is low, say 10 % then about 1 % of data is expected as rare homozygous. In this case the majority of data will lay on other two strata and the model with only one cross product term can reflect the model enough well as in the case of having only two strata. Also note that for very rare alleles when there is no third strata G2 and G are linearly dependent (if G gets values 0 or 1 and there is no G = 2, then G2 = G, if G gets the values 1 or 2 and there is no G = 0, then G2 = 3G − 2) the model should not have G2 terms, otherwise the model will have collinearity issues. Essentially, the use of only one cross-product term with three genotype categories imposes constraints on the interaction: it forces the slope (and also intercept) difference to be the same between adjacent genotypic groups (e.g., the difference in slope between the groups G = 0 and G = 1 is constrained to be the same as the slope difference between the groups where G = 1 and G = 2) and it forces the lines for
