True positives (PCR-cDNA library, 2.5Gb depth, known fusions) of JAFFAL JAFFA 2.3 (Dorney et al. 2026) on SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled
13 True positives (PCR-cDNA library, 2.5Gb depth, known fusions)
Methods
- Tested configuration
- JAFFAL JAFFA 2.3 (Dorney et al. 2026)
- Protocol
- MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026)
- Dataset
- SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled
- Procedure
- MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026)
- Evaluation
- JAFFAL on SG-NEx MCF7 ONT RNA-seq (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 · counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
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
- Distinct calls matching 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 13 Individual claims | A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber' 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","deterministic-table-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Read the pinned repository file with extract/extract_fusion_longread.py; header, row count and caller labels asserted. counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber' 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 13 Individual claims | LRFusionBenchmark repository (Dorney et al.): result tables and run scripts counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber' 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","deterministic-table-parse","independent-cell-check"] · 2026-10-11 independent paper Audit detailsExtraction: Read the pinned repository file with extract/extract_fusion_longread.py; header, row count and caller labels asserted. counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber' 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-jaffal-mcf7-pcr-cdna-2-5gb-knownnumber
- metric
- true-positive-count
- metric direction
- higher
- unit
- count
- printed value
- 13
- source locator
- counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
- review
- method: source-hash-verification; deterministic-table-parse; 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: c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e; retrieval url: https://github.com/RDorney/LRFusionBenchmark/tree/83e629fed3098881079fd9ac1c8bc13478ce69ed; note: Extraction: Read the pinned repository file with extract/extract_fusion_longread.py; header, row count and caller labels asserted. counts_SGNex_summary.tsv.gz, row Source 'SGNex_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber' 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
- 13
- metric qualifier
- PCR-cDNA library, 2.5Gb depth, known fusions
- unit detail
- counted entity: known MCF7 fusions called
- missing metadata
- uncertainty: reason: unreported