Infinium Human MethylationEPIC BeadChip Analysis

The Infinium Human MethylationEPIC BeadChip (Illumina) platform was used for DNA Methylation profiling. Samples were randomized on 2 slides and processed by the core facility for Bioinformatics and Expression Analysis (BEA), Karolinska Institutet, Huddinge campus. Idat files were loaded into R using scripts adapted from the ChAMP package (version 2.6.0) [13 (link)] referred to as “mEPIC.loading.Script.R” and “Champ.load.mEPIC.Script.R” available in Additional files 31 and 32, respectively. Furthermore, an R script for normalization of mEPIC probes with Subset-quantile within array normalization (SWAN) [16 (link)] and BMIQ [21 (link)], referred to as “Champ.norm.mEPIC.Script.R” is available in Additional file 33. Hierarchical clustering was performed with the ward.D2 method of the hclust function in R.