Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
eQTL effect-size ranking (AlphaGenome paper)
Can sequence-derived expression changes predict the ranking and sign of measured eQTL effects?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15At a glance
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Dataset and biological context | GTExv8 SuSiE fine-mapped SNP eQTLs with PIP≥0.9; target-gene/tissue pairs.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 |
| Split | Zero-shot scorer development uses validation chromosomes 1,2,4,5,7,8,10,11,13,14,15,17,20,22,X; final test chromosomes are 3,6,9,12,16,18,19,21. This partitions variant evaluation labels; the distilled model’s teachers were trained on all reference-genome folds.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 |
| Allowed inputs and adaptation | Gene-specific RNA-seq scores respecting the dataset’s REF/ALT orientation even when its REF differs from the reference genome; matched GTEx tissue.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 |
| Metrics as reported | tissue_weighted_mean_spearmanrAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 |
| Aggregation | Tissue-count-weighted mean Spearman correlation.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 |
| Uncertainty | Not reported for these summary-table scores. · Not reported in inspected sourcesAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 |
| Entity type | protocol |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
How it works
Conceptual summary of the cited procedure; model-specific conditions are given below.
Read the diagram as text
- Select fine-mapped test eQTLs
- Match allele orientation, gene and tissue
- Predict RNA fold changes
- Aggregate effect-size rank correlation
What is tested
Can sequence-derived expression changes predict the ranking and sign of measured eQTL effects?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15Procedure
Compare signed predicted scores against SuSiE beta posterior ranks in each GTEx tissue.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15Tested models and results
Release 2026-09-17-a757f4af4277 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
Strengths and limitations
Limitations and conditions
- These endpoints condition on fine-mapped causal variants; they do not measure discrimination of causal versus noncausal variants. Current repository notebook output is a separate versioned artifact and must not silently replace the workbook result.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15
- This is an author-reported protocol, not a rewire rerun. Different datasets, processing and adaptations cannot support an unrestricted leaderboard.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15
- Primary artifact values differ and their evaluation equivalence is unresolved. The affected comparison is withheld from published result tables.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15
Profile review details
Primary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction.
Stable record: alphagenome-2026-t4-protocol-13Evidence table
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
45 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram caption Conceptual summary of the cited procedure; model-specific conditions are given below. Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Diagram steps ["Select fine-mapped test eQTLs","Match allele orientation, gene and tissue","Predict RNA fold changes","Aggregate effect-size rank correlation"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram steps ["Select fine-mapped test eQTLs","Match allele orientation, gene and tissue","Predict RNA fold changes","Aggregate effect-size rank correlation"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram steps ["Select fine-mapped test eQTLs","Match allele orientation, gene and tissue","Predict RNA fold changes","Aggregate effect-size rank correlation"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Diagram title eQTL effect-size ranking: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Diagram title eQTL effect-size ranking: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplement to Nature version of record, 28 January 2026; content hash pinned | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact publisher PDF bytes Format: original_pdf |
| Diagram title eQTL effect-size ranking: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature version of record, 28 January 2026 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx |
| Dataset and biological context GTExv8 SuSiE fine-mapped SNP eQTLs with PIP≥0.9; target-gene/tissue pairs. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A15:P15; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods pp.32–33, eQTL effect size and sign; methods: pp.32–33, Expression Quantitative Trait Loci (eQTL) Variants; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 13; sheet rows 15 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated source review. No human sign-off or independent experimental reproduction. Field: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-09-17-a757f4af4277 · Record review: needs review
- AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
- AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
- alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied
Technical metadata and extraction receipts
Stable ID: alphagenome-2026-t4-protocol-13
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 13
- source table
- 4
- reference levels
- metric: tissue_weighted_mean_spearmanr; printed value: 0; numeric value: 0; source locator: Suppl Table 4 Variant performan!J15; note: Source reference quantity for relative-performance calculation, not a measured baseline run.