Supplementary Figure 1 Depths and coverages in whole-exome and targeted deep sequencing data. Depth (top) and coverage (bottom) of whole-exome sequencing for 38 independent JPN cases (mean depth = 130) (a), ten serial sampling cases (mean depth = 119) (b), four multi-regional sampling cases (mean depth = 142) (c), 425 TCGA cases (mean depth = 94) (d) and targeted deep sequencing for 332 JPN cases (mean depth = 178) (e). The genetic fractions analyzed by the indicated coverage are shown by color.
Supplementary Figure 2 Number of somatic mutations detected by whole-exome sequencing in the JPN and TCGA cohorts. Number of somatic mutations detected by whole-exome sequencing in the JPN and TCGA cohorts. (a) Thirty-eight independent JPN cases, (b) 10 serial sampling cases, (c) 4 multi-regional sampling cases and (d) 425 TCGA cases.
Supplementary Figure 3 Mutational spectra in grade II and III glioma. Mutational spectra of primary grade II and III glioma cases (n = 476) except for TCGA-DU-6392-01A (a) and relapsed hypermutated cases (n = 2) (b). Each plot organizes the 96 mutational patterns. Colors indicate the base substitution type. Each substitution is divided into the 16 pairs of immediately 5 and 3 bases. The height of each block is the frequency.
Supplementary Figure 4 Genetic landscape of 425 grade II and III glioma cases from the TCGA cohort. Molecular classification, histology types, WHO grades (on top rows), and types of mutations and CNVs are shown by color as indicated. The number of samples that had alterations in frequently mutated genes and CNVs are shown in a bar plot (right). PI3K, phosphatidylinositol 3-kinase; RTK, receptor tyrosine kinase; HMT, histone methyltransferase.
Supplementary Figure 5 Genetic landscape of 757 grade II and III glioma cases from the JPN and TCGA cohorts. The representation is the same as that used in Supplementary Figure 4.
Supplementary Figure 6 Impact of histopathological subtypes on overall survival. (a) Kaplan-Meier curves for each histopathological subtype from the combined JPN and TCGA cohort (n = 664). (b) Kaplan-Meier curve for type III tumors separated by histopathological diagnoses (n = 128). As a reference, the corresponding curve for primary GBM is also depicted based on combined JPN (n = 79) and TCGA (n = 583) data. P values were calculated using the log-rank test. DA, diffuse astrocytoma; AA, anaplastic astrocytoma; OA, oligoastrocytoma; AOA, anaplastic oligoastrocytoma; OD, oligodendroglioma; AO, anaplastic oligodendroglioma.
Supplementary Figure 7 DNA methylation analysis of grade II and III gliomas and glioblastomas. (a) Consensus clustering matrix of 425 grade II and III glioma and 144 glioblastoma samples for k = 3. (b) Cumulative distribution function plots from the consensus matrices for k = 2 to k = 6. (c) Integrated view of DNA methylation clustering combined with genetic subtypes, IDH1 and IDH2 mutations, and histopathological diagnosis. GBM, glioblastoma; NA, not available
Supplementary Figure 8 DNA expression analysis of grade II and III gliomas and glioblastomas. (a) Consensus clustering matrix of 422 grade II and III glioma and 160 glioblastoma samples for k = 4. (b) Cumulative distribution function plots from the consensus matrices for k = 2 to k = 6. (c) Integrated view of expression clustering combined with genetic subtypes, IDH1 and IDH2 mutations, and histopathological diagnosis. GBM, glioblastoma; NA, not available.
Supplementary Figure 9 The frequency of affected samples. The frequency of affected samples from the JPN cohort (left) (n = 332) and the TCGA cohort (right) (n = 425). Types of mutation are shown by color as indicated.
Supplementary Figure 10 Mutational patterns of representative genes detected by exome and targeted deep sequencing (n = 757). Mutation distributions for TP53, ATRX, CIC, FUBP1, NOTCH1, NOTCH2, NOTCH3, NOTCH4, EGFR, PDGFRA, PIK3CA, PIK3R1, PTEN, NF1, ARID1A, ARID1B, SMARCA4, SETD2, MLL2 and MLL3 in 757 grade II and III glioma cases. Types of mutation are distinguished by the indicated colors.
Supplementary Figure 11 Spectrum of genetic alteration in each grade II and III glioma type. The frequencies of representative gene mutations and CNVs in each grade II and III glioma type are shown by different colors. These mutations and CNVs were globally mutually exclusive among grade II and III glioma types. PI3K, phosphatidylinositol 3-kinase; HMT, histone methyltransferase; RTK, receptor tyrosine kinase.
Supplementary Figure 12 Temporal patterns of clonal evolution in nine cases with tumor samples collected at multiple time points. The bar plots show the tumor cell fraction of each somatic mutation and CNV (left). A phylogenetic tree depicts the patterns of clonal evolution inferred from somatic mutations and CNVs (right). HD, homozygous deletion; N, normal tissue; P, primary tumor; R, relapse tumor.
