Evidence claim

Relevance of OpenSplice MPRA delta PSI prediction for 283,121 single-nucleotide substitutions in 599 exons (SpliceAI2 paper, Spearman) to use case use-case-splicing-follow-up

Use case: Prioritise variants for splicing experiments
Assessed by: OpenSplice MPRA delta PSI prediction for 283,121 single-nucleotide substitutions in 599 exons (SpliceAI2 paper, Spearman)
Relevance: Proxy evidence
Endpoint: Spearman correlation between predicted and measured exon-inclusion change (delta PSI) for 283,121 single-nucleotide substitutions across 599 exons in the OpenSplice MPRA, for SpliceAI, Pangolin, AlphaGenome and SpliceAI2

Experimentally measured splicing of human SNVs in a reporter assay, with four predictors on the same variants: the same kind of endpoint as the MFASS reporter evidence for choosing variants for a splicing experiment. Proxy: a rank correlation over all substitutions, not precision among variants selected for follow-up, and the comparator scores are those released with OpenSplice while SpliceAI2 was scored by its developers.

4 reviewed evaluations

Evidence

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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 3 values source id rna-splicing-20261013-spliceai2-source-article locator Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)' source id rna-splicing-20261013-spliceai2-source-article locator Fig. 1d source id rna-splicing-20261013-spliceai2-source-article locator Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Comparison group spliceai2-2026-opensplice Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Comparison title OpenSplice MPRA delta PSI (SpliceAI2 paper, developer-reported) Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Constraints 4 values Inspect every linked evaluation's source locator and configuration before citing a result. Do not combine this mapping's evaluations with any other protocol's results; truth sets, inputs and metrics differ between sources. Do not pool with the MFASS protocols; assay, exons and metric differ. Settings differ between systems: comparators use the OpenSplice-released scores, SpliceAI2 an exon-skipping formula from its own outputs. Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Endpoint Spearman correlation between predicted and measured exon-inclusion change (delta PSI) for 283,121 single-nucleotide substitutions across 599 exons in the OpenSplice MPRA, for SpliceAI, Pangolin, AlphaGenome and SpliceAI2 Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Claimed field links:assessed_by:rna-splicing-20261013-spliceai2-protocol-opensplice-mpra Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Headline metric spearman-correlation Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Limitations 6 values Developer-reported; the OpenSplice dataset is from another group (reference 23), but this comparison was run by the SpliceAI2 authors. Spearman over all substitutions; no precision at a follow-up capacity and no uncertainty printed. Training overlap: SpliceAI2 was trained on all human genes outside chromosomes 21 and 22, including the reference splicing of most OpenSplice exons' genes. The use case's baseline, MaxEntScan, is not evaluated. Comparator scores come from the OpenSplice release; this paper does not describe their settings. Preprint (bioRxiv v1), not peer reviewed. Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
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09442cd33f8941b2e764e137cb843ca4a962a185fba4f3d7419d13f1981a5de1 record id use-case-splicing-follow-up fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 a811d697e1ee1733fb4ed295b0083737c626980c1af83116dc2e404cbf01821b Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.pins` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact
Rationale Experimentally measured splicing of human SNVs in a reporter assay, with four predictors on the same variants: the same kind of endpoint as the MFASS reporter evidence for choosing variants for a splicing experiment. Proxy: a rank correlation over all substitutions, not precision among variants selected for follow-up, and the comparator scores are those released with OpenSplice while SpliceAI2 was scored by its developers. Context-only references	A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Original source ↗ rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) Retrieved: 2026-10-13T12:40:34Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b` Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. Inspected artifact

