control group and 1: AUD group), and XS is the subject ID. In this model, β0, β1, β2, and β12 are coefficients of fixed effects, while b is the coefficient for random effect that models the differences between subjects. Our null hypothesis (H0) is: β12 = 0. Rejecting the null hypothesis indicates that the allelic imbalance differs between the AUD and control groups. False discovery rate (FDR) was calculated using the Benjamini–Hochberg procedure [20]. Ingenuity pathway analysis (IPA) (Qiagen) was used for deriving the pathways of the genes with AUD-associated allelic differences.