Supplementary Figure 13 Spatial patterns of clonal evolution in three cases with multi-regional sampling. Left, the sampling positions (T1 T5 or T6) in three cases LGG172, LGG173 and LGG175 are overlaid onto a three-dimensional magnetic resonance image. Center left, schematic diagram of spatial clonal evolution. Center right, major driver and parallel mutations are mapped in a phylogenetic tree. Right, landscape of genetic lesions in the 5 6 regional samples, showing mutations shared by all samples (orange), those shared by partial subsets of samples (green) and private mutations (blue). Dom, dominant tumor; min, minor tumor; N, normal tissue; T, tumor sample.
Supplementary Figure 14 Clonal architecture estimated by PyClone. Genetic alterations existing in the same clone are shown in the same color by Dinamic Tree Cut. Red clusters indicate the clusters with the highest frequency.
Supplementary Table 4: Significantly mutated genes in 477 grade-ii and III gliomas gene % of sample number of sample number of nonsilent mutations number of silent mutations p-value q-value ATRX 37.1 177 190 4 <1.00E-16 <1.89E-13 CIC 19.3 92 107 2 <1.00E-16 <1.89E-13 FUBP1 9.0 43 44 0 <1.00E-16 <1.89E-13 IDH1 76.7 366 366 0 <1.00E-16 <1.89E-13 IDH2 3.6 17 17 0 <1.00E-16 <1.89E-13 NOTCH1 8.6 41 52 3 <1.00E-16 <1.89E-13 PIK3CA 5.7 27 29 0 <1.00E-16 <1.89E-13 PIK3R1 3.6 17 21 1 <1.00E-16 <1.89E-13 PTEN 4.6 22 22 0 <1.00E-16 <1.89E-13 TCF12 2.3 11 11 0 <1.00E-16 <1.89E-13 TP53 48.6 232 290 1 <1.00E-16 <1.89E-13 EGFR 5.5 26 27 1 9.50E-12 1.49E-08 ZBTB20 3.4 16 16 2 2.99E-09 4.34E-06 ARID1A 3.6 17 18 2 5.15E-08 6.94E-05 CREBZF 1.0 5 5 0 4.69E-05 5.90E-02
Supplementary Table 5: The list of genes analyzed by targeted deep sequencing Targeted genes Categories for correlation and Bradley- Terry model analysis Significant mutated genes by Mutsig CV (premature 270 cases) ATRX IDH1 IDH1/2 CREBZF NUDT11 TP53 FUBP1 CIC NOTCH1 NOTCH family PIK3R1 PI3K classi PIK3CA PI3K classi ARID1A PTEN TPTE SMARCA4 IDH2 IDH1/2 Interacting or same family genes with significant mutated genes DAXX ATRX interact KDM2A related with IDH1/2 TET2 related with IDH1/2 ATF4 CREBZF interact ATF6 CREBZF interact CREB3 CREBZF interact HEY1 CREBZF interact NOTCH2 NOTCH family NOTCH family NOTCH3 NOTCH family NOTCH family NOTCH4 NOTCH family NOTCH family NOTCH2NL NOTCH family NOTCH family TPTE2 TPTE family Known significant mutated genes in pediatric low grade glioma or pilocytic glioma FGFR1 Pilocytic astrocytoma/pediatric low grade glioma Receptor tyrosine kinases(rtk) FGFR2 Pilocytic astrocytoma Receptor tyrosine kinases(rtk) FGFR3 Pilocytic astrocytoma Receptor tyrosine kinases(rtk) PTPN11 Pilocytic astrocytoma BRAF Pediatric low grade glioma NF1 Pediatric low grade glioma H3F3A Pediatric low grade glioma Known significant mutated genes in pediatric low grade glioma or pilocytic glioma PIK3R1 Gliobllastoma PI3K classi PIK3CA Gliobllastoma PI3K classi PTEN Gliobllastoma RB1 Gliobllastoma RB signaling TP53 Gliobllastoma EGFR Gliobllastoma Receptor tyrosine kinases(rtk)
