Figure 1

Groups of stage IIIC CM patients identified by whole-genome methylation profiling. Genome-wide DNA methylation profile was evaluated by Illumina HumanMethylation27 Bead-Chip whole-genome assay in short-term cultures of CM cells generated from neoplastic lesions of 45 stage IIIC CM patients. Cells were analyzed at 6^th in vitro passage. Patients were divided into 2 classes (LM and HM) based on the whole genome methylation profile of their tumor cells through the k-means algorithm. Panel a, the whole genome methylation profiles in the patients’ population have been reported as a heatmap. Patient identifier numbers and the k-means-defined groups have been reported on top of the heatmap. Each color patch represents the methylation level of one gene in each patient, with a continuum of methylation levels from dark blue (completely unmethylated, β = 0) to dark red (completely methylated, β = 1). Panel b, the genome-wide methylation profile of each patient was summarized by the “methylation score”, where “methylation scores” > and < 0 represent methylation above and below the population’s mean, respectively. Separate box plots have been generated for the LM and HM whole methylome defined patients’ groups. Black horizontal bars represent the median values of “methylation score” for each group. *, P = 0.001 as evaluated by Student’s T test.