Skip to main content

Table 3 Distribution of genomic alterations associated with normal-like (NL) and other-type (OT) tumors

From: A machine learning analysis of a “normal-like” IDH-WT diffuse glioma transcriptomic subgroup associated with prolonged survival reveals novel immune and neurotransmitter-related actionable targets

IDH-WT gliomas (n = 238) NL (n = 14) OT (n = 224) p value (Fisher’s test)
TERT promoter status
 Mutant 1 (7.1%) 62 (27.7%)  
 WT 10 (71.4%) 9 (4%) 4.2e−07
 Unknown 3 (21.4%) 153 (68.3%)  
Chr 7 gain/chr 10 loss
 Gain chr 7 and loss chr 10 2 (14.3%) 150 (67%)  
 No combined CNA 11 (78.6%) 70 (31.2%) 0.00022
 Unknown 1 (7.1%) 4 (1.8%)  
BRAF V600E status
 Mutant 1 (7.1%) 2 (0.9%)  
 WT 13 (92.9%) 218 (97.3%) 0.17
 Unknown 0 (0%) 4 (1.8%)  
BRAF-KIAA1549 fusion
 Fusion 0 (0%) 1 (0.4%)  
 WT 14 (100%) 217 (96.9%) 1
 Unknown 0 (0%) 6 (2.7%)  
ATRX status
 Mutant 0 (0%) 8 (3.6%)  
 WT 14 (100%) 212 (94.6%) 1
 Unknown 0 (0%) 4 (1.8%)  
EGFR
 EGFR amplification 6 (42.9%) 198 (88.4%) 0.000082
 EGFR deletion 0 (0%) 1 (0.4%)  
 WT 8 (57.1%) 24 (10.7%)  
 Unknown 0 (0%) 1 (0.4%)  
FGFR1
 FGFR1 amplification 0 (0%) 20 (8.9%) 0.61
 FGFR1 deletion 1 (7.1%) 29 (12.9%)  
 WT 13 (92.9%) 174 (77.7%)  
 Unknown 0 (0%) 1 (0.4%)  
CDKN2A
 CDKN2A amplification 0 (0%) 6 (2.7%)  
 CDKN2A deletion 5 (35.7%) 166 (74.1%) 0.0021
 WT 9 (64.3%) 51 (22.8%)  
 Unknown 0 (0%) 1 (0.4%)  
CDKN2B
 CDKN2B amplification 0 (0%) 7 (3.1%)  
 CDKN2B deletion 5 (35.7%) 164 (73.2%) 0.0025
 WT 9 (64.3%) 52 (23.2%)  
 Unknown 0 (0%) 1 (0.4%)  
MYB
 MYB amplification 0 (0%) 6 (2.7%) 0.12
 MYB deletion 1 (7.1%) 69 (30.8%)  
 WT 13 (92.9%) 148 (66.1%)  
 Unknown 0 (0%) 1 (0.4%)  
MYBL1
 MYBL1 amplification 0 (0%) 22 (9.8%) 0.68
 MYBL1 deletion 1 (7.1%) 25 (11.2%)  
 WT 13 (92.9%) 176 (78.6%)  
 Unknown 0 (0%) 1 (0.4%)  
MGMT_promoter_status
 Methylated 4 (28.6%) 72 (32.1%)  
 Unmethylated 10 (71.4%) 121 (54.0%) 0.58
 Unknown 0 (0.0%) 31 (13.8%)