First, consider separately each of the 19 non-MHC SNPs showing strong evidence for association on either the trend or genotypic test in Table 3. For four of these 19, the P value on the 2-d.f. genotypic test was smaller than that on the 1-d.f. trend test (Table 3). When comparing disease models, these were also the four SNPs with evidence for departure from a simple model in which odds of disease increase multiplicatively with the number of copies of the risk allele (Supplementary Table 8). This supports our view that the genotypic test should be carried out in addition to the trend test, although should perhaps be viewed more cautiously for two reasons: it is more susceptible to genotyping errors; and (on the basis of our findings) experience does not favour strong dominance effects.
