Methylation Quantitative Trait Loci

To determine methylation levels at CpG sites that may be influenced by nearby DNA sequence, methylation quantitative trait loci (meQTL) analyses were performed for the 13 replicated BP CpGs in EA individuals from ARIC (N = 948), FHS (N = 2,357), and RS (N = 731) and AA individuals from ARIC (N = 2,173) and GENOA (N = 422). Residuals were obtained from regressing inverse-normal transformed methylation beta values on the first ten methylation principal components (PCs) and up to the first ten genetic PCs. The residuals were then regressed on 1000 Genomes Phase I imputed SNPs within 50 kb of the probe (CpG position ± 25 kb, GRCh37/hg19). SNPs with low imputation quality (r² < 0.3), low frequency variants (MAF < 0.05), and SNPs present in only one cohort were removed from analyses. Results for each probe were combined using race-stratified p value-based meta-analysis weighted by sample size and direction of effects using METAL.²² Significant meQTLs were determined using a Bonferroni correction for all meQTLs tested in each race (EA: 0.05/1,447 = 3.5 × 10⁻⁵; AA: 0.05/1,952 = 2.6 × 10⁻⁵). To maximize statistical power for identifying meQTLs associated with BP, we then searched the largest genome-wide association studies (GWASs) for BP in each race for suggestive association of meQTL regions with BP.

To assess the association of SNPs reported by Kato et al.²³ whose association may be mediated by DNA methylation, we additionally performed meQTL analyses for 35 sentinel SNPs and additional GWAS loci in high linkage disequilibrium (LD) with these regions.^{3, 4, 5, 23, 24, 25, 26, 27, 28, 29, 30} We assessed the association of DNA methylation within 1 Mb (CpG position ± 500 kb) of GWAS SNPs among ARIC EAs (N = 790) using the previously described methodology. SNPs associated with methylation after Bonferroni correction for the 28 meQTLs reported by Kato et al.²³ (p < 0.0018) were then assessed for association with BP before and after adjustment for methylation at the CpG site. We additionally assessed the association of these CpG sites with BP in our overall meta-analysis.