Illumina Methylation Bead-Array Analyses.
Bisulphite-converted DNA from each sample was hybridised to HumanMethylation450 BeadChip arrays (Illumina, San Diego, USA), and processed by Bart’s and the London Genome Centre, UK. Array data were processed by GenomeStudio software and the Novel Identification of Methylation Biomarker Lists (NIMBL) platform[9]. NIMBL also assessed internal control data, and performed peak-based correction to compensate for probe-type sensitivity. CpGs where: (i) probe detection p-values were >0.05, (ii) with missing β-values, or (iii) known to be associated with single nucleotide polymorphisms (SNPs), were excluded.