1. Supplementary Table S1. Patient demographics of the RRBS discovery set. Characteristics RRBS discovery set TotalIDH1/2 WT IDH1 MUT No. of Patients311120 Age at Diagnosis Median44.6863.3338.14 >50/ ≤ 5012 /198/34/16 Gender Male/ Female18 /137/411/9 Tissue Pathology Astrocytoma (Grade II)303 Oligodendroglioma (Grade II)404 Oligoastrocytoma (Grade II)000 Astrocytoma (Grade III)523 Oligodendroglioma (Grade III)624 Oligoastrocytoma (Grade III)000 Glioblastoma (Grade IV)1376 Karnofsky Performance status ≥ 70 311 <70 281018 Unknown101 Extent of Resection Biopsy (0-9%)303 Subtotal resection (STR) (10-90%)1697 Gross total resection (GTR) (90-100%)1129 Unknown101 1

2. Total Reads 30 343 031 Aligned Reads 17 583 403 CpG Sites Covered2 160 341 Ave. Reads per CpG site21.98 Total CpG island26 567 CpG Islands Covered24 063 % Coverage within Island0.57 Total Unique Refseq Genes21 338 Unique Refseq Genes Covered20 600 Total Unique Promoters21 338 Unique Promoters Covered17 097 % Methylated CpG sites (>0.5)0.52 Supplementary Table S2. RRBS Mean Coverage per sample. 2

3. Supplementary Table S3. RRBS coverage of CpG islands associated with miRNAs. Total Data Data Covered by RRBS No. of CpG islands No. of associated miRNA No. of CpG islands (% of Total) No. of associated miRNA (% of Total) Total known CpG islands26 642NA22 646 (85%)NA Within 5000bp of miRNA coding region605491510 (84.29%)430 (87.57%) Within 500bp of miRNA coding region216231182 (84.25%)198 (85.71%) 3

4. Supplementary Table S4. Hypermethylated CpG islands within 5000 bp of miRNAs in IDH1 MUT versus IDH1/2 WT gliomas (G-CIMP). 4

5. Supplementary Table S5. Targeted bisulfite sequencing results for miR-148a associated CpG island (Region 1). Characteristics IDH1 WT IDH1/2 MUT miR-148a Methyl. No. (% of IDH1 WT ) miR-148a Unmethyl. No. (% of IDH1 WT ) miR-148a Methyl. No. (% of IDH1/2 MUT ) miR-148a Unmethyl. No. (% of IDH1/2 MUT ) Normal Brain Tissue Sample (n=17)0 (0%)17 (100%)0 (0%) Total Glioma Tissue Sample (n=291)12 (5.4%)207 (94.6%)70 (97.2%)2 (2.8%) Astrocytoma grade II (n=2)0020 Oligodendroglioma grade II (n=18)02160 Oligoastrocytoma grade II (n=5)0050 Astrocytoma grade III (n=17)2780 Oligodendroglioma grade III (n=15)01131 Oligoastrocytoma grade III (n=10)0370 Glioblastoma grade IV (GBM) (n=224)10194191 miR-148a Methyl.: methylated miR-148a; miR-148a Unmethyl.: unmmethylated miR-148a 5

6. Supplementary Table S6. Targeted bisulfite sequencing results for miR-148a associated CpG island (Region 2). Characteristics IDH1 WT IDH1/2 MUT miR-148a Methyl. % of the No. of IDH1 WT miR-148a Unmethyl. % of the No. of IDH1 WT miR-148a Methyl. % of the No. of IDH1/2 MUT miR-148a Unmethyl. % of the No. of IDH1/2 MUT Normal Brain Tissue Sample (n=17)0 (0%)17 (100%)0 (0%) Total Glioma Tissue Sample (n=63) 6 (28.5%)15 (71.5%)36 (85.7%)6 (14.3%) Astrocytoma grade II (n=2) 0020 Oligodendroglioma grade II (n=16) 02131 Oligoastrocytoma grade II (n=4) 0040 Astrocytoma grade III (n=12) 3531 Oligodendroglioma grade III (n=10) 0082 Oligoastrocytoma grade III (n=7) 1150 Glioblastoma grade IV (GBM) (n=12) 2712 6 miR-148a Methyl.: methylated miR-148a; miR-148a Unmethyl.: unmmethylated miR-148a

