3.3. Expression by Genotype Interaction of HLA-DPA1
The same cohort of subjects which had brain gene expression measured for HLA-DPA1 (Table 2) was genotyped for SNPs around the HLA-DPA1 gene and an F-ratio was calculated for association. The HLA-DPA1 expression levels were measured by qPCR for the association analysis with the genotypes of SNP rs9277341.This intronic SNP was located in intron two of HLA-DPA1. We sequenced the specific amplicon resulting from qPCR amplification reactions (Supplementary Table S1) to find the expected product and ensuring that SNPs or large exonic deletions were not within the primer region of the qPCR amplicon.
The results for HLA-DPA1 SNP rs9277341 by brain region are shown (Figure 6). The main effect for rs9277341was significant (p = 0.0002), the major ‘T’ allele showed increased expression, while the homozygous minor “C” allele has significantly lower expression. The interaction of region (five brain regions tested) by SNP rs9277341 genotype (0, 1, 2) was not significant. The overall effect of diagnosis factor (SZ, BD, MDD, C) on HLA-DPA1 expression was significant (p = 1.68 × 10−6). Post hoc comparisons between each psychiatric diagnosis and controls were significant, and decreased significantly in expression (Table 8 and Table 9).