We propose a statistical model for dissecting a multilocus genotypic value into its main (additive and dominant) effects and epistatic effects between different loci in a case-control association study. The model can discern four different kinds of epistasis, additive×additive, additive×dominant, dominant×additive, and dominant×dominant interactions. To test each kind of epistasis, a X2 test statistic was computed for a two by two contingency table derived from combined genotypes in both case and control groups. We derived an analytical approach for estimating the asymptotic distribution of the X2 test statistic for epistatic tests under the null hypothesis, with the result being consistent with that from Monte Carlo simulations. The new model was used to analyze a case-control data set for candidate gene studies of stroke, leading to the identification of several significant interactions between causal SNPs on this disease.
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