Table 2 For the methylation-based signatures: overall diagnostic accuracy, sensitivity, and specificity
From: DNA methylation signatures for 2016 WHO classification subtypes of diffuse gliomas
1. Low-grade glioma IDH WT versus mutant: for 14 CpG methylation signatures | |||||||||
Cohort | Dataset | Overall accuracy (%)a | Sensitivity (%)b | Specificity (%)c | Overall error (%) | IDH mutant error (%) | IDH WT error (%) | ||
IDH mutant | IDH WT | IDH mutant | IDH WT | ||||||
TCGA | Training set | 100 (266/266) | 100 (217/217) | 100 (49/49) | 100 (49/49) | 100 (217/217) | 0 | 0 | 0 |
TCGA | Test set | 99.62 (263/264) | 99.53 (215/216) | 100 (48/48) | 100 (48/48) | 99.53 (215/216) | 0.38 | 0.47 | 0 |
TCGA | Combined set | 99.81 (529/530) | 99.76 (432/433) | 100 (97/97) | 100 (97/97) | 99.76 (432/433) | 0.19 | 0.24 | 0 |
GSE58218 | Validation dataset | 98.5 (192/195) | 99.36 (156/157) | 94.7 (36/38) | 94.7 (36/38) | 99.36 (156/157) | 1.5 | 0.64 | 5.3 |
GSE48462 | Validation dataset | 85.8 (48/56) | 96.55 (28/29) | 74.07 (20/27) | 74.07 (20/27) | 96.55 (28/29) | 14.2 | 3.4 | 25.9 |
2. Diffuse astrocytoma (IDH mutant and non-codeletion of 1p/19q; DA) versus oligodendroglioma (IDH mutant and 1p/19q codeletion; ODG): for 14 CpG methylation signatures | |||||||||
Cohort | Dataset | Overall accuracy (%)a | Sensitivity (%)b | Specificity (%)c | Overall error (%) | DA error (%) | ODG error (%) | ||
DA | ODG | DA | ODG | ||||||
TCGA | Training set | 99.07 (215/217) | 98.47 (129/131) | 100 (86/86) | 100 (86/86) | 98.47 (129/131) | 0.93 | 1.53 | 0 |
TCGA | Test set | 96.29 (208/216) | 94.61 (123/130) | 98.83 (85/86) | 98.83 (85/86) | 94.61 (123/130) | 3.71 | 5.39 | 1.17 |
TCGA | Combined set | 97.69 (423/433) | 96.55 (252/261) | 99.41 (171/172) | 99.41 (171/172) | 96.55 (252/261) | 2.31 | 3.45 | 0.59 |
GSE58218 | Validation dataset | 97.5 (153/157) | 96.25 (77/80) | 98.70 (77/78) | 98.70 (77/78) | 96.25 (77/80) | 2.5 | 3.75 | 1.29 |
GSE48462 | Validation dataset | 78.57 (22/28) | 71.42 (10/14) | 85.71 (12/14) | 85.71 (12/14) | 71.42 (10/14) | 21.43 | 28.58 | 14.29 |
3. For GBM IDH WT versus mutant: for 13 CpG methylation signatures | |||||||||
Cohort | Dataset | Overall accuracy (%)a | Sensitivity (%)b | Specificity (%)c | Overall error (%) | GBM IDH mutant error (%) | GBM IDH WT error (%) | ||
GBM IDH mutant | GBM IDH WT | GBM IDH mutant | GBM IDH WT | ||||||
TCGA | Training set | 100 (63/63) | 100 (4/4) | 100 (59/59) | 100 (59/59) | 100 (4/4) | 0 | 0 | 0 |
TCGA | Test set | 98.36 (60/61) | 100 (3/3) | 98.27 (57/58) | 98.27 (57/58) | 100 (3/3) | 1.64 | 0 | 1.73 |
TCGA | Combined set | 99.19 (123/124) | 100 (7/7) | 99.14 (116/117) | 99.14 (116/117) | 100 (7/7) | 0.81 | 0 | 0.86 |
GSE36278 | Validation dataset | 96.10 (74/77) | 87.5 (14/16) | 98.36 (60/61) | 98.36 (60/61) | 87.5 (14/16) | 3.9 | 12.5 | 1.64 |