Evidence claim

Relevance of Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets) to "Select a patient-RNA splicing-variant validation workflow"

Use case: Select a patient-RNA splicing-variant validation workflow
Assessed by: Splice-defect classification of OPA1 variants with thresholds tuned on the same sets (Alavi Table III, evaluation sets)
Relevance: Proxy evidence
Endpoint: Accuracy, PPV, specificity, sensitivity and error rates of SpliceAI, AlphaGenome, Borzoi and the genomic foundation models NTv3 650M, Evo2 40B and Genos 10B on OPA1 LOVD evaluation sets (49 splicing, 79 benign)

Proxy: DNA-sequence models, including genomic foundation models, classify variants with established splicing defects against benign variants; this is the sequence-classification kind of evidence, not recovery of events in patient RNA-seq.

12 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 rna-splicing-20261011-alavi2026-source-article locator Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Comparison group alavi2026-opa1-splice-variants Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Comparison title Splice predictors and genomic foundation models on OPA1 and multi-gene splice variants (Alavi 2026) Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Constraints 2 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; variant sets and thresholds differ. Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Endpoint Accuracy, PPV, specificity, sensitivity and error rates of SpliceAI, AlphaGenome, Borzoi and the genomic foundation models NTv3 650M, Evo2 40B and Genos 10B on OPA1 LOVD evaluation sets (49 splicing, 79 benign) Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Claimed field links:assessed_by:rna-splicing-20261011-alavi2026-protocol-opa1-evaluation Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Headline metric accuracy Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Limitations 6 values In-sample: thresholds were optimised on these 128 variants, so the values are optimistic. Positives are LOVD entries annotated as splicing defects; the assay behind each annotation is not stated. Thresholds were set by one-dimensional grid search on the OPA1 evaluation sets, optimising accuracy and specificity (Methods B). Single-author preprint; no uncertainty intervals are printed for the tabulated metrics. Foundation-model scores are zero-shot log-likelihood ratios with author-chosen context windows, aggregation and strand rules (Methods F to H). Preprint (bioRxiv v1), not peer reviewed. Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
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rna-splicing-20261011-alavi2026-result-opa1-evaluation-spliceai-type-ii-error fields status attributes.metric attributes.metric_qualifier attributes.printed_value attributes.numeric_value sha256 df2a6b051663c22a2f7f5a757afdf430cdbd445c366ce856c24285ab011c6fa7 record id rna-splicing-20261011-alavi2026-source-article fields status attributes.artifact_sha256 sha256 5199dd076c879678874cff038417208915a8ea24545fc4ba21270e68f3e8e5b1 record id use-case-patient-rna-splicing-validation fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 b85cad56e15fbfad66a2e70c3b193ed56c464e5e44b62a19b12f391e409ec897 Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact
Rationale Proxy: DNA-sequence models, including genomic foundation models, classify variants with established splicing defects against benign variants; this is the sequence-classification kind of evidence, not recovery of events in patient RNA-seq. Context-only references	Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Original source ↗ rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5 Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) Retrieved: 2026-10-11T21:42:49Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (ModDate and the second document ID), so later retrievals differ. A reviewer retrieval on 2026-10-12 of the same length (1,823,372 bytes) had SHA-256 e22491e217c7c158528668b38bcb8b9855b89617b807c60b740795a204c84b0a and ModDate D:20261011221204-07'00'. All 168 Table III and IV cells in that copy match the stored results. Inspected artifact

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

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Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-splicing-20261011-alavi2026-opa1-evaluation

field: links:assessed_by:rna-splicing-20261011-alavi2026-protocol-opa1-evaluation
value: rna-splicing-20261011-alavi2026-protocol-opa1-evaluation
relevance: proxy
endpoint: Accuracy, PPV, specificity, sensitivity and error rates of SpliceAI, AlphaGenome, Borzoi and the genomic foundation models NTv3 650M, Evo2 40B and Genos 10B on OPA1 LOVD evaluation sets (49 splicing, 79 benign)
rationale: Proxy: DNA-sequence models, including genomic foundation models, classify variants with established splicing defects against benign variants; this is the sequence-classification kind of evidence, not recovery of events in patient RNA-seq.
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; variant sets and thresholds differ.
limitations: In-sample: thresholds were optimised on these 128 variants, so the values are optimistic.; Positives are LOVD entries annotated as splicing defects; the assay behind each annotation is not stated.; Thresholds were set by one-dimensional grid search on the OPA1 evaluation sets, optimising accuracy and specificity (Methods B).; Single-author preprint; no uncertainty intervals are printed for the tabulated metrics.; Foundation-model scores are zero-shot log-likelihood ratios with author-chosen context windows, aggregation and strand rules (Methods F to H).; Preprint (bioRxiv v1), not peer reviewed.
citation locators: source id: rna-splicing-20261011-alavi2026-source-article; locator: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5
source locator: rna-splicing-20261011-alavi2026-source-article: Table III columns 'Accuracy' to 'Type II error'; Methods B and I; Equations 1 to 5
headline metric: accuracy
comparison group: alavi2026-opa1-splice-variants
comparison title: Splice predictors and genomic foundation models on OPA1 and multi-gene splice variants (Alavi 2026)
stratum label: OPA1 evaluation sets (thresholds tuned here)
stratum order: 1
reason: Recorded from the 2026-10-11 use-case literature pass (data/omics/use-case-coverage-rna-splicing-20261011-alavi2026). Independently reviewed in docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md.
review: method: pdf-text-parse; independent-cell-check; automated-source-review; scope-review; reviewer: claude; reviewer note: Independent Claude review agent reviewer-scnv; did not extract this batch; no human review claimed; date: 2026-10-12; artifact sha256: e11f4bd8818992a831cb2829d934287c2587b108881c9785c2ef5c8cdc730004; retrieval url: https://www.biorxiv.org/content/10.64898/2026.10.02.756289v1.full.pdf; method note: Drafted by the collector agent uc-splicing-cnv from the pinned source.; note: Checked by reviewer-scnv against the pinned source; verdict in docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md and in this batch's review.md.
reviewed evaluations: rna-splicing-20261011-alavi2026-eval-opa1-evaluation-alphagenome-either-module; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-alphagenome-junction-scorer; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-alphagenome-splice-scorer; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-borzoi-128-bp; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-borzoi-32-bp; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-evo2-40b-human-identifier; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-evo2-40b-without-human-identifier; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-genos-10b; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-genos-10b-clinvar; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-ntv3-650m-post; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-ntv3-650m-pre; rna-splicing-20261011-alavi2026-eval-opa1-evaluation-spliceai
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