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.