Evidence claim

Relevance of GFMBench-API BRCA1, zs-embedding to "Interpret BRCA1/BRCA2 germline variants"

Use case: Interpret BRCA1/BRCA2 germline variants
Assessed by: GFMBench-API BRCA1, zs-embedding
Relevance: Proxy evidence
Endpoint: Zero-shot AUROC and AUPRC of embedding distance scores for genomic language models against 3,893 BRCA1 variants labelled LOF, INT or FUNC from experimentally measured DNA-repair activity

GFMBench-API zero-shot embedding distance scores scores against BRCA1 DNA-repair function classes as evidence for BRCA1 variant review.

5 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Citation locations 1 values source id lit-genomics-20261011-gfmbench-source-larey2026 locator Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group gfmbench-brca1 Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title GFMBench-API zero-shot scores on BRCA1 function classes Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 3 values Inspect every linked evaluation's source locator before citing a result. Do not combine this mapping's evaluations with any other protocol's results. Not a calibrated evidence-strength estimate; do not translate AUROC into ACMG/AMP points. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Zero-shot AUROC and AUPRC of embedding distance scores for genomic language models against 3,893 BRCA1 variants labelled LOF, INT or FUNC from experimentally measured DNA-repair activity Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric auroc Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 5 values Preprint, not peer reviewed. Single run; no uncertainty printed. The source does not state how the three function classes (LOF, INT, FUNC) were made binary for AUROC. BRCA1 only; no BRCA2 task. Assay labels, not clinical classifications. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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use-case-brca1-brca2-germline-interpretation fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 9681ae92e727dde7a801aec8d4884ec28b009d134a52d806a266f7d3b64bd5bd Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale Proxy, not direct: assay-derived function classes are one line of evidence a BRCA1 reviewer weighs, and this shows how well unsupervised scores track them; it does not test a classification workflow or ACMG/AMP evidence strength. Context-only references	GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models Original source ↗ lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task Version: bioRxiv preprint version 2, posted 2026-08-11 Retrieved: 2026-10-11T00:44:58Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `df9934c88ee245b1e19e155174169d6b6da57ae07c1a04bbea7115423facdf72` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Original source · bioRxiv preprint version 2, posted 2026-08-11

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-lit-genomics-20261011-gfmbench-brca1-zs-embedding

field: links:assessed_by:lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding
value: lit-genomics-20261011-gfmbench-protocol-brca1-zs-embedding
relevance: proxy
endpoint: Zero-shot AUROC and AUPRC of embedding distance scores for genomic language models against 3,893 BRCA1 variants labelled LOF, INT or FUNC from experimentally measured DNA-repair activity
rationale: Proxy, not direct: assay-derived function classes are one line of evidence a BRCA1 reviewer weighs, and this shows how well unsupervised scores track them; it does not test a classification workflow or ACMG/AMP evidence strength.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results.; Not a calibrated evidence-strength estimate; do not translate AUROC into ACMG/AMP points.
limitations: Preprint, not peer reviewed.; Single run; no uncertainty printed.; The source does not state how the three function classes (LOF, INT, FUNC) were made binary for AUROC.; BRCA1 only; no BRCA2 task.; Assay labels, not clinical classifications.
citation locators: source id: lit-genomics-20261011-gfmbench-source-larey2026; locator: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task
source locator: lit-genomics-20261011-gfmbench-source-larey2026: Table 3, task 'BRCA1'; Supplementary Note, BRCA1 task
headline metric: auroc
reason: Add a relevance judgement for a genomic foundation model benchmark protocol from the 2026-10-11 genomics suite pass, reviewed in docs/reviews/2026-10-11-genomics-gfm-suites.md.
comparison group: gfmbench-brca1
comparison title: GFMBench-API zero-shot scores on BRCA1 function classes
stratum label: embedding distance scores
stratum order: 1
reviewed evaluations: lit-genomics-20261011-gfmbench-eval-caduceus-ps-zero-shot-brca1-zs-embedding; lit-genomics-20261011-gfmbench-eval-dna-bert-zero-shot-brca1-zs-embedding; lit-genomics-20261011-gfmbench-eval-dnabert-2-zero-shot-brca1-zs-embedding; lit-genomics-20261011-gfmbench-eval-evo2-zero-shot-brca1-zs-embedding; lit-genomics-20261011-gfmbench-eval-ntv3-zero-shot-brca1-zs-embedding
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the proxy rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude review agent reviewer-gen-3, independent of the extractor lit-genomics; no human review claimed; reviewed at: 2026-10-11T14:40:00Z; note: Automated review; not human scientific review.
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