Select a patient-RNA splicing-variant validation workflow: attributes.setting
Setting of Select a patient-RNA splicing-variant validation workflow
FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. Separate, proxy sequence-classification results for DNA foundation models (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M classifying variants with established splicing defects against benign variants) are also linked, scoped as a different endpoint. Feng et al. 2025 Table 1 splice acceptor and donor classification is linked to 'Prioritise variants for splicing experiments', not here.
The setting said Feng et al. 2025 Table 1 is the proxy sequence-classification evidence linked to this use case. The Feng protocols are linked to use-case-splicing-follow-up; the linked foundation-model proxy is Alavi et al. 2026. Change of citation, not of meaning; 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.setting 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.setting 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 FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. A separate, proxy sequence-classification AUC for DNA foundation-model embeddings (Feng et al. 2025, Table 1 Acceptor/Donor) is also linked, scoped as a different endpoint. 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 FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. A separate, proxy sequence-classification AUC for DNA foundation-model embeddings (Feng et al. 2025, Table 1 Acceptor/Donor) is also linked, scoped as a different endpoint. 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 FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. Separate, proxy sequence-classification results for DNA foundation models (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M classifying variants with established splicing defects against benign variants) are also linked, scoped as a different endpoint. Feng et al. 2025 Table 1 splice acceptor and donor classification is linked to 'Prioritise variants for splicing experiments', not here. 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 FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. Separate, proxy sequence-classification results for DNA foundation models (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M classifying variants with established splicing defects against benign variants) are also linked, scoped as a different endpoint. Feng et al. 2025 Table 1 splice acceptor and donor classification is linked to 'Prioritise variants for splicing experiments', not here. 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 setting said Feng et al. 2025 Table 1 is the proxy sequence-classification evidence linked to this use case. The Feng protocols are linked to use-case-splicing-follow-up; the linked foundation-model proxy is Alavi et al. 2026. Change of citation, not of meaning; 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 setting said Feng et al. 2025 Table 1 is the proxy sequence-classification evidence linked to this use case. The Feng protocols are linked to use-case-splicing-follow-up; the linked foundation-model proxy is Alavi et al. 2026. Change of citation, not of meaning; 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-setting
- field
- attributes.setting
- previous value
- FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. A separate, proxy sequence-classification AUC for DNA foundation-model embeddings (Feng et al. 2025, Table 1 Acceptor/Donor) is also linked, scoped as a different endpoint.
- value
- FRASER, applied to a retrospective Kremer rare-mitochondrial-disorder skin-fibroblast RNA cohort (119 samples/105 individuals, 13 known pathogenic splicing events), recovers a mean 85% (11 of 13) of known events at a reduced 30-sample subsample. Separate, proxy sequence-classification results for DNA foundation models (Alavi et al. 2026: Evo 2 40B, Genos 10B and NTv3 650M classifying variants with established splicing defects against benign variants) are also linked, scoped as a different endpoint. Feng et al. 2025 Table 1 splice acceptor and donor classification is linked to 'Prioritise variants for splicing experiments', not here.
- 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 links and the 18 assessed_by judgements read on the PR branch; each judgement's rationale treats proxies as sequence-classification evidence kept separate from patient-RNA recovery, which the new text keeps.; 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: Applied by the independent reviewer; the 18 judgements, the baseline and the summary were re-pinned. See docs/reviews/2026-10-14-gfm-guide-sources.md.