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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
  1. 1. low-grade glioma IDH WT versus mutant, 2. diffuse astrocytoma (DA) versus oligodendroglioma (ODG), 3. GBM IDH WT versus mutant
  2. a(the number of samples predicted correctly)/(total number of samples analyzed)×100
  3. b(the number of positive samples predicted)/(the number of true positives)×100
  4. c(the number of negative samples predicted)/(the number of true negatives)×100