Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML)

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Records in this release that cite this source. A record can cite several sources.

• 26 methods
• 97 configurations
• 1 benchmark
• 6 protocols
• 2 datasets
• 570 evaluations
• 667 results
• 1 source
• 19 evidence claims
• 1 use case

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Claims

Statements this source supports, each with where in the source it was checked.

• Relevance of vep-lit-20261014-protocol-livesey2025-clinical-auroc to use-case-brca1-brca2-germline-interpretation: Assessed by Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S8; Methods)
• Relevance of vep-lit-20261014-protocol-livesey2025-clinical-auroc to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S8; Methods 'ClinVar and gnomAD data', 'AUROC and AUPRC')
• Relevance of vep-lit-20261014-protocol-livesey2025-clinical-auroc to use-case-rare-disease-candidate-ranking: Assessed by Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S8; Methods 'ClinVar and gnomAD data', 'AUROC and AUPRC')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-all to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-all to use-case-protein-variant-effect-prediction: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score'; vep-lit-20261014-source-livesey2025-article: Methods 'DMS datasets')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-all to use-case-rare-disease-candidate-ranking: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, all 36 DMS sets (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S3; Methods 'Spearman's correlation and rank score')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-direct to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-direct to use-case-protein-variant-effect-prediction: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results; vep-lit-20261014-source-livesey2025-article: Methods 'DMS datasets')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-direct to use-case-rare-disease-candidate-ranking: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, direct assays only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-indirect to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-indirect to use-case-protein-variant-effect-prediction: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results; vep-lit-20261014-source-livesey2025-article: Methods 'DMS datasets')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-indirect to use-case-rare-disease-candidate-ranking: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, indirect assays only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S5; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S6; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv to use-case-protein-variant-effect-prediction: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S6; Results; vep-lit-20261014-source-livesey2025-article: Methods 'DMS datasets')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv to use-case-rare-disease-candidate-ranking: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S6; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv-filled to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filled (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S7; Results)
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv-filled to use-case-protein-variant-effect-prediction: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filled (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S7; Results; vep-lit-20261014-source-livesey2025-article: Methods 'DMS datasets')
• Relevance of vep-lit-20261014-protocol-livesey2025-dms-snv-filled to use-case-rare-disease-candidate-ranking: Assessed by Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions with gaps filled (vep-lit-20261014-source-livesey2025-supplementary-2: Supplementary Material 2 Table S7; Results)
• tables_not_extracted: vep-lit-20261014-source-livesey2025-supplementary-2: Tables not extracted Not extracted as results: the pairwise win-rate matrix bodies of Tables S3 (97 x 97) and S8 (85 x 85), kept only through each VEP's rank_score, proteins and top_5_winrate columns; Table S4 (bootstrap counts behind the Figure 2 error bars); the absolute_difference column of Table S5 (a difference of two extracted values); Tables S1 and S2, used for dataset and configuration descriptions; Figures 1-4 and Supplementary Figs. S1-S6 (no printed values; the AUPRC ranking of Fig. S5 is figure-only); the figshare deposits of per-variant predictions and scripts. (Supplementary Material 2 Legends and Tables S1-S8; Figures 1-4; Data availability)

Models, benchmarks and other records

Evidence

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