Evidence claim
Evidence summary: tumour RNA fusion detection workflows
Summary of Select a tumour RNA fusion-detection workflow
Four comparisons join the Seraseq reference and paediatric NCH cohort evidence; values cannot be pooled across studies. Tamura et al. 2026 ran 12 short-read callers on haematologic cancer cell lines; one, Genomon, comes from a co-author's group. On 61 driver fusions in conventional RNA-seq of 170 cell lines, Arriba detected all 61 (TPR 1), FusionCatcher 0.98, STAR-Fusion 0.93, InFusion 0.43 and STARChip 0.41. On 24 driver fusions in targeted RNA-seq of 26 cell lines, Arriba again reached 1 and STAR-Fusion 0.92, InFusion 0.17 and STARChip 0. A driver fusion entered these truth sets only if at least four callers, including the one scored, found it and it had literature or RT-PCR support, so fusions that most callers miss are under-represented and these values may overstate sensitivity. Against a consensus of the other callers, the number of single-caller calls, a measure of review burden, ranged on conventional RNA-seq from 327 for TrinityFusion-D and 1,061 for STAR-Fusion (PPV 0.39) to 9,567 for Arriba (PPV 0.08), 22,445 for FusionCatcher and 695,295 for Pizzly. On nanopore long reads from 51 paediatric B-ALL samples (Lin et al. 2026), scored on the dominant fusion per sample, JAFFAL reached sensitivity 0.76, LongGF 0.70 and FusionSeeker 0.63, with precision 0.79 to 0.95; the authors' own FUSILLI reached 0.81. At about one eighth of the depth, sensitivity was 0.09 to 0.27. In an independent long-read benchmark (Dorney et al. 2026 preprint), no caller exceeded F1 0.35 on 400 simulated fusions at 100 Gb and 95% read identity: CTAT-LR-Fusion 0.35 (recall 0.28, precision 0.46), JAFFAL 0.29, Genion 0.20, FusionSeeker 0.14, GFSeeker 0.07 and LongGF 0.04. On all ONT PCR-cDNA reads of the MCF7 cell line, CTAT-LR-Fusion's calls matched 20 of 53 previously reported fusions, with 51 other calls; JAFFAL matched 19 with 38 other calls and FusionSeeker 11 with 359. The other calls mix real fusions missing from the literature list and false calls. On the Huh7 cell line, pooling six long-read callers per long-read platform and three short-read callers for Illumina, PacBio Kinnex recovered 20 of 34 previously reported fusions, ONT PCR-cDNA 17 and Illumina 15. Against karyotyping, FISH and RT-PCR in 101 adult and paediatric acute leukaemia patients (Kim et al. 2026), an Arriba workflow with manual review detected 40 of 48 conventionally detected fusions (sensitivity 83.3%) and called fusions in 21.4% of 56 conventionally negative results; these count against specificity, although the authors describe several as well-known recurrent fusions and confirmed one by RT-PCR and Sanger sequencing. These are cell lines, simulations and leukaemia samples: no linked comparison covers solid-tumour specimens, FFPE tissue or novel-fusion discovery, only Kim et al. score against orthogonal clinical assays, none reports interval estimates, and none establishes clinical performance.
Plain-language summary of what the reviewed evidence shows. Draft until reviewed.
