Given the potential influence of cell composition on gene expression, we also examined the cell type proportion associated with genetic ancestry and any potential confounding effects on gene expression. To this end, we performed cell type deconvolution (Supplementary Data 12). When we examined the BA population, we found that most cell types across brain regions showed no correlation with genetic ancestry (Supplementary Fig. 36); only oligodendrocytes in the DLPFC showed a significant association (Spearman P < 0.05) with genetic ancestry. In contrast, when we included non-Hispanic WA donors, we found that seven of the ten cell types showed a significant association (Spearman P < 0.05) with genetic ancestry in at least one brain region (Supplementary Fig. 37). These cell type proportions also showed high correlation with confounders (Supplementary Fig. 38). As such, our model also accounted for cell type proportions for each brain region (Supplementary Fig. 39).
