y=Xβ+g+e where y is a vector of case (y = 1) or control (y = 0) status (the observed scale), β is a vector for fixed effects of the overall mean (intercept), sex, sample cohort and 20 ancestry principal components, g is the vector of random additive genetic effects based on aggregate SNP information and e is a vector of random error effects. X is an incidence matrix for the fixed effects relating these effects to individuals. The variance structure of phenotypic observations is