IDH1 Gliobllastoma IDH1/2 SPTA1 Gliobllastoma NF1 Gliobllastoma GABRA6 Gliobllastoma KEL Gliobllastoma CDH18 Gliobllastoma SEMA3C Gliobllastoma STAG2 Gliobllastoma PDGFRA Gliobllastoma Receptor tyrosine kinases(rtk) ATRX Gliobllastoma COL1A2 Gliobllastoma ABCC9 Gliobllastoma NLRP5 Gliobllastoma TCHH Gliobllastoma SCN9A Gliobllastoma LZTR1 Gliobllastoma Genes in frequently aberrated pathway with GBM AKT1 AKT2 AKT3 ARAF BRAF CCND2 CDKN1A CDKN1B CDKN1C CDKN2A CDKN2A/B CDKN2B CDKN2A/B CDKN2C EGFR Receptor tyrosine kinases(rtk) EP300 ERBB2 Receptor tyrosine kinases(rtk) ERBB3 Receptor tyrosine kinases(rtk) FGFR1 Receptor tyrosine kinases(rtk) FGFR2 Receptor tyrosine kinases(rtk) HRAS KRAS MDM2 MDM2/MDM4 MDM4 MDM2/MDM4 MET NF1 NRAS PDGFRA Receptor tyrosine kinases(rtk) PDGFRB Receptor tyrosine kinases(rtk) PIK3C2A PI3K classii PIK3C2B PI3K classii PIK3C2G PI3K classii PIK3CA PI3K classi PIK3CB PI3K classi PIK3CD PI3K classi
PIK3CG PIK3R1 PIK3R2 PTEN RAF1 RB1 TP53 TSC1 TSC2 MTOR RHEB CCND1 MSH2 MSH3 MSH5 MSH6 MLH1 MLH3 PMS1 PMS2 TDG ACTB ACTL6A ACTL6B ARID1A ARID1B ARID2 BRD7 DPF1 DPF2 DPF3 HLTF PBRM1 PHF10 SMARCA1 SMARCA2 SMARCA4 SMARCA5 SMARCAL1 SMARCB1 SMARCC1 SMARCC2 SMARCD1 SMARCD2 SMARCD3 SMARCE1 Chromatin modifers BAP1 CREBBP PI3K classi PI3K classi PI3K classi RB signaling
SRCAP TEP1 TERT Histone methyltransferases ASH1L BMI1 DOT1L EHMT1 EHMT2 EZH1 EZH2 MLL MLL2 MLL3 MLL5 NSD1 PRDM2 PRMT1 SETD1A SETD1B SETD2 SETD7 SETD8 SETDB1 SETDB2 SETMAR SMYD3 SUV39H1 SUV39H2 SUV420H1 SUV420H2 Histone Deacetylases HDAC1 HDAC2 HDAC3 HDAC4 HDAC5 HDAC6 HDAC7 HDAC8 HDAC9 HDAC10 HDAC11 SIRT1 Migration ANXA1 CFL1 CXCR2 GPX1 LYPD3
MSN PAFAH1B1 PODXL POU4F2 PTEN S100A9 SELPLG TPM1 Negative regulation of apoptosis ADAM10 ADAMTSL4 ANXA1 ATG5 CD40LG CDKN1B CFL1 CLU CSTB CXCR2 EGFR FAF1 GPX1 HDAC2 ING3 MATK NF1 NOTCH1 PIK3CA PTEN RB1 SQSTM1 SSTR4 TNFRSF9 TP53 VAV3 VSIG4 Receptor tyrosine kinases(rtk) NOTCH family PI3K classi RB signaling *RB signaling contains CDK4 amplification.
Supplementary Table 7: Significant arm level copy number changes Arm q-value(gains) q-value(losses) 1p 1 7.83E-237 1q 1 1 2p 1 1 2q 1 1 3p 1 1 3q 1 1 4p 1 0.015852613 4q 1 8.22E-11 5p 1 1 5q 1 1 6p 1 1 6q 1 0.02192716 7p 3.96E-127 1 7q 9.87E-234 1 8p 0.015319732 1 8q 2.13E-11 1 9p 1 5.86E-15 9q 1 1 10p 5.81E-14 1.24E-06 10q 1 6.95E-16 11p 0.264543764 0.007282432 11q 8.07E-11 1 12p 2.29E-13 1 12q 1 1 13q 1 9.02E-09 14q 1 0.000653449 15q 1 0.899802777 16p 1 1 16q 1 1 17p 1 1 17q 1 1 18p 1 4.13E-04 18q 1 1.00E-05 19p 1.03E-04 1 19q 0.888616879 8.86947240292981e-317 20p 1.03E-04 1 20q 5.07E-04 1 21q 1 1 22q 1 0.553603782
Supplementary Table 9: Significantly mutated genes in targeted deep sequensing gene % of sample number of samples number of nonsilent mutations p-value q-value IDH1 70.7 198 198 <1.00E-160 <1.00E-160 TP53 38.6 108 130 <1.00E-160 <1.00E-160 CIC 28.6 80 86 3.01E-122 1.86E-120 ATRX 25.7 72 81 5.58E-98 2.58E-96 FUBP1 16.4 46 49 9.51E-79 3.52E-77 NOTCH1 11.8 33 38 5.29E-35 1.63E-33 PIK3R1 7.1 20 20 3.28E-25 8.68E-24 PIK3CA 7.1 20 20 8.67E-22 2.01E-20 SETD2 7.9 22 25 1.45E-19 2.99E-18 IDH2 3.9 11 11 1.35E-14 2.51E-13 PDGFRA 4.3 12 13 1.42E-12 2.39E-11 PTEN 2.5 7 7 3.23E-09 4.98E-08 SMARCA4 4.3 12 12 3.83E-09 5.45E-08 EGFR 3.2 9 10 1.19E-08 1.58E-07 ARID1B 4.6 13 13 1.47E-08 1.81E-07 ARID1A 4.3 12 13 1.78E-08 2.06E-07 ADAM10 1.8 5 8 2.42E-08 2.63E-07 NF1 3.6 10 13 2.42E-07 2.49E-06 H3F3A 1.1 3 3 6.67E-06 6.49E-05 NOTCH2 3.6 