With slight modification of the above technique, we can use our simulation to investigate how the dTDT is affected by population stratification. Simulating different populations to have different prevalences, we can choose two sets of trios using different allele frequencies. Applying the dTDT to this combined set of trios, we can test whether the power is lowered or heightened because of the prevalence difference within the populations. Since there is no information on phase of two markers in a trio, we have not introduced the recombination frequency (θ) in the simulation.