7. Supplementary Table S7. Demographics and miR-148a methylation status of GBM and Grade III glioma patient cohort. Characteristics GBM Patient CohortGrade III Patient Cohort Total No. (% of Total) miR-148a methyl. No. (% of Total) miR-148a Unmethyl. No. (% of Total) Total No. (% of Total) miR-148a methyl. No. (% of Total) miR-148a Unmethyl. No. (% of Total) Number of Patients224 (100%)29 (13%)195 (87%)42 (100%)30 (71%)12 (29%) Age at Diagnosis Median57.4645.4558.3140.0235.6051.70 >50151 (67%)11 (38%)140 (72%)11 (26%)4 (13%)7 (58%) ≤ 5073 (33%) 18 (62%)55 (28%)31 (74%)26 (87%)5 (42%) Gender Male141 (63%)18 (62%)123 (63%)27 (64%)20 (67%)7 (58%) / Female83 (37%)11 (38%)72 (37%)15 (36%)10 (33%)5 (42%) MGMT Methylation Methylated83 (37%)16 (55%)67 (34%)17 (40%)13 (43%)4 (33%) Unmethylated127 (57%)8 (28%)119 (61%)11 (26%)5 (17%)6 (50%) Unknown14 (6%)5 (17%)9 (5%)14 (33%)12 (40%)2 (17%) IDH1/2 Genotype IDH1 WT 204 (91%)10 (34%)194 (99.5%)13 (31%)2 (7%)11 (92%) IDH1/2 MUT 20 (8.5%)19 (62%)1 (0.5%)29 (69%)28 (93%)1 (8%) Treatment protocol Treated with RT at any time220 (98%)28 (97%)192 (98%)37 (88%)26 (87%)11 (92%) Treated with TMZ at any time221 (99%)28 (97%)193 (99%)32 (76%)21 (70%)11 (92%) Pre-treatment sample212 (95%)25 (86%)187 (96%)36 (86%)24 (80%)12 (100%) Pre-treatment data not available3 (1%)1 (3%)2 (1%)5 (12%)4 (13%)1 (8%) Karnofsky Performance status ≥ 70210 (94%)28 (97%)182 (93%)29 (69%)20 (67%)9 (75%) <7014 (6%)1 (3%)13 (7%)8 (19%)5 (17%)3 (25%) Unknown0 (0%) 5 (12%)5 (17%)0 (0%) Extent of Resection biopsy (0-9%)31 (14%)1 (3%)30 (15%)9 (21%)6 (20%)3 (25%) subtotal resection (STR) (10-90%)103 (46%)15 (52%)88 (45%)19 (45%)12 (40%)7 (58%) gross total resection (GTR) (90-100%)87 (39%)13 (45%)74 (38%)14 (33%)12 (40%)2 (17%) Unknown3 (1%)0 (0%)3 (2%)0 (0%) 7

8. GBMGrade III Univariate AnalysisMultivariate AnalysisUnivariate AnalysisMultivariate Analysis HR (95%CI) P-Value HR (95%CI) P-Value HR (95%CI) P-Value HR (95%CI) P-Value KPS (<70) 3.00 (1.73-5.21) 9.04E-05 2.20 (1.25-3.88) 0.006 3.01 (0.37-24.32) 0.3 5.54 (0.53-57.80) 0.151 Extent of Resection (STR + Biopsy) 1.63 (1.21-2.20) 0.001 1.51 (1.11-2.05) 0.008 3.72 (1.07-12.85) 0.037 4.03 (1.02-15.91) 0.046 Age at Diagnosis 1.65 (1.21-2.26) 0.001 1.35 (0.96-1.89) 0.075 2.79 (1.00-7.78) 0.049 1.85 (0.56-6.16) 0.311 Gender (Male) 1.37 (1.02-1.84) 0.036 1.32 (0.97-1.79) 0.068 0.32 (0.125-0.81) 0.017 0.45 (0.17-1.18) 0.104 miR-148a (Unmethyl.) 1.82 (1.14-2.90) 0.011 1.59 (0.98-2.6) 0.059 4.28 (1.58-11.59) 0.004 5.83 (1.47-23.08) 0.012 Supplementary Table S8. Univariate and Multivariate Cox Proportional Hazards Analysis of Factors Affecting OS in GBM and Grade III gliomas. KPS, Karnofsky Performance Status; HR, hazard ratio; miR-148a Unmethyl.:unmmethylated miR-148a 8

9. Supplementary Table S9. Predicted miR-148a targets. 9

10. Supplementary Table S10. Bisulfite sequencing primer sets. Sequencing PositionPrimers Region 1Stage 1 Forward Primer: 5’-GTTTTAGGTGGTTATTTGGTT- 3’ (CpG Island 101-115) Reverse Primer: 5’-ACTAAATTTAAAAAAAAAAACTCC- 3’ Stage 2 Forward Primer: 5’-GTTTTAGGTGGTTATTTGGTT- 3’ Reverse Primer: 5’-CATTCAAAAACATCTTACAAAAC-3’ Region 2Stage 1 Forward Primer: 5’-TTTTTTTGAGATTTTTTTTTTTAGTTATTTT-3’ (CpG Island 11-24) Reverse Primer: 5’-AAAAAAAATCTACTAAAATAAAAAACAAAATAATC-3’ Stage 2 Forward Primer: 5’-TTTTTTTGAGATTTTTTTTTTTAGTTATTTT-3’ Reverse Primer: 5’-AAAAAAAAAACAATCTTAAAAACTATATACAAAA-3’ 10

11. 11 Supplementary Table S11. Methylation Specific PCR (MSP) primer sets. Sequencing PositionPrimers Region 1Stage 1 Forward Primer: 5’-GTTTTAGGTGGTTATTTGGTT- 3’ Reverse Primer: 5’-ACTAAATTTAAAAAAAAAAACTCC- 3’ Stage 2 Methyl. Forward Primer: 5’-GTTATTTGGTTCGACGTTTCGTTTC-3’ Methyl. Reverse Primer: 5’-CTAACCGAAAACAACGCCCG-3’ Unmethyl. Forward Primer: 5’-TGGTTATTTGGTTTGATGTTTTGTTTT-3’ Unmethyl. Reverse Primer: 5’-ACAAAACTAACCAAAAACAACACCCA-3’