If the overall test for significant genetic effect is significant, we then test for heterogeneity of genetic effect across the two population samples by comparing the above full model to the model ln(P1−P)=α0+α1x1+...+αnxn+β1s+β2G; that is, the interaction term is removed. If the resulting likelihood ratio chi-square statistic is significant, we conclude that the genetic effect is not similar in the two population samples and thus the SNP is lower priority for follow-up; the population-specific odds ratios defined above can then indicate how the effects differ in the two populations.
