Fig. 4

Validation of the 14 CpG methylation signatures of LGG IDH mutant versus WT in an independent validation dataset GSE58218. a Heat map of the 14 CpG discriminatory probes identified in PAM analysis in IDH mutant (n = 157) and WT (n = 38) LGG patient samples in the entire TCGA dataset. A dual color code was used where yellow indicates more methylation (hypermethylation) and blue indicates less methylation (hypomethylation). b PCA was performed using β (methylation) values of 14 PAM-identified CpG probes between IDH mutant (n = 157) and WT (n = 38) LGG patient samples in the entire TCGA dataset. A scatter plot is generated using the first two principal components for each sample. The color code of the samples is as indicated. c The detailed probabilities of 10-fold cross-validation for the samples of training set based on the β values of 14 CpG probes are shown. For each sample, its probability as IDH mutant (red color) and WT (green color) of LGG patient samples is shown and it was predicted by the PAM program as either LGG IDH mutant or WT based on which grade’s probability is higher. The original histological grade of the samples is shown on the top