Fig. 5

A DNA methylation-based classifier to predict BCBM subtypes. a Boxplots describing the CV performance across 100 repeats for RF classifiers to predict breast cancer subtypes. From left to right, decreasing numbers of features were used to construct the model (x-axis). The top and bottom of each box represent the first and third quartile, respectively; the internal red line represents the median values. Light blue bars depict the performance based on permuted class labels and represent the random background distribution. b Bar plots depicting the prediction performance as measured by sensitivity and specificity for each of the three subtypes. The bars show the average performance and interquartile range (error bars) across all models with 10 features or more across all repeats (HR+/HER2−; n = 12, HER2+; n = 11, and HR−/HER2−; n = 5). c Bar plots depicting the RF feature importance (mean decreases in Gini impurity score; GIS) of the 15 most predictive regions averaged across all models with 10 or more features and across all repeats. d Boxplots of DNAm levels (β-values) across our cohort stratified by subtypes (HR+/HER2−; n = 12, HER2+; n = 11, and HR−/HER2−; n = 5) and TCGA-BRCA cohort of primary breast tumors stratified to match our molecular subtype definitions (HR+/HER2−; n = 443, HER2+; n = 83, and HR−/HER2−; n = 117). Differences in the DNAm levels among the groups were statistically significant for all the cases (Kruskal–Wallis test; P-value < 0.0001). e DNAm levels assessed by qMSP for six genomic regions with differential DNAm among the three BCBM subtypes (n = 31). ***Wilcoxon test; P-value < 0.001. f ROC curves showing the prediction potential for the breast cancer subtypes (n = 31) for each of the six differentially methylated regions and combinations of three or six regions into BCBM molecular subtype-specific scores: HR+/HER2-score = DNAm level of HR+/HER2− minus DNAm level of HER2+ minus DNAm level of HR−/HER2; HER2+ score = DNAm level of HER2+ minus DNAm level of HR+/HER2− minus DNAm level of HR−/HER2; and HR−/HER2-score = DNAm level of HR−/HER2− minus DNAm level of HR+/HER2− minus DNAm level of HER2+; see Supplementary Data 10 for details about these regions. The AUC values are indicated between square brackets