The relationship between 5HTTLPR genotype and SLC6A4 mRNA expression was explored using the commercially available primer probe set and our “in house” primer probe set that specifically recognizes transcripts containing exon 1 of SLC6A4. Consistent with our prior results [Philibert et al., 2007a], the correlation of SLC6A4 gene expression as measured by the two primer probe sets was only 0.75 (Pearson’s). The relationship between gene expression as measured by each of these primer probe sets and 5HTTLPR genotype is shown in Figure 3. When expression of the commercially available primer probe set which recognizes the sequence in exons 8 and 9 is examined, the s allele had a nominal but not a statistically significant effect upon SLC6A4 transcripts levels. In contrast, when the primer probe set specifically designed to assay the expression of transcripts containing exon 1 is used, there is a significant effect of genotype on SLC6A4 mRNA expression (ANOVA, Adjusted R square, 0.034, P < 0.02). The difference in Z scores for the exon 1 primer probe set between the s,s and l,l corresponds to a 0.84 cycles (i.e., on average, lymphoblasts with l,l genotypes produce 79% more of the mRNA that cells with the s,s genotypes produce).
