2. For a given disease model simulate the alleles at the disease locus of the new individual conditional upon case-control status. At the disease locus we use a general genotype model in which the frequencies of the genotypes aa, Aa and AA in control individuals are given by (1−p)2, 2p(1−p) and p2 respectively. This assumes that the control individuals are so-called population controls (as used by the WTCCC study [5]) rather than individuals who have been selected to specifically not have the disease. For case individuals the genotype frequencies are determined by specification of the two relative risks (4)where denotes the probability that an individual is a case conditional upon having genotype g. Under this model (5)where γ = (1−p)2+2αp(1−p)+βp2. As an example, if p = 0.1, α = 2 and β = 4 the control and case genotype frequencies are (0.81, 0.18, 0.01) and (0.67, 0.30, 0.03) respectively.
