reported as the susceptibility allele D with probability 0.01), then the probabilities for the three genotypes DD, Dd and dd were set to 0.094249 [0.09 + 0.01(0.42) + (0.01)2(0.49)], 0.425502 [(0.99)(0.42) + 2(0.99)(0.01)(0.49)] and 0.480249 [(0.99)2(0.49)], respectively. This calculation takes into consideration that subjects with true genotype dd could be mistakenly scored Dd (with probability = 2×0.99×0.01) or DD (with probability (0.01)2) and subjects with true genotype Dd could be mistakenly scored DD (with probability 0.01). We did not assume any additional random error in our calculations (in the above example, subjects with true genotype DD were assumed to be scored DD with probability = 1). We considered systematic allele calling error probabilities for a given genotype platform of + 0.01, 0.00, and − 0.01, where + (−) corresponds to erroneously over (under) calling of the susceptibility allele.
