For methylation analyses, DNA was purified by using DNeasy kit (69504, Qiagen), quantified (Qubit dsDNA BR Assay, Life Technologies) and bisulfite-converted (EZDNA Methylation Kit, Zymo Research) according to the manufacturer's protocol. Bisulfite-converted DNA was then labelled and hybridized to the Infinium Human Methylation 450 K beadchip (Illumina) and scanned on a HiScan (Illumina). Samples were normalized and filtered using the statistical programming language R (http://www.r-project.org/) (v.3.0.1) and the R package minfi (v.1.6.0). Briefly, samples were first control-normalized using Illumina's internal bead controls and probes with a detection P value >0.01 in at least one sample were discarded. The samples were then SWAN normalized using the minfi package and β values (Methylated allele intensity/ Unmethylated allele intensity+methylated allele intensity) were exported. Probes with less than a max β—min β of 0.5 were removed.