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

1 source record and release history

A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) · Original source · bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-splicing-20261013-spliceai2-opensplice

field: links:assessed_by:rna-splicing-20261013-spliceai2-protocol-opensplice-mpra
value: rna-splicing-20261013-spliceai2-protocol-opensplice-mpra
relevance: proxy
endpoint: Spearman correlation between predicted and measured exon-inclusion change (delta PSI) for 283,121 single-nucleotide substitutions across 599 exons in the OpenSplice MPRA, for SpliceAI, Pangolin, AlphaGenome and SpliceAI2
rationale: Experimentally measured splicing of human SNVs in a reporter assay, with four predictors on the same variants: the same kind of endpoint as the MFASS reporter evidence for choosing variants for a splicing experiment. Proxy: a rank correlation over all substitutions, not precision among variants selected for follow-up, and the comparator scores are those released with OpenSplice while SpliceAI2 was scored by its developers.
constraints: Inspect every linked evaluation's source locator and configuration before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; truth sets, inputs and metrics differ between sources.; Do not pool with the MFASS protocols; assay, exons and metric differ.; Settings differ between systems: comparators use the OpenSplice-released scores, SpliceAI2 an exon-skipping formula from its own outputs.
limitations: Developer-reported; the OpenSplice dataset is from another group (reference 23), but this comparison was run by the SpliceAI2 authors.; Spearman over all substitutions; no precision at a follow-up capacity and no uncertainty printed.; Training overlap: SpliceAI2 was trained on all human genes outside chromosomes 21 and 22, including the reference splicing of most OpenSplice exons' genes.; The use case's baseline, MaxEntScan, is not evaluated.; Comparator scores come from the OpenSplice release; this paper does not describe their settings.; Preprint (bioRxiv v1), not peer reviewed.
citation locators: source id: rna-splicing-20261013-spliceai2-source-article; locator: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; source id: rna-splicing-20261013-spliceai2-source-article; locator: Fig. 1d; source id: rna-splicing-20261013-spliceai2-source-article; locator: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph
source locator: rna-splicing-20261013-spliceai2-source-article: Extended Data Fig. 2 panel 'OpenSplice MPRA (ρ)'; rna-splicing-20261013-spliceai2-source-article: Fig. 1d; rna-splicing-20261013-spliceai2-source-article: Methods 'Variant effect benchmarks', OpenSplice MPRA paragraph
comparison group: spliceai2-2026-opensplice
comparison title: OpenSplice MPRA delta PSI (SpliceAI2 paper, developer-reported)
stratum label: All substitutions and exon or intron strata
stratum order: 1
headline metric: spearman-correlation
reason: Drafted from the 2026-10-13 SpliceAI2 extraction (data/omics/use-case-coverage-rna-splicing-20261013-spliceai2), issue #127. Independently reviewed in docs/reviews/use-cases/spliceai2-2026-10-13.md.
review: method: scope-review; independent-cell-check; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent reviewer; did not extract this batch; no human review claimed; date: 2026-10-13; artifact sha256: f8f3db2c3943d4827b670bc2e962e0cec8fbe96e0b1acf9d4a9b9f0c7a78c06b; retrieval url: https://www.biorxiv.org/content/10.64898/2026.10.08.757673v1.full.pdf; method note: Judged against the use case's question, inputs and output in data/entities/use-cases.jsonl and the existing judgements for the same use case; endpoint, limitations and every evaluation on the protocol re-read in the pinned PDF.; note: Checked against the pinned source by the independent reviewer; verdict and correction list in docs/reviews/use-cases/spliceai2-2026-10-13.md and this batch's review.json. Developer-reported value, not reproduced. Extraction method: Drafted by the extractor against the use case's question, inputs and output and the existing judgements for the same use case; not a review.
reviewed evaluations: rna-splicing-20261013-spliceai2-eval-opensplice-mpra-alphagenome-opensplice-released; rna-splicing-20261013-spliceai2-eval-opensplice-mpra-pangolin-opensplice-released; rna-splicing-20261013-spliceai2-eval-opensplice-mpra-spliceai-opensplice-released; rna-splicing-20261013-spliceai2-eval-opensplice-mpra-spliceai2-ensemble
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