Select a patient-RNA splicing-variant validation workflow: attributes.evidence_gaps[2]
Evidence gaps[2] of Select a patient-RNA splicing-variant validation workflow
Feng et al. 2025 Table 1 splice-site classification is not linked to this use case: it measures AUC on benchmark splice-site sequences (DNABERT-2/NT datasets), not patient RNA, and is linked to 'Prioritise variants for splicing experiments'. The DNA foundation-model results linked here (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M) are threshold classifications of variants with established splicing defects, also proxies; none recovers events from patient RNA-seq.
The text said Feng et al. 2025 Table 1 is linked to this use case. Its acceptor and donor protocols are linked to use-case-splicing-follow-up only. Historical releases retain the previous value.
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.
14 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field attributes.evidence_gaps[2] Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Claimed field attributes.evidence_gaps[2] Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Previous value The sequence-classification proxy mapping (Feng Table 1) measures AUC on a different population (DNABERT-2/NT benchmark splice-site datasets), not minigene reporter exon inclusion or patient RNA, and must not be pooled with the FRASER recovery figure. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Previous value The sequence-classification proxy mapping (Feng Table 1) measures AUC on a different population (DNABERT-2/NT benchmark splice-site datasets), not minigene reporter exon inclusion or patient RNA, and must not be pooled with the FRASER recovery figure. Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Source location Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Source location Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Claimed value Feng et al. 2025 Table 1 splice-site classification is not linked to this use case: it measures AUC on benchmark splice-site sequences (DNABERT-2/NT datasets), not patient RNA, and is linked to 'Prioritise variants for splicing experiments'. The DNA foundation-model results linked here (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M) are threshold classifications of variants with established splicing defects, also proxies; none recovers events from patient RNA-seq. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Claimed value Feng et al. 2025 Table 1 splice-site classification is not linked to this use case: it measures AUC on benchmark splice-site sequences (DNABERT-2/NT datasets), not patient RNA, and is linked to 'Prioritise variants for splicing experiments'. The DNA foundation-model results linked here (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M) are threshold classifications of variants with established splicing defects, also proxies; none recovers events from patient RNA-seq. Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
| Description The text said Feng et al. 2025 Table 1 is linked to this use case. Its acceptor and donor protocols are linked to use-case-splicing-follow-up only. Historical releases retain the previous value. Context-only references | Benchmarking DNA foundation models for genomic and genetic tasks Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12663285.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Description The text said Feng et al. 2025 Table 1 is linked to this use case. Its acceptor and donor protocols are linked to use-case-splicing-follow-up only. Historical releases retain the previous value. Context-only references | Probing Genomic Foundation Models with Splice-Variant Perturbations (Alavi, bioRxiv 2026) Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-10-09; full-text PDF (11 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: 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. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Benchmarking DNA foundation models for genomic and genetic tasks · Original source · PMC12663285.1
- 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)
Technical metadata and extraction receipts
Stable ID: metadata-correction-gfm-guide-20261014-patient-rna-splicing-evidence-gaps-2
- field
- attributes.evidence_gaps[2]
- previous value
- The sequence-classification proxy mapping (Feng Table 1) measures AUC on a different population (DNABERT-2/NT benchmark splice-site datasets), not minigene reporter exon inclusion or patient RNA, and must not be pooled with the FRASER recovery figure.
- value
- Feng et al. 2025 Table 1 splice-site classification is not linked to this use case: it measures AUC on benchmark splice-site sequences (DNABERT-2/NT datasets), not patient RNA, and is linked to 'Prioritise variants for splicing experiments'. The DNA foundation-model results linked here (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M) are threshold classifications of variants with established splicing defects, also proxies; none recovers events from patient RNA-seq.
- source locator
- Store links: use-case-splicing-follow-up assessed_by amp-feng-20261007-protocol-splice-acceptor and -splice-donor, none from this use case; this use case assessed_by rna-splicing-20261011-alavi2026-protocol-opa1-evaluation and -multigene, whose evaluations include the Evo 2 40B, Genos 10B and NTv3 650M configurations
- review
- method: scope-review; method note: Use case assessed_by links, judgement claim subjects and the configurations of every evaluation on the linked protocols read from the store on the PR branch.; reviewer: claude; reviewer note: Independent Claude (Opus 5.5) review agent for PR #150; did not extract this batch; no human review claimed; date: 2026-10-14; note: The extractor's replacement text said no DNA foundation-model result is linked to this use case; Alavi et al. 2026 foundation-model evaluations are linked, so the review replaced it. Extractor's text: No DNA foundation-model result is linked to this use case. Feng et al. 2025 Table 1 splice-site classification is linked to 'Prioritise variants for splicing experiments' instead, because it measures AUC on benchmark splice-site sequences (DNABERT-2/NT datasets), not on patient RNA.