Examining SNCA Expression and Genotypes

The SNCA gene expression dataset and analysis methods used here have been described previously^{49 (link)}. In brief, SNCA expression levels were assayed from 165 samples using quantitative real-time polymerase chain reaction. The Relative Standard Curve Method was used to transform the Ct values into quantity units. The base 10 logarithm of the SNCA expression values was used for all analyses, to ensure the normal distribution of data required by the statistical tests performed. SNP genotyping was performed as part of the US PD-GWAS Consortium meta-analysis replication sample^{50 (link)}. As described in the consortium study, the samples were genotyped at the Center for Inherited Disease Research (CIDR) using a custom Illumina genotyping array of 768 SNPs. Because the tested SNP dataset did not include the top reported PD-associated SNP rs356182 in the SNCA locus, we included rs356229 as proxy for this SNP (R² = 0.62) in our analysis. After QC, genotyping and expression data was available for 86 cases and 41 controls for eQTL analysis. Expression models were analyzed including adjustment for disease status, sex, pH, age at death, as well as for the interaction between PMI and disease status and significance was assessed using a one sided test based on the a priori hypothesis of an association of the G-allele at rs356168 with increased SNCA expression.