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We compared four haplotype-based approaches for the analysis of gene-environment interactions when haplotype-phase is ambiguous. The methods employ different versions of the expectation maximization algorithm and differ in the choice of the reference group and in the way the risk of disease is modeled (retrospective versus prospective). Furthermore, the methods are based on distinct assumptions (such as Hardy Weinberg equilibrium). The haplotype-based methods were also compared to single-marker logistic regression (LR).

human heredity

Comparison of Different Haplotype-Based Haplotype-Based Association Methods for Gene-Environment (G×E) Interactions in Case-Control Studies when Haplotype-Phase Is Ambiguous