Validation of the Illumina methylation assay. (A) Average β-levels for 15 to 17 samples (y-axis) according to bisulfite pyrosequencing results. Bisulfite pyrosequencing was considered methylated at a cut-off of 15%. P = .03, .01, and .06 for CDKN2B, HIC1, and CDH1, respectively. There were no methylated samples of CDKN2A according to bisulfite pyrosequencing. (B) Technical replicates; 2 samples were replicated on the 27k array (top panel) and 2 replicates on both the 27k and 450k array (bottom panel). All were highly correlated (P < .0001) with Pearson correlation coefficients of r = 0.99, 0.94 and r = 0.98, 0.98, clockwise from top left. (C) There is an inverse relationship between promoter methylation assessed by the Illumina HumanMethylation27 array and global CpG methylation as measured by LUMA (Pearson r = −0.45, P = .02, n = 29).