Fig. 3

DNA methylation classifiers to predict the tissue of origin of brain metastases. a CV performance across 100 repeats for the RF classifiers to predict tumor of origin, in order of decreasing number of features used in model construction, from left to right (x-axis). Red bars on the boxplots indicate medians and 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 BM types. The bars show the average performance and interquartile range (error bars) across all models with 40 features or more across all repeats. c Bar plots depicting the RF feature importance (mean decreases in Gini impurity score; GIS) of the 15 most predictive genomic regions averaged across all models with 40 features or more and across all repeats. d For three genomic regions in the top 15: boxplots of DNAm β-values across our cohort stratified by tumor of origin (BCBM n = 28, LCBM n = 22, and MBM n = 44) in the upper panels and TCGA cohorts of primary breast tumors (n = 401), primary lung tumors (n = 307), and primary melanomas (n = 83) in the lower panels. 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 three regions differentially methylated among the three BM types (n = 59). The top and bottom of each box represent the first and third quartile, respectively; the internal line represents the median. ***Wilcoxon test; P-value < 0.001. f ROC curves showing the prediction potential for the tumor of origin (n = 59) for each of the differentially methylated regions and combinations into BM type-specific scores: MBMscore = DNAm level of MBM-B minus DNAm level of LCBM-C minus DNAm level of BCBM-C; LCBMscore = DNAm level of LCBM-C minus DNAm level of BCBM-C minus DNAm level of MBM-B; and BCBMscore = DNAm level of BCBM-C minus DNAm level of LCBM-C minus DNAm level of MBM-B; see Supplementary Data 6 for details about these genomic regions. The AUC values are indicated between square brackets