10 10 1.17E-05 1.08E-04 CDKN2A 1.1 3 3 1.48E-05 0.000130071 MSH6 2.5 7 7 2.64E-05 0.000221796 FGFR1 1.8 5 5 1.03E-04 0.000826556 PTPN11 1.4 4 4 0.00017048 0.001314108 MLL5 2.1 6 7 0.0002217 0.001640576 SETD8 1.1 3 3 0.00025439 0.001810087 TET2 2.5 7 7 0.00036243 0.002394651 SMARCB1 1.1 3 3 0.00035581 0.002394651 CDKN1A 0.7 2 2 0.00040008 0.00255226 CDKN2C 0.7 2 2 0.00042882 0.002644376 SEMA3C 1.4 4 4 0.00049713 0.002966762 PIK3C2B 2.1 6 6 0.00055665 0.003218153 NLRP5 1.8 5 5 0.00062177 0.003485671 SETDB1 1.4 4 5 0.00090379 0.004873295 PHF10 1.1 3 3 0.00092197 0.004873295 ERBB3 1.4 4 5 0.00109989 0.00565219 COL1A2 1.8 5 5 0.00120272 0.006013607 MSH2 1.4 4 4 0.00130258 0.006341507 TNFRSF9 0.7 2 2 0.00141171 0.006696558 ARAF 1.1 3 3 0.00187958 0.00863186 TPM1 0.7 2 2 0.00191301 0.00863186 BRD7 1.1 3 3 0.0024422 0.010757301 SMARCC1 1.4 4 4 0.00268335 0.011544635
MLL2 3.6 10 11 0.00312714 0.013148207 HDAC11 0.7 2 2 0.00334901 0.013768162 PIK3R2 1.1 3 3 0.00360835 0.014511851 ERBB2 1.4 4 4 0.00457529 0.018009134 EP300 1.8 5 6 0.00488782 0.018453996 CDH18 1.1 3 3 0.00480194 0.018453996 TDG 0.7 2 2 0.00530578 0.019631394 SQSTM1 0.7 2 2 0.00643403 0.023339113 GABRA6 0.7 2 2 0.00696381 0.024775079 SCN9A 1.8 5 5 0.00719832 0.025126206 NUDT11 0.4 1 1 0.00876195 0.030017795 CFL1 0.4 1 1 0.00896572 0.030157421 SMARCD1 0.7 2 2 0.00984061 0.032509155 KRAS 0.4 1 1 0.01145872 0.037190598 PIK3CD 1.1 3 3 0.01239032 0.038851016 PODXL 0.7 2 2 0.01218481 0.038851016 MSN 0.7 2 2 0.01331366 0.041050458 ASH1L 2.1 6 6 0.01392739 0.042238814 PDGFRB 0.7 2 3 0.01498657 0.044717983 PRDM2 1.4 4 4 0.01606009 0.047160576 FAF1 0.7 2 2 0.01818953 0.051770202 RAF1 0.7 2 2 0.01804447 0.051770202 ARID2 0.7 2 4 0.02063459 0.056465565 SMARCC2 1.1 3 3 0.02027732 0.056465565 SETMAR 0.7 2 2 0.02075491 0.056465565 SETDB2 0.7 2 2 0.02359212 0.063254224 SETD1B 1.1 3 4 0.02458402 0.064350495 KEL 0.7 2 2 0.02469668 0.064350495 EHMT1 1.1 3 3 0.02509403 0.064477724 CCND1 0.4 1 1 0.02623477 0.066485375 BRAF 0.7 2 2 0.02771523 0.069288081 CDKN1C 0.4 1 1 0.02974517 0.073371422 BMI1 0.4 1 1 0.03147873 0.076625853 FGFR2 0.7 2 2 0.03309407 0.079511716 PIK3C2G 1.1 3 3 0.03505285 0.081080259 LZTR1 0.7 2 2 0.03492978 0.081080259 ANXA1 0.4 1 1 0.03506173 0.081080259 VAV3 0.7 2 2 0.0356576 0.081176801 ATF4 0.4 1 1 0.03598107 0.081176801 CXCR2 0.4 1 1 0.0376591 0.083938965 HDAC8 0.4 1 1 0.04090852 0.090096147 DOT1L 1.1 3 3 0.04229339 0.092050326 SSTR4 0.4 1 1 0.0430653 0.092640463 RB1 0.7 2 2 0.04464041 0.094925002 VSIG4 0.4 1 1 0.04526353 0.095156286 NOTCH3 1.4 4 4 0.04829575 0.099274598 SUV39H1 0.4 1 1 0.0479136 0.099274598 SELPLG 0.4 1 1 0.05125064 0.101950206 ACTL6B 0.4 1 1 0.05082905 0.101950206 HDAC3 0.4 1 1 0.05125064 0.101950206
HDAC7 0.7 2 2 0.05232641 0.102982836 SPTA1 1.4 4 4 0.05566088 0.108392235 SRCAP 1.4 4 5 0.05786668 0.109238112 CREBBP 1.4 4 4 0.05747799 0.109238112 SETD1A 1.1 3 3 0.05771837 0.109238112 SUV420H2 0.4 1 1 0.05860601 0.10951628 SMARCA1 0.7 2 2 0.06060385 0.112117122 AKT3 0.4 1 1 0.062412 0.114319007 HDAC4 0.7 2 2 0.0647471 0.115479537 HDAC2 0.4 1 1 0.06446005 0.115479537 MDM4 0.4 1 1 0.06491823 0.115479537 MTOR 1.4 4 4 0.06637289 0.116114451 MDM2 0.4 1 1 0.06653044 0.116114451 PIK3CG 0.7 2 2 0.067294 0.116349444 TERT 0.7 2 