Exploiting gene-environment independence for analysis of case-control studies: An empirical Bayes-type shrinkage estimator to trade-off between bias and efficiency

Biometrics

Volumn 64, Issue 3, 2008, Pages 685-694

  Mukherjee, Bhramar ^a   Chatterjee, Nilanjan ^b  

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

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Case only designs; Gene environment interaction; Profile likelihood; Retrospective analysis; Semiparametrics

Indexed keywords

ECONOMIC AND SOCIAL EFFECTS; EFFICIENCY; MAXIMUM LIKELIHOOD ESTIMATION; REGRESSION ANALYSIS; SHRINKAGE;

CASE-CONTROL; CASE-CONTROL STUDY; CASE-ONLY DESIGN; CONTROL DATA; EMPIRICAL BAYES; GENE-ENVIRONMENT INTERACTION; PROFILE LIKELIHOOD; RETROSPECTIVE ANALYSIS; SEMIPARAMETRIC; SHRINKAGE ESTIMATOR;

GENES;

BAYESIAN ANALYSIS; EMPIRICAL ANALYSIS; GENOTYPE; MAXIMUM LIKELIHOOD ANALYSIS; REGRESSION ANALYSIS;

ARTICLE; CASE CONTROL STUDY; ENVIRONMENTAL FACTOR; EXPOSURE; GENE INTERACTION; RETROSPECTIVE STUDY;

EID: 49749089301     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2007.00953.x     Document Type: Article

References (27)

1. Albert, P. S., Ratnasinghe, D., Tangrea, J., and Wacholder, S. (2001). Limitations of the case-only design for identifying gene-environment interactions. American Journal of Epidemiology 154, 687 693.
2. Andersen, E. B. (1970). Asymptotic properties of conditional maximum likelihood estimators. Journal of the Royal Statistical Society, Series B 32, 283 301.
3. Berger, J. O. (1985). Statistical Decision Theory and Bayesian Analysis. New York : Springer Verlag.
4. Carlin, B. P. and Louis, T. A. (2000). Bayes and empirical Bayes methods for data analysis, 2nd edition. Boca Raton, FL : Chapman and Hall/CRC Press.
5. Chatterjee, N. and Carroll, R. J. (2005). Semiparametric maximum likelihood estimation exploiting gene-environment independence in case-control studies. Biometrika 92, 399 418.
6. Chen, J. and Chatterjee, N. (2007). Exploiting Hardy-Weinberg equilibrium for efficient screening of single SNP associations from case-control studies. Human Heredity 63, 196 204.
7. Cox, D. R. (1975). A note on partially Bayes inference and the linear model. Biometrika 62, 651 654.
8. Efron, B. (1993). Bayes and likelihood calculations from confidence intervals. Biometrika 80, 3 26.
9. Efron, B. and Morris, C. (1972). Empirical Bayes on vector observations: An extension of Stein's method. Biometrika 59, 335 347.
10. Epstein, M. P. and Satten, G. A. (2003). Inference on haplotype effects in case-control studies using unphased genotype data. American Journal of Human Genetics 73, 1316 1329.
11. Gohagan J. K., Prorok P. C., Hayes R. B., and Kramer B. S. (2000). Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial Project Team. Design of the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. Controlled Clinical Trials 21 (6 suppl. 273S 309S.
12. Greenland, S. (1993). Methods for epidemiologic analyses of multiple exposures: A review and comparative study of maximum likelihood, preliminary-testing, and empirical Bayes regression. Statistics in Medicine 12, 717 736.
13. Hayes R. B., Sigurdson A., Moore L., Peters U., Huang W. Y., Pinsky P., Reding D., Gelmann E. P., Rothman N., Pfeiffer R. M., Hoover R. N., and Berg C. D. (2005). Methods for etiologic and early marker investigations in the PLCO Trial. Mutation Research 592, 147 154.
14. Lin, D. Y. and Zeng, D. (2006). Likelihood-based inference on haplotype effects in genetic association studies. Journal of the American Statistical Association 101, 89 104.
15. Liu, X., Fallin, M. D., and Kao, W. H. (2004). Genetic dissection methods: Designs used for tests of gene-environment interaction. Current Opinions in Genetics and Development 14, 241 245.
16. Marcus, P. M., Hayes, R. B., Vineis, P., et al. (2000). Cigarette smoking: N-acteyltransferease 2 acetylation status, and bladder cancer risk: A case series meta-analysis of a gene-environment interaction. Cancer Epidemiology, Biomarkers and Prevention 9, 461 467.
17. Modan, B., Hartge, P., Hirsh-Yechezkel, G., et al. (2001). Parity, oral contraceptives and the risk of ovarian cancer among carriers and non-carriers of a BRCA1 or BRCA2 mutation. New England Journal of Medicine 345, 235 240.
18. Morris, C. N. (1983). Parametric empirical Bayes inference: Theory and applications. Journal of the American Statistical Association 78, 47 55.
19. Moslehi, R., Chatterjee, N., Church, T. R., Chen, J., Yeager, M., Weissfield, J., Hein, D. W., and Hayes, R. B. (2006). Cigarette smoking n-acetyltransferase genes and the risk of advanced colorectal adenoma. Pharmacogenomics 7, 819 829.
20. Piegorsch, W. W., Weinberg, C. R., and Taylor, J. (1994). Nonhierarchical logistic models and case-only designs for assessing susceptibility in population-based case-control studies. Statistics in Medicine 13, 153 162.
21. Prentice, R. L. and Pyke, R. (1979). Logistic disease incidence models and case-control studies. Biometrika 66, 403 411.
22. Satten, G. A. and Epstein, M. P. (2004). Comparison of prospective and retrospective methods for haplotype inference in case-control studies. Genetic Epidemiology 27, 192 201.
23. Satten, G. A. and Kupper, L. L. (1993). Inferences about exposure-disease associations using probability-of-exposure information. Journal of the American Statistical Association 88, 200 208.
24. Schmidt, S. and Schaid, D. J. (1999). Potential misinterpretation of the case-only study to assess gene-environment interaction. American Journal of Epidemiology 150, 878 885.
25. Spinka, C., Carroll, R. J., and Chatterjee, N. (2005). Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity. Genetic Epidemiology 29, 108 127.
26. Tibshirani, R. (1989). Noninformative priors for one parameter of many. Biometrika 76, 604 608.
27. Umbach, D. M. and Weinberg, C. R. (1997). Designing and analysing case-control studies to exploit independence of genotype and exposure. Statistics in Medicine 16, 1731 1743.