Expanding our analysis to the isoform level (transcripts, exons and junctions), we also found a significant association with immune-related pathways, with consistent upregulation for the AA proportion in the caudate nucleus and the EA proportion in the dentate gyrus, DLPFC and hippocampus. Additionally, we found significant enrichment of these DEGs for genes with population differences in macrophages18 associated with the innate immune response to infection (Fisher’s exact test, false discovery rate (FDR) < 0.05; Supplementary Fig. 7). Moreover, we found significant enrichment (Fisher’s exact test, FDR < 0.01) for global ancestry-associated DEGs in gene coexpression network modules (weighted gene coexpression network analysis22; Supplementary Fig. 8). Like our DEG analysis, immune response pathway enrichment in these modules showed a consistent opposite direction of effect based on brain region (Supplementary Fig. 9 and Supplementary Data 4 and 5).