2 0.07163857 0.12271422 TEP1 1.4 4 4 0.07331211 0.124428806 SMARCD2 0.4 1 1 0.07454566 0.12537225 KDM2A 0.7 2 2 0.07610543 0.12684239 CSTB 0.0 0 0 0.0797961 0.131806053 EHMT2 0.7 2 2 0.0834997 0.136703041 HDAC6 0.7 2 2 0.08428704 0.136781595 STAG2 0.7 2 2 0.09282526 0.14804029 S100A9 0.0 0 0 0.0920809 0.14804029 HDAC10 0.4 1 1 0.1098105 0.171321319 ATF6 0.4 1 1 0.11007987 0.171321319 CDKN2B 0.0 0 0 0.11020128 0.171321319 MLL 1.4 4 5 0.12165522 0.187551804 MLH1 0.4 1 1 0.13385168 0.204649262 RHEB 0.0 0 0 0.14392732 0.218250444 NRAS 0.0 0 0 0.14751529 0.220083289 HRAS 0.0 0 0 0.14751529 0.220083289 FGFR3 0.4 1 1 0.14873189 0.220123195 CDKN1B 0.0 0 0 0.15393577 0.226016805 MSH5 0.4 1 1 0.156584 0.227610396 GPX1 0.0 0 0 0.15748179 0.227610396 PIK3C2A 0.7 2 2 0.17064484 0.243801378 SUV420H1 0.4 1 1 0.17131989 0.243801378 NOTCH2NL 0.0 0 0 0.18051567 0.254926707 PMS1 0.4 1 1 0.1853681 0.259796206 TSC2 0.7 2 2 0.19586674 0.272446216 CD40LG 0.0 0 0 0.1975454 0.272730591 ATG5 0.0 0 0 0.206927 0.283566623 CCND2 0.0 0 0 0.21619891 0.294094103 PIK3CB 0.4 1 1 0.22738592 0.30646869 HEY1 0.0 0 0 0.22860908 0.30646869 MLL3 1.8 5 5 0.2348725 0.312600095 NOTCH4 0.7 2 2 0.23839079 0.315016398 HDAC5 0.4 1 1 0.24370971 0.319760965 LYPD3 0.0 0 0 0.25284304 0.32940819 TSC1 0.4 1 1 0.2563691 0.331261907
CREBZF 0.0 0 0 0.25784711 0.331261907 DPF3 0.0 0 0 0.25971498 0.331360487 CREB3 0.0 0 0 0.26836974 0.335462173 SETD7 0.0 0 0 0.26529043 0.335462173 PRMT1 0.0 0 0 0.26836974 0.335462173 ACTB 0.0 0 0 0.27082389 0.336257851 DPF2 0.0 0 0 0.28055846 0.346022095 SUV39H2 0.0 0 0 0.2919496 0.351290718 POU4F2 0.0 0 0 0.29135459 0.351290718 PAFAH1B1 0.0 0 0 0.2919496 0.351290718 DPF1 0.0 0 0 0.29432466 0.351290718 SMARCE1 0.0 0 0 0.29254411 0.351290718 ING3 0.0 0 0 0.29669175 0.351845981 ACTL6A 0.0 0 0 0.30316038 0.354966272 SMYD3 0.0 0 0 0.30257479 0.354966272 CLU 0.0 0 0 0.3147695 0.366241241 MET 0.4 1 1 0.33142281 0.376839204 AKT1 0.0 0 0 0.33238258 0.376839204 SMARCD3 0.0 0 0 0.33406286 0.376839204 AKT2 0.0 0 0 0.33294315 0.376839204 HDAC1 0.0 0 0 0.33350324 0.376839204 MATK 0.0 0 0 0.34790173 0.390071631 TPTE2 0.0 0 0 0.35552549 0.396218161 TPTE 0.0 0 0 0.37103521 0.411027028 ABCC9 0.4 1 1 0.37388529 0.411718926 SMARCA2 0.4 1 1 0.38603146 0.422578822 EZH1 0.0 0 0 0.46651269 0.498382175 EZH2 0.0 0 0 0.4683022 0.498382175 DAXX 0.0 0 0 0.46874864 0.498382175 SIRT1 0.0 0 0 0.46651269 0.498382175 BAP1 0.0 0 0 0.45838507 0.498382175 TCHH 0.4 1 1 0.48565 0.513401429 PMS2 0.0 0 0 0.51563668 0.542004468 SMARCAL1 0.0 0 0 0.55165847 0.576592189 HLTF 0.0 0 0 0.57190066 0.594391132 SMARCA5 0.0 0 0 0.58708768 0.606766593 ADAMTSL4 0.0 0 0 0.59464822 0.607789619 HDAC9 0.0 0 0 0.59294216 0.607789619 MSH3 0.0 0 0 0.61554172 0.625688012 NSD1 0.4 1 1 0.66110781 0.668333028 MLH3 0.0 0 0 0.70517107 0.709003525 PBRM1 0.0 0 0 0.73985601 0.739856012
Supplementary Table 13: Hot-spot domains in TP53, ATRX, CIC, NOTCH1 and SMARCA4 Gene refseq Domain amino acid amino acid start end TP53 NM_000546 transcription activation (acidic) 1 44 TP53 NM_000546 DNA binding domain 100 292 TP53 NM_000546 oligomerization domain 325 356 ATRX NM_138270 ADD 159 296 ATRX NM_138270 Helicase domain 1581 2205 CIC NM_015125 DNA_binding HMG box 200 268 CIC NM_015125 Pre_Pro-rich 1450 1523 NOTCH1 NM_017617 anterior part of EGF-like repeats 20 500 NOTCH1 NM_017617 ANK 1927 2089 SMARCA4 NM_001128845 SNF2 family N terminal domain 757 1052
