The CpG methylation measure of each sample was profiled using the HumanMethylation27K array by Illumina, which assays 27,578 CpG sites per sample. These 27,578 sites represent 14,475 consensus coding sequences across the genome, providing approximately 2 CpG assays per gene, with increased targeting of cancer related genes. Then the CpG methylation status was determined by discretization CpG methylation measure with cut-off values of 0.2, 0.4 and 0.6 (Figure S4B, related to Figure 1).
