Evidence claim

Relevance of MCF7 known-fusion recovery (Dorney et al. 2026) to "Select a tumour RNA fusion-detection workflow"

Use case: Select a tumour RNA fusion-detection workflow
Assessed by: MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026)
Relevance: Direct evidence
Endpoint: Known MCF7 fusions recovered (of 53) and other calls per long-read caller, by ONT library type and depth

Real cancer cell-line long-read RNA-seq scored against previously reported fusions measures sensitivity for known fusions and, through the other-call count, the review burden the use case asks about.

6 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.

38 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 2 values source id rna-fusion-longread-20261011-source-dorney2026 locator Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests source id rna-fusion-longread-20261011-source-dorney2026-repository locator Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Citation locations 2 values source id rna-fusion-longread-20261011-source-dorney2026 locator Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests source id rna-fusion-longread-20261011-source-dorney2026-repository locator Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Comparison group dorney2026-longread Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group dorney2026-longread Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Comparison title Long-read fusion callers, independent benchmark (Dorney et al. 2026) Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Long-read fusion callers, independent benchmark (Dorney et al. 2026) Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz 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; truth sets, specimens, sequencing and caller versions differ between sources. Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record 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; truth sets, specimens, sequencing and caller versions differ between sources. Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.constraints` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Endpoint Known MCF7 fusions recovered (of 53) and other calls per long-read caller, by ONT library type and depth Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Known MCF7 fusions recovered (of 53) and other calls per long-read caller, by ONT library type and depth Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.endpoint` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact

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

2 source records and release history

A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing · Original source · bioRxiv preprint version 1, posted 2026-08-12; JATS XML
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Original source · Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-fusion-longread-20261011-sgnex-mcf7

field: links:assessed_by:rna-fusion-longread-20261011-protocol-sgnex-mcf7
value: rna-fusion-longread-20261011-protocol-sgnex-mcf7
relevance: direct
endpoint: Known MCF7 fusions recovered (of 53) and other calls per long-read caller, by ONT library type and depth
rationale: Real cancer cell-line long-read RNA-seq scored against previously reported fusions measures sensitivity for known fusions and, through the other-call count, the review burden the use case asks about.
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; truth sets, specimens, sequencing and caller versions differ between sources.
limitations: Independent benchmark: the authors developed none of the six callers (Competing interests: none). Preprint, not peer reviewed.; Caller versions for CTAT-LR-Fusion and GFSeeker are not stated.; The known list (53 fusions) comes from the literature; fusions missing from it count as other calls, so the other-call count mixes real unlisted fusions and false calls.; No read-support filter is applied in the counting script; the run-level two-read filter stated in Methods may or may not apply here.; Counts only; no precision or recall printed. Single run per library and depth.; knownnumber is the number of distinct call records the authors' script labels known (grouped by gene pair, chromosomes and fusion type); the script does not deduplicate them to listed fusions, so it is an upper bound on the number of listed fusions recovered.
citation locators: source id: rna-fusion-longread-20261011-source-dorney2026; locator: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; source id: rna-fusion-longread-20261011-source-dorney2026-repository; locator: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R
source locator: rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R
headline metric: true-positive-count
reason: Add a relevance judgement from the 2026-10-11 oncology use-case literature pass.
comparison group: dorney2026-longread
comparison title: Long-read fusion callers, independent benchmark (Dorney et al. 2026)
stratum label: MCF7, ONT libraries
stratum order: 3
reviewed evaluations: rna-fusion-longread-20261011-eval-ctat-lr-fusion-sgnex-mcf7; rna-fusion-longread-20261011-eval-fusionseeker-sgnex-mcf7; rna-fusion-longread-20261011-eval-genion-sgnex-mcf7; rna-fusion-longread-20261011-eval-gfseeker-sgnex-mcf7; rna-fusion-longread-20261011-eval-jaffal-sgnex-mcf7; rna-fusion-longread-20261011-eval-longgf-sgnex-mcf7
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the relevance 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 research agent reviewer-onc-2, independent of the extractor uc-oncology; no human review claimed; reviewed at: 2026-10-11T23:30:00Z; note: Automated review; not human scientific review. See docs/reviews/use-cases/tumour-rna-fusion-detection-2026-10-11.md.
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