Figure 3.
Construction of SVM to identify patients with IM. (A) Using DREAM data of the 38 cases from the discovery cohort that were known to belong to consensus HM (n = 30) and consensus IM (n = 8) subgroups, a volcano plot showing DNA methylation fold changes and P values between consensus HM and IM subgroups was constructed. Red dots indicate 35 CpG sites that showed a distinct difference (>0.3) in mean methylation level. (B) To develop an SVM that classified HM and IM, 60% of the samples were randomly assigned to the training data and the remaining 40% to the test data. (C) In the best SVM model, optimal γ, cost parameter, and MSE were 0.0095, 1.05, and 0.1, respectively. (D) Volcano plot shows DNA methylation fold changes and P values between consensus LM (n = 60) and IM (n = 8) subgroups from the discovery cohort. Red dots indicate 12 CpG sites that showed a distinct difference (>0.3) in mean methylation level. (E) To develop an SVM that classified LM and IM, 60% of the samples were randomly assigned to the training data and the remaining 40% to the test data. (F) In the best SVM model, optimal γ, cost parameter, and MSE were 0.0095, 3.02, and 0.05, respectively. (G) Using these SVM models, 3 of the 38 patients in the validation cohort were classified as belonging to the IM subgroup (IM_SVM). Kaplan-Meier curves for OS were presented using data from 37 cases, excluding 1 case of NS/MPD.