer NB, Sabattisabatti C, Eskineeskin E. 2010. Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42:348-354.
9. Kauermann G, Carroll RJ. 2001.A note on the efficiency of sandwich covariance matrix estimation. J Am Stat Assoc 96:1387-1396.
10. Liang KY, Zeger SL. 1986. Longitudinal data analysis using generalized linear models. Biometrika 73:13-22.
11. Lipsitz SR, Dear BG, Zhao LP. 1994. Jackknife estimators of variance for parameter estimated from estimating equations with applications to clustered survival data. Biometrics 50:842-846.
12. Paik MC. 1988. Repeated measurement analysis for nonnormal data in small samples. Commun Stat B Simulation Comput 17:1155-1171.
13. Pinheiro JC, Bates DM. 1995. Approximations to the log-likelihood function in the nonlinear mixed-effects model. J Comput Graph Stat 4:12-35.
14. Slager SL, Schaid DJ. 2001. Evaluation of candidate genes in case-control studies: a statistical method to account for related subjects. Am J Hum Genet 68:1457-1462.
15. Slager SL, Schaid DJ, Wang L, Thibodeau SN. 2003. Candidate-gene association studies with pedigree data: controlling for environmental covariates. Genet Epidemiol 24:273-283.
16. Yan J, Fine J. 2004. Estimating equations for association structures. Stat Med 23:859-874.
17. Yang Q, Köttgen A, Dehghan A, Smith AV, Glazer NL, Chen MH, Chasman DI, Aspelund T, Eiriksdottir G, Harris TB, Launer L, Nalls M, Hernandez D, Arking DE, Boerwinkle E, Grove ML, Li M, Kao WL, Chonchol M, Haritunians T, Li G, Lumley T, Psaty BM, Shlipak M, Hwang SJ, Larson MG, O'Donnell CJ, Upadhyay A, van Duijn CM, Hofman A, Rivadeneira F, Stricker B, Uitterlinden AG, Paré G, Parker AN, Ridker PM, Siscovick DS, Gudnason V, Witteman JC, Fox CS, Coresh J. 2010. Multiple genetic loci influence serum urate and their relationship with gout and cardiovascular disease risk factors. Circ Cardiovasc Genet 3:523-530.
18. Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES. 2010. Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355-360.