Table 4. FDA-approved or -recognized biomarkers (therapeutic, diagnostic, and prognostic) from the rule-based model and the deep learning model (OPAI) in CancerVar.
| Gene | Alternation | Cancers | Levels | Rule-based CancerVar | OPAI |
| ABL1 | T315I | B-lymphoblastic leukemia/lymphoma/ chronic myelogenous leukemia |
Therapeutic (ponatinib) | Tier II (score 8) | 0.93 |
| AKT1 | E17K | Breast cancer/ovarian cancer/endometrial cancer |
Therapeutic (AZD5363) | Tier II (score 10) | 0.98 |
| BRAF | V600E | Melanoma/non–small cell lung cancer |
Therapeutic (dabrafenib + trametinib; vemurafenib) |
Tier I (score 11) | 0.98 |
| EGFR | T790M | Non–small cell lung cancer |
Therapeutic (osimertinib) |
Tier II (score 9) | 0.98 |
| EGFR | L861Q | Non–small cell lung cancer |
Therapeutic (afatinib) | Tier II (score 10) | 0.99 |
| EGFR | S768I | Non–small cell lung cancer |
Therapeutic (afatinib) | Tier I (score 11) | 0.99 |
| EZH2 | Y646F | Follicular lymphoma | Therapeutic (tazemetostat) |
Tier I (score 11) | 0.99 |
| Y646H | Tier I (score 11) | 0.99 | |||
| Y646N | Tier I (score 11) | 0.99 | |||
| Y646S | Tier I (score 11) | 0.99 | |||
| FGFR3 | R248C | Bladder cancer | Therapeutic (erdafitinib) |
Tier II (score 9) | 0.99 |
| S249C | Tier II (score 9) | 0.99 | |||
| Y373C | Tier II (score 10) | 0.99 | |||
| JAK2 | V617F | Primary myelofibrosis | Prognostic | Tier I (score 11) | 0.87 |
| KIT | A829P | Gastrointestinal stromal tumor |
Therapeutic (imatinib, regorafenib, ripretinib, and sunitinib) |
Tier II (score 9) | 0.83 |
| T670I | Tier II (score 9) | 0.98 | |||
| V654A | Tier I (score 11) | 0.99 | |||
| Y823D | Tier II (score 10) | 0.99 | |||
| D816V | Systemic mastocytosis | Diagnostic | Tier II (score 9) | 0.99 | |
| KRAS | G12C | Non–small cell lung cancer |
Therapeutic (AMG-510) | Tier I (score 11) | 0.99 |
| PDGFRA | D842V | Gastrointestinal stromal tumor |
Therapeutic (avapritinib) |
Tier II (score 9) | 0.97 |
| D842Y | Tier II (score 10) | 0.99 |