Evidence claim

Relevance of Huh7 known-fusion recovery by platform (Dorney et al. 2026) to "Select a tumour RNA fusion-detection workflow"

Use case: Select a tumour RNA fusion-detection workflow
Assessed by: Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026)
Relevance: Proxy evidence
Endpoint: Known Huh7 fusions recovered (of 34) by the union of callers on PacBio Kinnex, ONT PCR-cDNA and Illumina libraries of the same RNA

Proxy, not direct: the same Huh7 RNA sequenced on PacBio Kinnex, ONT PCR-cDNA and Illumina gives the first linked short- versus long-read comparison on identical samples, but each value pools several callers (six long-read callers, three short-read callers for Illumina), so it compares platforms with unequal caller pools, not workflows a user would run.

3 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 1 values source id rna-fusion-longread-20261011-source-dorney2026 locator Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests 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 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 1 values source id rna-fusion-longread-20261011-source-dorney2026 locator Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests 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 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 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 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 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 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 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 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 Huh7 fusions recovered (of 34) by the union of callers on PacBio Kinnex, ONT PCR-cDNA and Illumina libraries of the same RNA 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 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 Huh7 fusions recovered (of 34) by the union of callers on PacBio Kinnex, ONT PCR-cDNA and Illumina libraries of the same RNA 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 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

How to read the evidence

Sources and history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-fusion-longread-20261011-huh7-known-fusions

field: links:assessed_by:rna-fusion-longread-20261011-protocol-huh7-known-fusions
value: rna-fusion-longread-20261011-protocol-huh7-known-fusions
relevance: proxy
endpoint: Known Huh7 fusions recovered (of 34) by the union of callers on PacBio Kinnex, ONT PCR-cDNA and Illumina libraries of the same RNA
rationale: Proxy, not direct: the same Huh7 RNA sequenced on PacBio Kinnex, ONT PCR-cDNA and Illumina gives the first linked short- versus long-read comparison on identical samples, but each value pools several callers (six long-read callers, three short-read callers for Illumina), so it compares platforms with unequal caller pools, not workflows a user would run.
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.; Union of several callers per platform, so it compares sequencing platforms, not individual callers.; The Figure 4C legend refers to 25 curated known Huh7 or HCC fusions, while the text counts 34 previously reported Huh7 fusions, 21 of them recovered; the relation between the two lists is not explained.; None of the three RT-PCR or Sanger validated Huh7 fusions was detected by any library (Results).; ONT direct cDNA and direct RNA counts are shown only in Figure 4C and are not recorded.; Short-read callers' versions are not stated.
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 locator: rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests
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: Huh7, platform comparison
stratum order: 4
reviewed evaluations: rna-fusion-longread-20261011-eval-union-illumina-huh7; rna-fusion-longread-20261011-eval-union-ont-pcr-cdna-huh7; rna-fusion-longread-20261011-eval-union-pacbio-kinnex-huh7
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.
pins: record id: rna-fusion-longread-20261011-eval-union-illumina-huh7; fields: status; links; attributes.origin; attributes.comparison; sha256: cd06549fb5c84af3a22d777dddb42ce668f47ff8011377830910f00e664b5bcd; record id: rna-fusion-longread-20261011-eval-union-ont-pcr-cdna-huh7; fields: status; links; attributes.origin; attributes.comparison; sha256: c46edd6d15c75c41355ce4fd9837af7b237894983b6c460efb0204e674f5e699; record id: rna-fusion-longread-20261011-eval-union-pacbio-kinnex-huh7; fields: status; links; attributes.origin; attributes.comparison; sha256: fdd72ce1234acf0d35682683f10c972773241b21b543ffd0abfe5fbb4f088246; record id: rna-fusion-longread-20261011-protocol-huh7-known-fusions; fields: status; name; description; facets; source_ids; links; attributes; sha256: d24320afc634b8d7a322d44e384a139694a24cdce71833c496ac37a91dc37c3b; record id: rna-fusion-longread-20261011-result-union-illumina-huh7-known; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: ae827269c9332077d59bf8dbf40a40f1ccc110687983fa1d162e8622594edcfe; record id: rna-fusion-longread-20261011-result-union-ont-pcr-cdna-huh7-known; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 55ea04e913970ea6411790ab9a522c9c1f19f843160c80cde9566b126ce29bab; record id: rna-fusion-longread-20261011-result-union-pacbio-kinnex-huh7-known; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 00052fffaea9313fc36305c8d9d97cad28d01f71da349a8556fd9e60d249fe7a; record id: rna-fusion-longread-20261011-source-dorney2026; fields: status; attributes.artifact_sha256; sha256: aeda3f021bd2c06aff8a5811545c403310881bcb55e891090d270276fe45a653; record id: rna-fusion-longread-20261011-source-dorney2026-repository; fields: status; attributes.artifact_sha256; sha256: 4b9ba39531d80aad2b619045fdf206edc54f32decf84b18bbf9abaa88268c215; record id: use-case-tumour-rna-fusion-detection; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: 813ef5e1275c5b78b486810d5445b67c9069bf366d78399aa2098727d56b2d15

Related records

subject: Select a tumour RNA fusion-detection workflow

Suggest a correction