Figure 6

The methylation profile of vHMEC hypermethylated loci can identify tumour from normal in the TCGA breast cancer cohort. (A) HM450 probes overlapping with vHMEC DMR chr19-37205 are hypermethylated in tumours in the TCGA-BRCA cohort. (B) DMR chr19-37205 overlaps the COX7A1 promoter associated CpG island. Methylation at the locus was able to separate tumour from normal tissue in the TCGA-BRCA cohort (AUC > 0.94). (C) vHMEC DMR chr5-12238 overlapped two HM450 probes; however, in the TCGA-BRCA cohort, several adjacent probes also exhibited increased methylation. (D) Hypermethylation of DMR chr5-12238 overlapping and adjacent probes (covering the LCT4S promoter) was specific to tumours in the TCGA-BRCA cohort (ROC analysis AUC > 0.97). Additionally, a small independent cohort of HM27 profiled samples also exhibited tumour-specific methylation at this locus (AUC = 0.94).