500ng genomic DNA from cord blood (birth) or peripheral blood (age 7 and 9) was bisulfite-converted using the EZ-DNA methylation kit (Zymo Research, Orange, CA, USA). The protocol followed manufacturer instructions using the recommended alternative incubation conditions for use with Illumina Infinium arrays. Illumina HumanMethylation450 BeadChips (Illumina, USA) were run following the manufacturer’s protocol with no modifications and arrays were scanned using an Illumina iScan (software version 3.3.28). Initial quality control of data generated was conducted using GenomeStudio (version 2011.1) to determine the status of staining, extension, hybridization, target removal, bisulfite conversion, specificity, non-polymorphic and negative controls. DNA methylation data was only available on samples that passed this stage. Samples were quantile normalised using the dasen function within the wateRmelon package (wateRmelon_1.0.3; 19) in R and batch corrected using the ComBat package (20).
