TABLE 5.
MNP and SVM model display contrasting performance for classification of glioneuronal tumours.
| Sample | Histology | BRAF/FGFR1 | Consensus clustering | SVM | MNP |
|---|---|---|---|---|---|
| VAL1 | GG | BRAF V600E | Group 1 | Group 1 | CONTR, REACT* |
| VAL2 | GG | BRAF V600E | Group 1 | Group 1 | CONTR, REACT* |
| VAL3 | GG | ‐ | Group 1 | Group 1 | CONTR, REACT* |
| VAL4 | GG | ‐ | Group 1 | Group 1 | PLEX, PED B* |
| VAL5 | GG | ‐ | Group 1 | Group 1 | MNG* |
| VAL6 | GG | ‐ | Group 1 | Group 1 | PLEX, PED B* |
| VAL7 | GNT NOS | BRAF V600E | Group 1 | Group 1 | LGG, PA/GG ST |
| VAL8 | GNT NOS | ‐ | Group 1 | Group 1 | LGG, PA/GG ST |
| VAL34 | DNET | ‐ | Group 2 | Group 1 | MB, G3* |
| VAL16 | DNET | FGFR1‐TACC1 | Group 2 | Group 2 | LGG, DNT |
| VAL17 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT* |
| VAL18 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL19 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL20 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL21 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL22 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL23 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL24 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL25 | DNET | FGFR1 TKD | Group 2 | Group 2 | LGG, DNT |
| VAL26 | DNET | ‐ | Group 2 | Group 2 | LGG, DNT |
| VAL27 | DNET | ‐ | Group 2 | Group 2 | LGG, DNT* |
| VAL28 | GNT NOS | ‐ | Group 2 | Group 2 | LGG, DNT* |
| VAL29 | GNT NOS | ‐ | Group 2 | Group 2 | LGG, DNT |
| VAL10 | GG | BRAF V600E | Control/Diffuse | Group 1 | LGG, GG |
| VAL11 | GG | BRAF V600E | Control/Diffuse | Group 1 | LGG, GG* |
| VAL12 | GG | BRAF V600E | Control/Diffuse | Group 1 | LGG, GG |
| VAL13 | GG | BRAF V600E | Control/Diffuse | Group 1 | LGG, GG* |
| VAL32 | GNT NOS | ‐ | Control/Diffuse | Group 1 | LGG, GG |
| VAL33 | GG | ‐ | Control/Diffuse | Group 1 | LGG, GG |
| VAL9 | GG | BRAF V600E | Control/Diffuse | Group 1 | LGG, GG |
| VAL15 | GG | BRAF V600E | Control/Diffuse | Group 2 | LGG, GG |
| VAL14 | GG | BRAF V600E | Control/Diffuse | Control | LGG, GG |
| VAL30 | DNET | FGFR1 TKD | Control/Diffuse | Control | CONTR, HEMI* |
| VAL31 | GG | ‐ | Control/Diffuse | Control | LGG, GG |
Note: Of the 23 tumours segregated by consensus clustering, MNP classifies 13/23 (56%) concordantly, rising to 16/23 (69%) when confidence threshold is ignored. MNP performs comparably with SVM for Group 2/DNET, whereas Group 1 sensitivity is lower. Both methods perform comparably for cases with weak methylation data, concordantly classifying 5/8 cases alongside adjuvant variant data. MNP column represents classification as listed in MNP reference.
*
Misclassifications and classifications below confidence threshold 0.5.