Methylation overview. A: Bar chart displaying promoter methylation frequencies across the three diagnosis groups. Methylation frequency is defined as the number of methylated samples within each category. The average values of methylation for all CpGs were calculated for each sample and each gene. A sample was scored as hypermethylated if the measured methylation values were two times above the standard deviation of the mean of the normal controls, and conversely, as hypomethylated if methylation values were below two times the standard deviation of the mean of the normal control tissues. DCIS = light grey, pure invasive = dark grey, and mixed = black. B: Methylation overview per gene across the three diagnosis groups. Black boxes indicate methylated and white boxes indicate unmethylated samples. For the imprinted gene IGF2; white boxes indicate the expected allele-specific methylation, black boxes indicate hypermethylation, and grey boxes indicate hypomethylation.