Conditionally independent rare variants associated with complex traits in a UK Biobank and All of Us meta-analysis, with frequency- and sample-size-matched controls.
2 evaluations · 2 results. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AVI six-model ensemble (AlphaGenome Atlas v1) | Protocol: Rare complex-trait SNVs versus matched controls, AUPRC (AlphaGenome Atlas) Dataset: Rare variants associated with complex traits, UK Biobank and All of Us meta-analysis (AlphaGenome Atlas) | 0.69 AUPRC (rare complex-trait SNVs) unitless · higher Uncertainty: Not reported by the source: Fig. 2B draws 95% bootstrap intervals (100 bootstraps) without printing them. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceavi on rare complex-trait SNVs (AlphaGenome Atlas Fig. 2B) ag-atlas-20261019-protocol-rare-complex-trait-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'State-of-the-art interpretable genome-wide variant prioritization with AVI' paragraph 1 (page 5), citing Fig. 2B: '(AUPRC 0.69 vs. GPN-Star-M’s 0.67)' |
| Configuration: GPN-Star (M), mammalian, mutation-rate calibrated (AlphaGenome Atlas v1) | Protocol: Rare complex-trait SNVs versus matched controls, AUPRC (AlphaGenome Atlas) Dataset: Rare variants associated with complex traits, UK Biobank and All of Us meta-analysis (AlphaGenome Atlas) | 0.67 AUPRC (rare complex-trait SNVs) unitless · higher Uncertainty: Not reported by the source: Fig. 2B draws 95% bootstrap intervals (100 bootstraps) without printing them. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcegpn-star-m on rare complex-trait SNVs (AlphaGenome Atlas Fig. 2B) ag-atlas-20261019-protocol-rare-complex-trait-snv-auprc Aggregation: Not reported AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) · Results 'State-of-the-art interpretable genome-wide variant prioritization with AVI' paragraph 1 (page 5), citing Fig. 2B: '(AUPRC 0.69 vs. GPN-Star-M’s 0.67)' |
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4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Population SNVs +2879/-2784; indels +628/-562 (fig. S7B) Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Methods 'Complex Trait Benchmark' (pages 28 to 29); Fig. 2B panel header; fig. S7B Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Source location Methods 'Complex Trait Benchmark' (pages 28 to 29); Fig. 2B panel header; fig. S7B Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Methods 'Complex Trait Benchmark' (pages 28 to 29); Fig. 2B panel header; fig. S7B Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Description Conditionally independent rare variants associated with complex traits in a UK Biobank and All of Us meta-analysis, with frequency- and sample-size-matched controls. Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Methods 'Complex Trait Benchmark' (pages 28 to 29); Fig. 2B panel header; fig. S7B Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
| Name Rare variants associated with complex traits, UK Biobank and All of Us meta-analysis (AlphaGenome Atlas) Context-only references | AlphaGenome Atlas: in silico mutagenesis of the entire human genome (Cheng, Taylor, Nicolaisen et al., medRxiv 2026) Methods 'Complex Trait Benchmark' (pages 28 to 29); Fig. 2B panel header; fig. S7B Version: medRxiv preprint version 1, posted 2026-09-20; full-text PDF with supplementary figures and tables (83 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the medRxiv PDF. A second retrieval at 2026-10-19T12:30:54Z had the same length (15,415,633 bytes) and the same SHA-256. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: ag-atlas-20261019-data-rare-complex-trait-variants