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Statistical Analysis for Haplotype‐Based Matched Case–Control Studies

Summary Using unphased genotype data, we studied statistical inference for association between a disease and a haplotype in matched case–control studies. Statistical inference for haplotype data is complicated due to ambiguity of genotype phases. An estimating equation‐based method is developed for estimating odds ratios and testing disease‐haplotype association. The method potentially can also be applied to testing haplotype‐environment interaction. Simulation studies show that the proposed method has good performance. The performance of the method in the presence of departures from Hardy–Weinberg equilibrium is also studied.