Infinium methylationepic epic dna methylation arrays

In addition to WGBS, existing DNA methylation data were available from NDBS for each sample from Illumina Infinium MethylationEPIC (EPIC) DNA methylation arrays [17 (link)]. In brief, DNA was isolated from a separate one-third portion of the NDBS, bisulfite conversion performed as above, and DNA samples were block-randomized (ensuring equivalent distribution of sex and race/ethnicity on each plate) for EPIC arrays [17 (link)]. QC of DNA methylation array data was conducted in R using “minfi,” “SeSAMe,” and “noob” packages, and trisomy 21 was confirmed from copy-number variation plots generated using the conumee R package [25 ], as described [17 (link)]. Global methylation for each sample is represented by the beta value, the ratio of the methylated probe intensity and the overall intensity [26 (link)]. As previously done [27 (link)], EPIC array beta values from all samples were correlated with WGBS global methylation values to assess consistency across platforms (see Sect. 2.5). DMRs associated with DS-CHDs were investigated using the ipDMR method with the ENmix R package [28 (link)].