DNA Methylation Analysis of Placental Samples

Extracted DNA from 139 placenta samples was run on Illumina Infinium EPIC Methylation arrays. The quality control pipeline was set up using the R-package minfi 1.36.0 [59 (link)]. Two samples were excluded as they showed artefacts in the beta-value distribution. Methylation beta-values were normalized using the swan normalization [60 (link)]. After normalization, slide was the most significant batch and removed using the Combat function in the R-package sva 3.30.1 [61]. We excluded any probes on chromosome X or Y, probes containing SNPs and cross-hybridizing probes according to [62 (link)–64 (link)]. Furthermore, any CpGs with a detection p value > 0.01 in at least 25% of the samples were excluded. The final dataset contained 793,213 CpGs and 137 participants. For 136 of these (52 BET and 84 controls), genotypes and hence MDS components were available. Using MixUpMapper 1.2.4 [65 (link)] we confirmed that methylation levels and genotypes matched and that no sample mix-ups were present.