Methylation quantitative trait loci analysis in Korean exposome study

Abstract

Background Environmental exposure and genotype variation influence DNA methylation. Studies on the effects of genotype variation were performed mainly on European ancestries. We analyzed the genetic effects on cord blood methylation of Koreans. Methods As part of the Korean Exposome study project, DNA was extracted from 192 cord blood samples for analysis. Cord blood samples were genotyped via Asian Precision Medicine Research Array analysis and methylation was measured using the Methylation EPIC Beadchip kits. The associations between genotypes and CpG methylation were analyzed with matrix eQTL. Results Conditional analysis revealed 34,425 methylation quantitative trait loci (mQTLs), and trans-mQTLs constituted 7.2% of all the associated CpG sites. About 80% of the total trans-associations were trans-chromosomal and the related SNPs were concentrated on chromosome 19. According to the results of DAVID, cis-mQTL-related SNPs resulting in amino acid substitutions were related to signal peptides or glycosylation. Conclusion We identified genotype variations associated with DNA methylation in the cord blood obtained from Koreans.