Based on the data noted, haplotypes marked by variants that tag mRNA and lie at the 5′ end of the PPP3CA gene are thus candidates to play roles in some of the association findings noted here. To seek allele-specific expression based on 5′ PPP3CA haplotypes, we compared effects of haplotypes marked by “B” versus “D” alleles in mRNAs extracted from postmortem brain samples, using genomic DNA from heterozygotes as a control. Using the linear range for amplification of cDNA and genomic DNA for each sample, we were able to determine the relative trinucleotide repeat expression by quantifying peak area ratios (i.e., B allele peak area to D allele peak area) produced using GENESCAN. In mRNA extracted from 13 medial temporal gyrus samples, we observed significant differences in the B/D allele ratio in comparison to control values observed in studies of genomic DNA (Figure 4) (p = .0154). Such data support the idea that the tri-nucleotide repeats identify 5′ PPP3CA haplotypes that can alter PPP3CA expression in ways that are preserved in postmortem cerebral cortical samples. Conceivably, the repeat sequences itself might even contribute to such differential expression.
