Extended Data Fig. 3: Integrated analysis of tumour mutation burden in hypermutated gliomas in the DFCI-Profile, MSKCC-IMPACK and FMI datasets.

a, Distribution of TMB, homopolymer indels, MMR mutations, and SNV mutational spectrum according to molecular status of IDH1/2, 1p/19q co-deletion (1p/19q), gain of chromosome 7 and/or deletion of chromosome 10 (7gain/10del), and MGMT promoter methylation, histological grade, age at initial diagnosis, and history of prior treatment with alkylating agents or radiation therapy (the distinction between photon and proton therapy was not systematically captured) in the DFCI-Profile dataset (n = 84, data not shown for the single sample from other gliomas, IDH1/2-wt subgroup). b, Top, distribution of histomolecular groups in non-hypermutated and hypermutated gliomas from the combined sequencing dataset (n = 2,173). Bottom, distribution of molecular groups in de novo and post-treatment hypermutated gliomas from the DFCI-Profile dataset (n = 85) (annotation not available for the MSKCC-IMPACT set). c, Prevalence of hypermutation according to MGMT promoter methylation and IDH1/2 mutation status in post-temozolomide gliomas from the DFCI-Profile dataset (n = 150). Two-sided Fisher’s exact test. d, Number of temozolomide cycles according to IDH1/2 mutation status in post-temozolomide diffuse gliomas from the DFCI-Profile dataset (n = 211 gliomas). Patients who received combined chemoradiation but no adjuvant temozolomide were included. Two-sided Wilcoxon rank-sum test. e, Boxplots of TMB in post-treatment hypermutated gliomas according to the number of temozolomide cycles received before surgery. Kruskal–Wallis test and Dunn’s multiple comparison test. f, TMB in recurrent gliomas according to treatments received before surgery. Patients who received multiple treatment modalities were excluded. Kruskal–Wallis test and Dunn’s multiple comparison test. Boxes, quartiles; centre lines, median ratio for each group; whiskers, absolute range (d–f). g, Integrated analysis of the FMI dataset (n = 8,121 gliomas) depicting tumour mutation burden, the number of indels at homopolymer regions, and the SNV mutation spectrum detected in each tumour according to molecular status of IDH1/2 and 1p/19q co-deletion (1p/19q), MSI status, and age at initial diagnosis. Dominant mutational signatures detected in hypermutated samples are depicted. The dotted line indicates the threshold for samples with a high mutation burden (8.7 mutations per Mb). h, Prevalence of hypermutation among molecularly defined subgroups in the FMI dataset (n = 8,121 gliomas). Chi-squared test. i, Dominant mutational signatures detected in hypermutated samples in the FMI dataset (n = 8,121 gliomas). Chi-squared test. j, Mutated genes and pathways enriched in hypermutated gliomas in the FMI dataset (n = 8,121). Enrichment was assessed using a permutation test to control for random effects of hypermutability in tumours with high TMB. k, l, Proportion of TMB^high versus TMB^low samples with mutations in selected DNA repair genes and glioma drivers (e) and in the MMR pathway (MSH2, MSH6, MLH1 and PMS2; f). Permutation test; ****P < 0.0001, ***P < 0.001, **P < 0.01; ns, not significant.