Fig. 4

Validation of EpiClass cutoff values and corresponding performance for identifying EOC from patient plasma. a The pooled epiallelic fractions of cfDNA methylated epialleles with varying methylation densities in the second EOC (red, n = 24) and healthy (blue, n = 12) patient plasma sample cohort. Purple shaded regions indicate overlap between the two plasma sets. b Performance of EpiClass at each methylation density cutoff for the EOC and healthy control plasma samples. Dotted line shows the optimal methylation density cutoff derived from EpiClass. The red dot indicates the ROC curve AUC for the mean methylation cutoff. Measurement metric refers to either 1—FPR, TPR, AUC, or TPR–FPR. c Receiver operating characteristic curve for the optimal 60% methylation density cutoff on the second plasma cohort. d Boxplots indicating the distribution of sample normalized read counts with intramolecular methylation densities greater than or equal to 60% (EpiClass), 95% (MSP*), or greater than 0% (mean* methylation). EOC epithelial ovarian carcinoma; EpiClass methylation density classifier, MDC methylation density cutoff, AUC area under the curve; *** indicates p < 0.001, two-sided Wilcoxon rank-sum test; ns = not significant; Mean* methylation was inferred from the fraction of all methylated epialleles. MSP* performance estimated using an MDC of 95%