Statistical Tests of genetic association in the presence of gene-gene and gene-environment interactions

Human Heredity

Volumn 69, Issue 2, 2010, Pages 131-142

  Pan, Wei ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Epistasis; Genome wide association study; Logistic regression; Main effects model; Score test; SNP; Sum of squared score tests

Indexed keywords

AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; CONTROLLED STUDY; GENE INTERACTION; GENETIC ASSOCIATION; GENOTYPE ENVIRONMENT INTERACTION; HUMAN; MATHEMATICAL GENETICS; MULTIVARIATE ANALYSIS; PARTIAL LEAST SQUARES REGRESSION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ENVIRONMENT; EPISTASIS, GENETIC; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, GENETIC;

EID: 71249121016     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000264450     Document Type: Article

References (31)

1. Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and hap-lotype maps. Bioinformatics 2005; 21:263-265.
2. Chatterjee N, Carroll RJ: Semiparametric maximum-likelihood estimation exploiting gene-environment independence in case-control studies. Biometrika 2005; 92:399-418.
3. Chatterjee N, Kalaliouglu Z, Moslehi R, Peters U, Wacholder S: Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions. Am J Hum Genet 2006: 79:1002-1016.
4. Clayton D, Chapman J, Cooper J: Use of un-phased multilocus genotype data in indirect association studies. Genet Epidemiol 2004; 27: 415-4 28.
5. Cox DR, Hinkley DV: Theoretical Statistics, Chapman and Hall, London.
6. Evans DM, Marchini J, Morris AP, Cardon LR: Two-stage two-locus models in genome-w ide association. PLoS Genet 2006; 2:e157.
7. Goeman JJ, van de Geer S, van Houwelingen HC: Testing against a high dimensional alternative. J R Stat Soc B 2006; 68:477-493.
8. Guo Y, Li J, Bonham A, Wang Y, Deng H: Gain in power for exhaustive analyses of haplo-types using variable-sized sliding window strategy: a comparison of association mapping strategies. To appear Eur J Hum Genet, 2009. Published on-line.
9. Johnson NL, Kotz S: Distributions in Statistics, Continuous Univariate Distributions, vol 2. Boston: Houghton-Miffin, 1970.
10. Kooperberg C, LeBlanc M: Increasing the power of identifying gene ! gene interactions in genome-wide association studies. Genet Epidemiol 2008;32:255-263.
11. Lou X, Chen G, Yan L, Ma JZ, Zhu J, Elston RC, Li MD: A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence. Am J Hum Genet 2007; 80: 11 2 5-113 7.
12. Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005; 37:413-417.
13. 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: 906-913. (Pubitemid 47014502)
14. Millstein J, Conti DV, Gilliland FD, Gauderman WJ: A testing framework for identifying susceptibility genes in the presence of epistasis. Am J Hum Genet 20 06; 78: 15-27.
15. Moore JH: The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 2003; 56:73-82.
16. Mukherjee B, Chatterjee N: Exploiting gene-environment in dependence for analysis of case-control studies: an empirical-Bayes type shrinkage estimator to trade off between bias and efficiency. Biometrics 2008; 64: 685-694.
17. Musani SK, Shriner D, Liu N, Feng R, Coffey CS, Yi N, Tiwari HK, Allison DB: Detection of gene ! gene interactions in genome-wide association studies of human population data. Hum Hered 2007; 63: 67-84.
18. Pan W: Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol 2009;33:497-507.
19. Piegorsch WW, Weinberg CR, Taylor JA: Non-hierarchical logistic models and case-only designs for assessing susceptibility in population based case-control studies. Stat Med 1994; 13:153-162.
20. Roeder K, Bacanu SA, Sonpar V, Zhang X, Devlin B: Analysis of single-locus tests to detect gene/disease associations. Genet Epidemiol 2005; 28:207-219.
21. Schymick JC, Scholz SW, Fung HC, et al: Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2007; 6:322-328.
22. Seaman SR, Muller-Myhsok B: Rapid simulation of p values for product methods and multiple testing adjustment in association studies. Am J Hum Genet 2005; 76: 399-408.
23. Servin B, Stephens M: Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genetics 2007; 3:e114.
24. Song M, Nicolae DL: Restricted parameter space models for testing gene-gene interaction. To appear Genet Epidemiol, 2008.
25. Tang HK, Siegmund D: Mapping multiple genes for quantitative or complex traits. Genet Epidemiol 2002;22:313-327.
26. Wang K: Genetic association tests in the presence of epistasis or gene-environment interaction. Genet Epidemiol 2008; 32:606-614.
27. Wang T, Ho G, Ye K, Strickler H, Elston RC: A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped. Genet Epidemiol 2009; 33: 6-15.
28. Zhang JT: Approximate and asymptotic distributions of Chi-squared-type mixtures with applications. J Am Stat Assoc 2005; 100:273-285.
29. Zhang Y, Liu JS: Bayesian inference of epistatic interactions in case-control studies. Nat Genet 2007; 39: 116 7-117 3.
30. Zhao JY, Jin L, Xiong MM: Test for interaction between two unlinked loci. Am J Hum Ge-net 20 06; 79: 831-845.
31. Zheng T, Wang H, Lo SH: Backward genotype-trait Association (BGTA)-based dissection of complex traits in case-control design. Hum Hered 2006; 62:196-212.