Analysis of separate molecular biomarkers confirmed the same changes as in subtype analysis according to hormone receptor status: ER+ cases more frequently had methylated PRKCB (86% vs. 40%) and RUNX3 (46% vs. 18%) than ER negative, while FILIP1L promoter hypermethylation was dominating in ER and PR negative BC (84% vs. 45% and 76% vs. 47%, respectively; in all cases p < 0.05). Here, FILIP1L is linked to breast cancer.