The derived expressions were compared to simulations in which the major assumptions were examined under realistic scenarios. These assumptions include a large number of markers with effects, for equality in equation 7, and small genetic effects, so that effects on the liability scale are approximately linear. In case/control designs the disease prevalence is assumed to be not too small, so that the variance of the ascertained genotypes remains near 1 as assumed in equation 13 and Text S1. Effects are assumed to be normally distributed on the standardised genotype scale. Sample sizes are assumed large so that estimates of genetic effects are normally distributed.
