True positives (known Huh7 fusions recovered of 34, union of callers) of Union of JAFFA-direct, Arriba and STAR-Fusion on Illumina (Dorney et al. 2026) on Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)
15 True positives (known Huh7 fusions recovered of 34, union of callers)
Methods
- Tested configuration
- Union of JAFFA-direct, Arriba and STAR-Fusion on Illumina (Dorney et al. 2026)
- Protocol
- Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026)
- Dataset
- Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)
- Procedure
- Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026)
- Evaluation
- Union of JAFFA-direct, Arriba and STAR-Fusion on Huh7 Illumina (Dorney et al. 2026)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedA comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Evaluation only
- Adaptation
- Not reported
- Scoring implementation
- Partner-gene match to the known list
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 15 Individual claims | A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15' 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 | source checked ["source-hash-verification","transcription","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Sentence in Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' asserted verbatim in the pinned XML by extract/extract_fusion_longread.py. Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md (docs/reviews/use-cases/tumour-rna-fusion-detection-2026-10-11.md). Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 15 Individual claims | LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15' 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 | source checked ["source-hash-verification","transcription","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Sentence in Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' asserted verbatim in the pinned XML by extract/extract_fusion_longread.py. Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md (docs/reviews/use-cases/tumour-rna-fusion-detection-2026-10-11.md). Field: Source artifact SHA-256: 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 Extraction artifact SHA-256: |
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
Technical metadata and extraction receipts
Stable ID: rna-fusion-longread-20261011-result-union-illumina-huh7-known
- metric
- true-positive-count
- metric direction
- higher
- unit
- count
- printed value
- 15
- source locator
- Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15'
- review
- method: source-hash-verification; transcription; independent-cell-check; method note: Independent re-retrieval and hash check; reviewer's own parser compared every table cell; stratified hand check against the rendered table or quoted sentence.; reviewer: claude; reviewer note: Claude research agent reviewer-onc-2, independent of the extractor uc-oncology; no human review claimed; date: 2026-10-11; artifact sha256: c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b; retrieval url: https://www.biorxiv.org/content/early/2026/08/12/2026.08.07.743439.source.xml; note: Extraction: Sentence in Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' asserted verbatim in the pinned XML by extract/extract_fusion_longread.py. Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15' Independent review 2026-10-11: value, locator, metric, unit, direction and linked configuration and protocol checked; corrections from the review applied by the extractor as listed in review.md (docs/reviews/use-cases/tumour-rna-fusion-detection-2026-10-11.md).
- numeric value
- 15
- metric qualifier
- known Huh7 fusions recovered of 34, union of callers
- unit detail
- counted entity: previously reported Huh7 fusions recovered
- missing metadata
- uncertainty: reason: unreported