| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.766 AUPRC (candidate gene set of 100 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'AUPR', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.93 AUROC (candidate gene set of 100 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'ROC AUC', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 82% Top-1 accuracy (candidate gene set of 100 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@1 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 85% Top-10 accuracy (candidate gene set of 100 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@10 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.799 AUPRC (candidate gene set of 25 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'AUPR', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.938 AUROC (candidate gene set of 25 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'ROC AUC', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 84% Top-1 accuracy (candidate gene set of 25 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'Hits@1 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 91% Top-10 accuracy (candidate gene set of 25 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'Hits@10 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.889 AUPRC (candidate gene set of 5 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'AUPR', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.967 AUROC (candidate gene set of 5 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'ROC AUC', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 89% Top-1 accuracy (candidate gene set of 5 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'Hits@1 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 100% Top-10 accuracy (candidate gene set of 5 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'Hits@10 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.789 AUPRC (candidate gene set of 50 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'AUPR', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.936 AUROC (candidate gene set of 50 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'ROC AUC', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 84% Top-1 accuracy (candidate gene set of 50 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'Hits@1 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 91% Top-10 accuracy (candidate gene set of 50 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'Hits@10 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.771 AUPRC (candidate gene set of 75 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'AUPR', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.932 AUROC (candidate gene set of 75 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'ROC AUC', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 82% Top-1 accuracy (candidate gene set of 75 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'Hits@1 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: Exomiser 12.1.0 'Exomiser score' gene ranking (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 86% Top-10 accuracy (candidate gene set of 75 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceExomiser on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'Hits@10 (%)', column 'ClinVar' 'Exomiser' |
|---|
| Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.668 AUPRC (candidate gene set of 100 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot' |
|---|
| Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.929 AUROC (candidate gene set of 100 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'ROC AUC', column 'ClinVar' 'GPT-4' 'One shot' |
|---|
| Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 70% Top-1 accuracy (candidate gene set of 100 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@1 (%)', column 'ClinVar' 'GPT-4' 'One shot' |
|---|
| Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 89% Top-10 accuracy (candidate gene set of 100 genes including the causative gene) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@10 (%)', column 'ClinVar' 'GPT-4' 'One shot' |
|---|
| Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) | Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3)
Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025) | 0.856 AUPRC (candidate gene set of 25 genes including the causative gene) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot' |
|---|