Genotype calls for the postmortem AD sample were generated as part of a larger GWAS and integrated with miRNA and mRNA hub genes to identify expression quantitative trait loci (eQTLs). The genotype data used to generate the eQTLs for the mRNA and miRNA genes are provided in S11 Table, respectively. Briefly, all samples were genotyped on the Affymetrix Genome-Wide Human SNP Array 6.0; imputed genotype probabilities greater than 98% were converted into hard call genotypes of 0,1, or 2 using GTOOL software and filtered to eliminate ambiguity, i.e. no “unknown” calls [104]. Genetic variants were then filtered with Plink v1.07 to exclude variants in LD (R2≥ 0.8) [105]. Based on a sample size of n = 34 (one individual was removed from the sample due to genotype missingness), for a reliable estimation of the eQTL effects on gene expression a minor allele frequency ≥24% was required.
