Comparison of different haplotype-based haplotype-based association methods for gene-environment (GxE) interactions in case-control studies when haplotype-phase is ambiguous

Human Heredity

Volumn 68, Issue 4, 2009, Pages 252-267

  Hein, Rebecca ^a   Beckmann, Lars ^a   Chang Claude, Jenny ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Case control studies; Expectation maximization algorithm; Hardy Weinberg equilibrium; Indirect association; Linkage disequilibrium; Logistic regression; Retrospective and prospective likelihood

Indexed keywords

ARTICLE; GENE INTERACTION; GENETIC ANALYSIS; GENOTYPE; HAPLOTYPE; RISK FACTOR; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; COMPUTER SIMULATION; ENVIRONMENT; GENES; GENETIC PREDISPOSITION TO DISEASE; GENETIC TECHNIQUES; HAPLOTYPES; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; REGRESSION ANALYSIS;

EID: 67650702872     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000228923     Document Type: Article

References (36)

1. Hirschhorn JN: Genetic approaches to studying common diseases and complex traits. Pediatr Res 2005; 57: 74R-77R.
2. Akey J, Jin L, Xiong M: Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur J Hum Genet 2001;9:291-300.
3. Clark AG: Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 1990;7:111-122. (Pubitemid 20129868)
4. Dempster AP, Laird NM, Rubin DB: Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc 1977;39:1-38.
5. Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995;12:921-927.
6. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001;68:978-989. (Pubitemid 32289743)
7. Niu T, Qin ZS, Xu X, Liu JS: Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 2002;70:157-169. (Pubitemid 34031705)
8. Lake SL, Lyon H, Tantisira K, Silverman EK, Weiss ST, Laird NM, Schaid DJ: Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous. Hum Hered 2003;55:56-65. (Pubitemid 36928747)
9. Tregouet DA, Barbaux S, Escolano S, Tahri N, Golmard JL, Tiret L, Cambien F: Specific haplotypes of the P-selectin gene are associated with myocardial infarction. Hum Mol Genet 2002;11:2015-2023. (Pubitemid 34919276)
10. Tregouet DA, Escolano S, Tiret L, Mallet A, Golmard JL: A new algorithm for haplotypebased association analysis: the Stochastic- EM algorithm. Ann Hum Genet 2004;68:165-177. (Pubitemid 38379847)
11. Lin DY, Zeng D, Millikan R: Maximum likelihood estimation of haplotype effects and haplotype-environment interactions in association studies. Genet Epidemiol 2005;29:299-312.
12. Lin DY, Zeng D: Likelihood-based inference on haplotype effects in genetic association studies. J Am Stat Assoc 2006;101:89-118.
13. Chen YH, Chatterjee N, Carroll RJ: Retrospective analysis of haplotype-based case control studies under a flexible model for gene environment association. Biostatistics 2008; 9: 81-99. (Pubitemid 350274583)
14. Prentice RL, Pyke R: Logistic disease incidence models and case-control studies. Biometrika 1979;66:403-411.
15. Rabinowitz D: A note on efficient estimation from case-control data. Biometrika 1997;84:486-488.
16. Breslow NE, Robins JM, Wellner JA: On the semi-parametric efficiency of logistic regression under case-control sampling. Bernoulli 2000;6:447-455.
17. Epstein MP, Satten GA: Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 2003;73:1316-1329.
18. Chatterjee N, Carroll RJ: Semiparametric maximum likelihood estimation exploiting gene-environment independence in casecontrol studies. Biometrika 2005;92:399-418. (Pubitemid 40937643)
19. Satten GA, Epstein MP: Comparison of prospective and retrospective methods for haplotype inference in case-control studies. Genet Epidemiol 2004;27:192-201. (Pubitemid 39447242)
20. Spinka C, Carroll RJ, Chatterjee N: Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity. Genet Epidemiol 2005;29:108-127. (Pubitemid 41209166)
21. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA: Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 2002;70:425-434.
22. R Development Core Team: R: A Language and Environment for Statistical Computing. 2005. Vienna, Austria, R Foundation for Statistical Computing. Ref Type: Computer Program.
23. Sinnwell JP, Schaid DJ, Yu Z. haplo.stats: Statistical Analysis of Haplotypes with Traits anc Covariates when Linkage Phase is Ambiguous. 2007. R package version 1.3.1. Ref Type: Computer Program.
24. Diebolt J, Ip EHS: Stochastic EM: method and application; in Gilks WR, Richardson S, Spiegelhalter DJ (eds): Markov Chain Monte Carlo in practice. London, Chapman and Hall, 1996.
25. Ip EHS: Using the Stochastic EM Estimator in the Presence of Missing Data - Theory and Applications. Department of Biostatistics, Stanford University 1994.
26. Tregouet DA, Garelle V: A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies. Bioinformatics 2007;23:1038-1039.
27. Fallin D, Schork NJ: Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 2000;67:947-959. (Pubitemid 30740145)
28. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA: Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 2002;70:425-434.
29. Zhao LP, Li SS, Khalid N: A method for the assessment of disease associations with single- nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet 2003;72:1231-1250.
30. Cordell HJ: Estimation and testing of genotype and haplotype effects in case-control studies: comparison of weighted regression and multiple imputation procedures. Genet Epidemiol 2006;30:259-275.
31. Zondervan KT, Cardon LR: The complex interplay among factors that influence allelic association. Nat Rev Genet 2004;5:89-100.
32. Hein R, Beckmann L, Chang-Claude J: Sample size requirements for indirect association studies of gene-environment interactions (G x E). Genet Epidemiol 2008;32:235-245. (Pubitemid 351550370)
33. Fallin D, Schork NJ: Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 2000;67:947-959. (Pubitemid 30740145)
34. Balding DJ: A tutorial on statistical methods for population association studies. Nat Rev Genet 2006;7:781-791. (Pubitemid 44413222)
35. Stram DO, Leigh PC, Bretsky P, Freedman M, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Thomas DC: Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals. Hum Hered 2003;55:179-190. (Pubitemid 37323455)
36. Piegorsch WW, Weinberg CR, Taylor JA: Non-hierarchical logistic models and caseonly designs for assessing susceptibility in population-based case-control studies. Stat Med 30-1-1994;13:153-162.