Supplementary Table 15: Results of TERT promoter mutations Sample Status Method LGG1T1 228G>A PCR_based_deep LGG1T2 228G>A Capture+PCR_based_deep LGG2T1 intact Capture+PCR_based_deep LGG2T2 intact PCR_based_deep LGG2T3 intact PCR_based_deep LGG2T4 intact PCR_based_deep LGG3T1 228G>A PCR_based_deep LGG3T2 228G>A PCR_based_deep LGG4T1 228G>A Capture+PCR_based_deep LGG4T2 228G>A PCR_based_deep LGG5T1 intact Sanger LGG5T2 intact Capture LGG5T3 intact Capture LGG6T1 228G>A Capture+PCR_based_deep LGG6T3 228G>A Capture+PCR_based_deep LGG7T1 228G>A Capture+PCR_based_deep LGG7T2 228G>A PCR_based_deep LGG8T1 250G>A Capture LGG8T2 250G>A Capture LGG9T 228G>A Sanger LGG10T intact Sanger LGG11T intact Capture LGG12T intact Sanger LGG13T intact Capture LGG14T 250G>A Sanger LGG15T intact Capture LGG16T intact Sanger LGG17T intact Capture LGG18T 228G>A Sanger LGG19T 250G>A Capture+PCR_based_deep LGG20T 228G>A PCR_based_deep LGG21T intact PCR_based_deep LGG22T 250G>A PCR_based_deep LGG23T 228G>A Sanger LGG24T 250G>A Sanger LGG25T 228G>A Capture+PCR_based_deep LGG26T 250G>A PCR_based_deep LGG27T 250G>A Sanger LGG28T 228G>A Capture LGG29T intact Sanger LGG30T intact Capture+Sanger LGG31T 228G>A PCR_based_deep LGG32T 228G>A Capture+PCR_based_deep LGG33T 228G>A Sanger LGG34T intact Sanger LGG35T 228G>A Capture+PCR_based_deep LGG36T 228G>A Capture+PCR_based_deep
LGG37T intact Sanger LGG38T intact Capture LGG39T intact Capture LGG40T 228G>A Capture LGG41T 228G>A Sanger LGG42T 228G>A Sanger LGG43T 228G>A Sanger LGG44T 250G>A Capture LGG45T 228G>A Capture LGG46T 228G>A Capture LGG47T 228G>A Capture LGG48T intact Capture LGG49T 228G>A Capture LGG50T 228G>A Sanger LGG51T 228G>A Capture+PCR_based_deep LGG52T 228G>A Capture+PCR_based_deep LGG54T intact Capture LGG55T 228G>A Capture LGG56T intact Sanger LGG58T intact Capture LGG59T intact Capture LGG60T intact Sanger LGG61T 250G>A PCR_based_deep LGG62T intact Sanger LGG63T 228G>A PCR_based_deep LGG64T intact Sanger LGG65T 250G>A Capture+PCR_based_deep LGG66T 228G>A PCR_based_deep LGG67T 228G>A Capture LGG68T 228G>A Capture+PCR_based_deep LGG69T intact Capture LGG70T intact Sanger LGG71T intact Capture LGG72T 228G>A Capture+PCR_based_deep LGG73T 228G>A Capture+PCR_based_deep LGG74T intact Sanger LGG75T 228G>A PCR_based_deep LGG76T 228G>A PCR_based_deep LGG77T intact Sanger LGG78T intact Capture LGG79T 228G>A Sanger LGG80T intact PCR_based_deep LGG81T intact Capture LGG82T intact Sanger LGG83T 228G>A PCR_based_deep LGG84T 250G>A Capture+PCR_based_deep LGG85T 228G>A PCR_based_deep LGG86T 228G>A Capture+PCR_based_deep LGG87T 228G>A Sanger LGG88T 228G>A PCR_based_deep
