Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
benchmark · protocol
Splicing-QTL causality (AlphaGenome paper)
Can splicing predictions distinguish fine-mapped sQTLs from matched control variants?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5At 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 | Borzoi-curated eQTL-catalogue sQTL data across GTEx tissues, with distance-matched non-sQTL controls.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 |
| 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'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 |
| Allowed inputs and adaptation | REF/ALT sequence, gene annotations and tissue-specific composite splicing scores.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 |
| Metrics as reported | tissue_weighted_mean_auprcAlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 |
| Aggregation | auPRC per tissue, averaged with variant-count weights.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 |
| 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'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 |
| 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
- Fine-mapped and matched-control variants
- Hold out test chromosomes
- Score tissue-specific splicing changes
- Weight tissue auPRCs
What is tested
Can splicing predictions distinguish fine-mapped sQTLs from matched control variants?
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5Procedure
Compare predicted splicing effects for causal sQTLs and matched negatives; keep the wide and proximal splice-distance analyses distinct.
AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5Tested models and results
Release 2026-09-17-a757f4af4277 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AlphaGenome distilled all-fold student: Splicing-QTL causality Model: AlphaGenome distilled all-fold student · Benchmark: Splicing-QTL causality (AlphaGenome paper) · Dataset: Splicing-QTL causality: evaluated data subset Compare predicted splicing effects for causal sQTLs and matched negatives; keep the wide and proximal splice-distance analyses distinct. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.76 tissue_weighted_mean_auprc Unit: dimensionless · Direction: higher Aggregation: auPRC per tissue, averaged with variant-count weights. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!M5 Source checking is not independent reproduction. |
| Pangolin (paper Table 4): Splicing-QTL causality Model: Pangolin (paper Table 4) · Benchmark: Splicing-QTL causality (AlphaGenome paper) · Dataset: Splicing-QTL causality: evaluated data subset Compare predicted splicing effects for causal sQTLs and matched negatives; keep the wide and proximal splice-distance analyses distinct. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.731911 tissue_weighted_mean_auprc Unit: dimensionless · Direction: higher Aggregation: auPRC per tissue, averaged with variant-count weights. | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L5 Source checking is not independent reproduction. |
Strengths and limitations
Limitations and conditions
- Fine-mapping and matching define the benchmark labels; they do not establish causality experimentally for every variant. The table does not explicitly name its distance threshold beyond the evaluation identifier.AlphaGenome Nature 2026 supplementary comparison tables; AlphaGenome Nature 2026 supplementary methods; alphagenome: Journal full-text XML · 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5
- 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'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5
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-4Evidence 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.
42 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'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 ["Fine-mapped and matched-control variants","Hold out test chromosomes","Score tissue-specific splicing changes","Weight tissue auPRCs"] Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 ["Fine-mapped and matched-control variants","Hold out test chromosomes","Score tissue-specific splicing changes","Weight tissue auPRCs"] Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 ["Fine-mapped and matched-control variants","Hold out test chromosomes","Score tissue-specific splicing changes","Weight tissue auPRCs"] Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 Splicing-QTL causality: evaluation procedure Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 Splicing-QTL causality: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary methods 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 Splicing-QTL causality: evaluation procedure Individual claims | AlphaGenome Nature 2026 supplementary comparison tables 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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 Borzoi-curated eQTL-catalogue sQTL data across GTEx tissues, with distance-matched non-sQTL controls. Individual claims | alphagenome: Journal full-text XML 'Suppl Table 4 Variant performan'!A5:P5; Supplementary Methods p.30, Chromosome Splits for Variant Benchmarks; Supplementary Methods p.30, sQTLs; methods: p.30, Splicing Quantitative Trait Loci; paper: Fig.3f; methods: p.30, Chromosome Splits for Variant Benchmarks; paper: Fig.1e; tables: Suppl Table 4 Variant performan; evaluation index 4; sheet rows 5 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-4
- areas
- dna-genomes
- entity level
- protocol
- version
- Nature version of record, 28 January 2026
- source evaluation index
- 4
- source table
- 4
- reference levels
- metric: tissue_weighted_mean_auprc; printed value: 0.4984; numeric value: 0.49840000000000001; source locator: Suppl Table 4 Variant performan!J5; note: Source reference quantity for relative-performance calculation, not a measured baseline run.