Shrinkage estimators for robust and efficient inference in haplotype-based case-control studies

Journal of the American Statistical Association

Volumn 104, Issue 485, 2009, Pages 220-233

  Chen, Yi Hau ^a   Chatterjee, Nilanjan ^b   Carroll, Raymond J ^c  

^a INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

^b NATIONAL CANCER INSTITUTE   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Empirical bayes; Genetic epidemiology; LASSO (Least Absolute Shrinkage and Selection Operator); Model averaging; Model robustness; Model selection

Indexed keywords

EID: 70350335073     PISSN: 01621459     EISSN: None     Source Type: Journal    
DOI: 10.1198/jasa.2009.0104     Document Type: Article

References (26)

1. Chang-Claude, J., Kropp, S., Jäger, B., Bartsch, H., and Risch, A. (2002), "Differential Effect of NAT2 on the Association between Active and Passive Smoke Exposure and Breast Cancer Risk," Cancer Epidemiology, Biomarkers & Prevention, 11, 698-704.
2. Chatterjee, N., and Carroll, R. J. (2005), "Semiparametric Maximum Likelihood Estimation in Case-Control Studies of Gene-Environment Interactions," Biometrika, 92, 399-418.
3. Chatterjee, N., and Chen, Y.-H. (2007), "Maximum Likelihood Inference on a Mixed Conditionally and Marginally Specified Regression Model for Genetic Epidemiologic Studies with Two-Phase Sampling," Journal of the Royal Statistical Society, Series B, 69, 123-142.
4. Claeskens, G., and Carroll, R. J. (2007), "Post-Model Selection Inference in Semiparametric Models," Biometrika, 94, 249-265.
5. Clark, A. G. (2004), "The Role of Haplotypes in Candidate Gene Studies," Genetic Epidemiology, 27, 321-333.
6. 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.
7. Fan, J., and Li, R. (2001), "Variable Selection via Nonconcave Penalized Likelihood and Its Oracle Properties," Journal of the American Statistical Association, 96, 1348-1360.
8. Gohagan, J. K., Prorok, P. C., Hayes, R. B., and Kramer, B. S. (2000), "The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial of the National Cancer Institute: History, Organization, and Status," Controlled Clinical Trials, 21(Suppl):251S-272S.
9. Hastie, T., Tibshirani, R., and Friedman, J. (2001): The Elements of Statistical Learning: Data Mining, Inference, and Prediction, New York: Springer-Verlag.
10. Hjort, N. L., and Claeskens, G. (2003), "Frequentist Model Average Estimators" (with discussion), Journal of the American Statistical Association, 98, 879-899.
11. Lake, S. L., Lyon, H., Tantisira, K., Silverman, E. K., Weiss, S. T., Laird, N. M., and Schaid, D. J. (2003), "Estimation and Tests of Haplotype-Environment InteractionWhen Linkage Phase Is Ambiguous," Human Heredity, 55, 56-65.
12. Lehmann, E. L. (1983): Theory of Point Estimation, NewYork: John Wiley and Sons.
13. Li, S. S., Khalid, N., Carlson, C., and Zhao, L. P. (2003), "Estimating Haplotype Frequencies and Standard Errors for Multiple Single Nucleotide Polymorphisms," Biostatistics (Oxford, England), 4, 513-522.
14. Lin, D. Y., and Zeng, D. (2006), "Likelihood-Based Inference on Haplotype Effects in Genetic Association Studies" (with discussion), Journal of the American Statistical Association, 101, 89-118.
15. Moslehi, R., Chatterjee, N., Church, T. R., Chen, J., Yeager, M., Weissfield, J., Hein, D. W., and Hayes, R. B. (2006), "Cigarette Smoking, Nacetyltransferase Genes and the Risk of Advanced Colorectal Adenoma," Pharmacogenomics, 7, 819-829.
16. Mukherjee, B., Ahn, J., Gruber, S.B., Rennert, G., Moreno, V., and Chatterjee, N. (2008), "Tests for Gene-Environment Interaction from Case-Control Data: A Novel Study of Type I Error, Power and Designs," Genetic Epidemiology, Epub PMID: 18473390.
17. Mukherjee, B., and Chatterjee, N. (2008), "Exploiting Gene-Environment Independence for Analysis of Case-Control Studies: A Shrinkage Approach to Trade Off Between Bias and Efficiency," Biometrics, 64, 685-694.
18. Prentice, R. L., and Pyke, R. (1979), "Logistic Disease Incidence Models and Case-Control Studies," Biometrika, 66, 403-411.
19. 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.
20. Schaid, D. J. (2004), "Evaluating Associations of Haplotypes with Traits," Genetic Epidemiology, 27, 348-364.
21. Schaid, D. J., Rowland, C. M., Tines, D. E., Jacobson, R. M., and Poland, G. A. (2002), "Score Tests for Association Between Traits and Haplotypes When Linkage Phase Is Ambiguous," American Journal of Human Genetics, 70, 425-434.
22. 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.
23. Stram, D. O., Pearce, C. L., Bretsky, P., Freedman, M., Hirschhorn, J. N., Altshuler, D., Kolonel, L. N., Henderson, B. E., and Thomas, D. C. (2003), "Modeling and E-M Estimation of Haplotype-Specific Relative Risks from Genotype Data for a Case-Control Study of Unrelated Individuals," Human Heredity, 55, 179-190.
24. Tibshirani, R. J. (1996), "Regression Shrinkage and Selection via the LASSO," Journal of the Royal Statistical Society: Series B, 58, 267-288.
25. Wallenstein, S., Hodge, S. E., and Weston, A. (1998), "Logistic Regression Model for Analyzing Extended Haplotype Data," Genetic Epidemiology, 15, 173-181.
26. Zhao, L. P., Li, S. S., and Khalid, N. A. (2003), "Method for the Assessment of Disease Associations with Single Nucleotide Polymorphism Haplotypes and Environmental Variables in Case-Control Studies," American Journal of Human Genetics, 72, 1231-1250.