Samples quality assessment and microarray analysis were conducted at The Sidney Kimmel Cancer Center Microarray Core Facility at Johns Hopkins University using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001; Illumina Inc., San Diego, CA, USA) according to the manufacturer’s manual. Images were processed in Illumina’s iScan scanner (Illumina Inc.) and data were extracted using Methylation Module of GenomeStudio v.1.0 Software (Illumina Inc.). Illumina probe type was corrected using the Beta2M function in the wateRmelon package in R. Methylation status of each CpG site was calculated as β (beta)-value based on following definition: β-Value=(signal intensity of methylation−detection probe)/(signal intensity of methylation−detection probe+signal intensity of non-methylation−detection probe+100).
