Kaplan-Meier plot showing survival of breast cancer case subsets defined by methylation-based consensus clustering or intrinsic subtyping. Consensus clustering of methylation β values for the 167 most variant CpG (cytosine preceding a guanosine) sites in 517 breast tumors defined four clusters. Kaplan-Meier plots show (A) breast cancer-specific survival or (B) overall survival for methylation-based clusters 1 through 4. Log-rank P values (P =0.02) indicate significant differences in survival among the methylation clusters. Intrinsic subtype information was available on 413 of the 517 tumors with methylation data. Subtypes defined by immunohistochemistry (IHC), as described in the Materials and methods section, were luminal A, luminal B, basal-like, human epidermal growth factor receptor 2-positive/hormone receptor-negative (HER2+/HR-), and unclassified. Kaplan-Meier plots for the five intrinsic subtypes show (C) breast cancer-specific survival and (D) overall survival. Numbers of cases and events within each group are noted in each plot.