Tests for gene-environment interaction from case-control data: A novel study of type I error, power and designs

Bhramar Mukherjee, Jaeil Ahn, Stephen B. Gruber, Gad Rennert, Victor Moreno, Nilanjan Chatterjee

Research output: Contribution to journalArticlepeer-review

56 Scopus citations


To evaluate the risk of a disease associated with the joint effects of -genetic susceptibility and environmental exposures, epidemiologic researchers often test for non-multiplicative gene-environment effects from case-control studies. In this article, we present a comparative study of four alternative tests for interactions: (i) the standard case-control method;-(ii) the case-only method, which requires an assumption of gene-environment independence for the underlying population; (iii) a two-step method that decides between the case-only and case-control estimators depending on a statistical test for the gene-environment independence assumption and (iv) a novel empirical-Bayes (EB) method that combines the case-control and case-only estimators depending on the sample size and strength of the gene-environment association in the data. We evaluate the methods in terms of integrated Type I error and power, averaged with respect to varying scenarios for gene-environment association that are likely to appear in practice. These unique studies suggest that the novel EB procedure overall is a promising approach for detection of gene-environment interactions from case-control studies. In particular, the EB procedure, unlike the case-only or two-step methods, can closely maintain a desired Type I error under realistic scenarios of gene-environment dependence and yet can be substantially more powerful than the traditional case-control analysis when the gene-environment independence assumption is satisfied, exactly or approximately. Our studies also reveal potential utility of some non-traditional case-control designs that samples controls at a smaller rate than the cases. Apart from the simulation studies, we also illustrate the different methods by analyzing interactions of two commonly studied genes, N-acetyl transferase type 2 and glutathione s-transferase M1, with smoking and dietary exposures, in a large case-control study of colorectal cancer.

Original languageEnglish (US)
Pages (from-to)615-626
Number of pages12
JournalGenetic epidemiology
Issue number7
StatePublished - 2008
Externally publishedYes


  • Case-only designs
  • Empirical bayes
  • Gene-environment interaction
  • Genome-wide scan
  • Molecular epidemiology of colorectal cancer

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)


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