LGG89T 250G>A Sanger LGG90T intact Sanger LGG91T intact Sanger LGG92T intact Capture LGG93T intact Sanger LGG94T intact Sanger LGG95T 228G>A Sanger LGG96T intact Sanger LGG97T 228G>A PCR_based_deep LGG98T intact Capture LGG99T intact Sanger LGG100T intact Sanger LGG101T intact Sanger LGG102T intact Sanger LGG103T 250G>A PCR_based_deep LGG104T 228G>A Sanger LGG105T 228G>A Sanger LGG106T intact Sanger LGG107T 250G>A PCR_based_deep LGG108T 228G>A Sanger LGG109T intact Capture LGG110T 250G>A PCR_based_deep LGG111T intact Capture LGG112T 228G>A PCR_based_deep LGG113T 250G>A PCR_based_deep LGG114T 228G>A PCR_based_deep LGG115T 250G>A PCR_based_deep LGG116T intact Sanger LGG117T intact Sanger LGG118T 228G>A Sanger LGG119T 228G>A Capture+PCR_based_deep LGG120T intact Sanger LGG121T intact Sanger LGG122T 250G>A Capture LGG123T 228G>A PCR_based_deep LGG124T intact Capture LGG125T intact Capture LGG126T intact Sanger LGG127T intact Capture LGG128T intact Capture LGG129T intact Capture LGG130T intact Sanger LGG131T intact Capture LGG132T 228G>A PCR_based_deep LGG133T intact Capture LGG134T 228G>A Sanger LGG135T intact Capture LGG136T intact Capture LGG137T 250G>A Capture LGG138T 228G>A Capture+PCR_based_deep
LGG139T intact Sanger LGG140T intact Capture LGG141T 250G>A PCR_based_deep LGG142T 250G>A Capture+PCR_based_deep LGG143T intact Capture LGG144T intact Capture LGG145T 250G>A Capture+PCR_based_deep LGG146T 250G>A PCR_based_deep LGG147T intact Capture LGG148T 250G>A Capture+PCR_based_deep LGG149T intact Capture LGG150T 228G>A PCR_based_deep LGG151T 250G>A Capture+PCR_based_deep LGG152T 228G>A Capture+PCR_based_deep LGG153T intact Capture+Sanger LGG154T intact Sanger LGG155T 228G>A PCR_based_deep LGG156T 250G>A Sanger LGG157T 250G>A Capture LGG158T 250G>A Capture LGG159T 228G>A Capture LGG160T intact Capture LGG161T 228G>A Capture LGG162T intact Capture LGG163T intact Sanger LGG164T intact Capture LGG165T 250G>A Capture+PCR_based_deep LGG166T 250G>A Sanger LGG167T 250G>A Capture LGG168T 250G>A Capture LGG169T 250G>A Capture LGG170T intact Sanger LGG171T 228G>A Capture LGG172T1 intact Capture+PCR_based_deep LGG172T2 intact Capture+PCR_based_deep LGG172T3 intact Capture+PCR_based_deep LGG172T4 intact Capture+PCR_based_deep LGG172T5 intact Capture+PCR_based_deep LGG173T1 228G>A Capture+PCR_based_deep LGG173T2 228G>A PCR_based_deep LGG173T3 228G>A Capture+PCR_based_deep LGG173T4 228G>A PCR_based_deep LGG173T6 228G>A PCR_based_deep LGG174T1 228G>A Capture+PCR_based_deep LGG174T2 228G>A PCR_based_deep LGG174T3 228G>A Capture+PCR_based_deep LGG174T4 228G>A PCR_based_deep LGG174T5 228G>A PCR_based_deep LGG174T6 228G>A Capture+PCR_based_deep LGG174T7 228G>A PCR_based_deep
LGG174T8 228G>A Capture+PCR_based_deep LGG174T9 228G>A Capture+PCR_based_deep LGG175T1 228G>A Capture+PCR_based_deep LGG175T2 228G>A PCR_based_deep LGG175T3 228G>A Capture+PCR_based_deep LGG175T4 228G>A Capture+PCR_based_deep LGG175T5 228G>A Capture+PCR_based_deep LGG175T6 228G>A PCR_based_deep LGG176T 228G>A Capture LGG177T intact Capture LGG178T 228G>A Capture+PCR_based_deep LGG179T 228G>A PCR_based_deep LGG180T intact Capture LGG181T 228G>A Capture+PCR_based_deep LGG182T intact Capture LGG183T 228G>A PCR_based_deep LGG184T intact Sanger LGG185T intact Capture LGG186T intact Capture LGG187T intact Capture LGG188T intact Capture LGG189T intact Capture LGG190T intact Capture LGG191T intact Capture LGG192T 250G>A Capture LGG193T intact Capture LGG194T intact Capture LGG195T intact Capture LGG196T 228G>A Capture LGG197T 228G>A Capture LGG198T intact Capture LGG199T intact Capture LGG200T intact Capture LGG201T 228G>A Sanger LGG202T1 228G>A Capture+PCR_based_deep LGG202T2 228G>A Capture LGG203T 228G>A Capture+PCR_based_deep LGG204T 228G>A Capture+PCR_based_deep LGG205T 228G>A Capture+PCR_based_deep LGG206T intact Capture LGG207T 228G>A Sanger LGG208T 228G>A Capture LGG209T 228G>A Capture LGG210T 228G>A Capture LGG211T intact Sanger LGG212T 228G>A Sanger LGG213T 250G>A Capture LGG214T 228G>A Capture LGG215T intact Sanger LGG216T 228G>A Capture
