Fig. 3

Identification of 14 CpG probe methylation signatures of LGG IDH mutant versus WT in training set (TCGA). a Plot demonstrating classification error for 9554 CpG probes from PAM analysis in training set. The threshold value 18.9 corresponded to 14 discriminatory CpG probes which classified IDH mutant (n = 217) and WT (n = 49) LGG samples with classification error of 0%. b Heat map of the 14 CpG discriminatory probes identified from the PAM analysis between LGG IDH Mut and WT patient samples in the training set (TCGA). A dual color code was used where yellow indicates more methylation (hypermethylation) and blue indicates less methylation (hypomethylation). c PCA was performed using beta (methylation) values of 14 PAM-identified CpG probes between IDH mutant (n = 217) and WT (n = 49) LGG samples in training set. A scatter plot is generated using the first two principal components for each sample. The color code of the samples is as indicated. d The detailed cross-validation probabilities of 10-fold cross-validation for the samples of training set based on the beta values of 14 CpG probes are shown. For each sample, its probability as LGG IDH Mut (red color) and WT (green color) is shown and it was predicted by the PAM program as either IDH Mut or WT in LGG samples based on which grade’s probability is higher. The original histological grade of the samples is shown on the top