At each SNP, the genotype label (0, 1, 2) is represented by the count of an arbitrarily chosen allele. Table I contains a summary of notation for the frequencies and genetic effect sizes (“phenotypic deviations”) of each genotype. Since allele frequency affects the power to detect phenotype association, we adjust the phenotypic deviations separately for each SNP, so that we may tabulate results over all SNPs. To accomplish this, we maintain constant genetic variance attributable to the marker VG, which we calculate with the following formula from Equation [8.8] (p. 129) of Falconer [1989]: (1)VG=2pq[a+d(q−p)]2+[2pqd]2, where p and q = 1 − p are allele frequencies, and a and d are additive and dominance effects (see Table I). We report genetic variance as a percent of total phenotypic variation (heritability), fixing this at 2.8% for n = 1,000, and 59.8% for n = 50. These values were calculated so as to achieve approximately 90% power at type-I error of 5 × 10−5 when analyzing the simulated genotypes under an additive genetic model with equal allele frequencies of one-half.
