Figure 3: Methylation profile stratifies TNBC tumours into survival subgroups.

(a) Unsupervised clustering with 4,987 HM450K probes overlapping 822 hypermethylated DMRs identified in the discovery cohort separates TCGA TNBC tumours (n=73) into three main clusters. The heatmap shows the methylation profile of TCGA TNBC tumours and cluster dendrogram. The three clusters are colour-coded with the red cluster exhibiting the highest methylation (TNBC.high), the blue cluster exhibiting the lowest methylation (TNBC.low) and the orange cluster exhibiting an intermediate level of methylation (TNBC.medium). β; methylation beta value. (b) A Kaplan–Meier plot showing survival curves for the patients in the three clusters defined in a. In addition, individual regions of hypermethylation in the discovery cohort overlap with survival-associated probes in the TCGA cohort, including (c) intergenic loci, (d) intragenic loci (for example, the HOXB13 gene body) and (e) promoter associate loci (for example, ZNF254 promoter). (f) Association with survival for three adjacent regions—chr11-11623, chr11-4047 and chr11-1210—spanning the WT1/WT1-AS locus is shown. These three regions are hypermethylated in the discovery cohort and overlap several probes showing statistically significant association with overall survival in both univariate and multivariate analyses. For each region, the methylation profile of TCGA TNBC tumour (n=73) and adjacent normal samples (n=9) across overlapping survival probes is shown as a heatmap. The Kaplan–Meier plots for each of the overlapping survival probes is shown as well with corresponding hazard ratios and P values from Cox proportional hazards model; values in parentheses correspond to multivariate analysis. HR, hazard ratio.