LGG217T intact Capture LGG218T 228G>A Capture LGG219T intact Sanger LGG220T intact Capture LGG222T intact Capture LGG223T intact Sanger LGG224T 228G>A Capture LGG225T intact Sanger LGG226T 228G>A Capture LGG227T intact Capture LGG228T 250G>A Capture LGG229T 228G>A Capture LGG230T intact Capture LGG231T 228G>A Sanger LGG232T intact Sanger LGG233T 228G>A Capture LGG234T intact Capture LGG235T intact Capture LGG236T intact Sanger LGG237T intact Capture LGG238T intact Capture LGG239T1 intact Capture LGG239T2 intact Capture LGG240T 250G>A Capture LGG241T intact Sanger LGG242T intact Capture+Sanger LGG242T intact Capture+Sanger LGG243T 228G>A Capture LGG244T 250G>A Capture LGG245T intact Capture LGG246T intact Sanger LGG247T 250G>A Capture LGG248T 228G>A Capture LGG249T 250G>A Capture+Sanger LGG249T 250G>A Capture LGG250T intact Capture LGG251T intact Capture LGG252T 228G>A Sanger LGG253T 228G>A Capture LGG254T 250G>A Sanger LGG255T 228G>A Sanger LGG256T 228G>A Capture LGG257T 250G>A Capture LGG258T intact Capture LGG259T intact Capture LGG260T intact Sanger LGG261T 228G>A Capture LGG262T intact Sanger LGG263T intact Capture LGG264T 228G>A Capture
LGG265T 250G>A Capture LGG266T intact Sanger LGG267T 228G>A Capture LGG268T intact Capture LGG269T intact Sanger LGG270T1 intact Sanger LGG270T2 intact Sanger LGG270T3 intact Sanger LGG271T intact Capture LGG272T 250G>A Capture LGG273T 250G>A Capture LGG274T intact Capture LGG275T intact Capture LGG276T 228G>A Capture LGG277T 228G>A Capture LGG278T intact Capture LGG279T intact Capture LGG280T intact Capture LGG281T 250G>A Capture+PCR_based_deep LGG282T 228G>A Sanger LGG283T 228G>A Capture LGG284T 228G>A Capture+PCR_based_deep LGG285T intact Capture+Sanger LGG286T 228G>A Capture LGG287T intact Capture LGG288T intact Capture LGG289T intact Sanger LGG290T intact Capture LGG291T intact Capture LGG292T 228G>A Capture LGG293T intact Sanger LGG294T intact Sanger LGG295T 228G>A Capture LGG296T intact Capture LGG297T 228G>A Capture+PCR_based_deep LGG298T 250G>A Capture LGG299T 250G>A Capture LGG300T intact Sanger LGG301T intact Sanger LGG302T intact Sanger LGG303T intact Sanger LGG304T 228G>A PCR_based_deep LGG305T intact Sanger LGG306T 228G>A Capture LGG307T intact Sanger LGG308T intact Sanger LGG309T intact Sanger LGG310T 250G>A Capture LGG311T 228G>A Sanger LGG312T 228G>A Capture
LGG313T 228G>A PCR_based_deep LGG314T 228G>A Sanger LGG315T 250G>A Sanger LGG316T 228G>A Capture LGG317T 228G>A Capture LGG318T 228G>A Capture LGG319T 250G>A Sanger LGG320T 228G>A Capture LGG321T 228G>A Capture+PCR_based_deep LGG322T intact Sanger LGG323T intact Sanger LGG324T 228G>A Capture LGG325T intact Sanger LGG326T intact Sanger LGG327T intact Sanger LGG328T intact Sanger LGG329T intact Capture LGG330T intact Capture LGG331T intact Capture LGG332T intact Sanger LGG333T intact Sanger LGG334T intact Capture LGG335T intact Capture