Evidence
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Evidence table
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42 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field summary Context-only references | Discovery of clinically relevant fusions in pediatric cancer amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC fullTextXML retrieved 2026-10-07T12:25:20.810843+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Journal of Molecular Diagnostics 28(5):406, published 2026-02-10; PMC13197905 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NPJ Precision Oncology 10:199, published 2026-04-04; PMC13230599 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | Tamura et al. 2026, Supplementary Information (Supplementary Tables 1-12) amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 41698_2026_1397_MOESM1_ESM.pdf as served by the publisher | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | Detection of Fusion Genes Using RNA Sequencing in Acute Leukemia amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Annals of Laboratory Medicine 46(3), epub 2025-10-16; PMC13071280 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | LRFusionBenchmark repository (Dorney et al.): result tables and run scripts amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch 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 | not individually reviewed No individual claim review recorded Audit detailsField: 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 |
Pinned records1112 values
| Discovery of clinically relevant fusions in pediatric cancer amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC fullTextXML retrieved 2026-10-07T12:25:20.810843+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records1112 values
| Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Journal of Molecular Diagnostics 28(5):406, published 2026-02-10; PMC13197905 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records1112 values
| Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: NPJ Precision Oncology 10:199, published 2026-04-04; PMC13230599 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
7 source records and release history
- Discovery of clinically relevant fusions in pediatric cancer · Original source · Europe PMC fullTextXML retrieved 2026-10-07T12:25:20.810843+00:00
- Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies · Original source · NPJ Precision Oncology 10:199, published 2026-04-04; PMC13230599 full-text XML
- Tamura et al. 2026, Supplementary Information (Supplementary Tables 1-12) · Original source · 41698_2026_1397_MOESM1_ESM.pdf as served by the publisher
- Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Original source · Journal of Molecular Diagnostics 28(5):406, published 2026-02-10; PMC13197905 full-text XML
- 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
- Detection of Fusion Genes Using RNA Sequencing in Acute Leukemia · Original source · Annals of Laboratory Medicine 46(3), epub 2025-10-16; PMC13071280 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-summary-tumour-rna-fusion-detection
- field
- summary
- value
- Four comparisons join the Seraseq reference and paediatric NCH cohort evidence; values cannot be pooled across studies. Tamura et al. 2026 ran 12 short-read callers on haematologic cancer cell lines; one, Genomon, comes from a co-author's group. On 61 driver fusions in conventional RNA-seq of 170 cell lines, Arriba detected all 61 (TPR 1), FusionCatcher 0.98, STAR-Fusion 0.93, InFusion 0.43 and STARChip 0.41. On 24 driver fusions in targeted RNA-seq of 26 cell lines, Arriba again reached 1 and STAR-Fusion 0.92, InFusion 0.17 and STARChip 0. A driver fusion entered these truth sets only if at least four callers, including the one scored, found it and it had literature or RT-PCR support, so fusions that most callers miss are under-represented and these values may overstate sensitivity. Against a consensus of the other callers, the number of single-caller calls, a measure of review burden, ranged on conventional RNA-seq from 327 for TrinityFusion-D and 1,061 for STAR-Fusion (PPV 0.39) to 9,567 for Arriba (PPV 0.08), 22,445 for FusionCatcher and 695,295 for Pizzly. On nanopore long reads from 51 paediatric B-ALL samples (Lin et al. 2026), scored on the dominant fusion per sample, JAFFAL reached sensitivity 0.76, LongGF 0.70 and FusionSeeker 0.63, with precision 0.79 to 0.95; the authors' own FUSILLI reached 0.81. At about one eighth of the depth, sensitivity was 0.09 to 0.27. In an independent long-read benchmark (Dorney et al. 2026 preprint), no caller exceeded F1 0.35 on 400 simulated fusions at 100 Gb and 95% read identity: CTAT-LR-Fusion 0.35 (recall 0.28, precision 0.46), JAFFAL 0.29, Genion 0.20, FusionSeeker 0.14, GFSeeker 0.07 and LongGF 0.04. On all ONT PCR-cDNA reads of the MCF7 cell line, CTAT-LR-Fusion's calls matched 20 of 53 previously reported fusions, with 51 other calls; JAFFAL matched 19 with 38 other calls and FusionSeeker 11 with 359. The other calls mix real fusions missing from the literature list and false calls. On the Huh7 cell line, pooling six long-read callers per long-read platform and three short-read callers for Illumina, PacBio Kinnex recovered 20 of 34 previously reported fusions, ONT PCR-cDNA 17 and Illumina 15. Against karyotyping, FISH and RT-PCR in 101 adult and paediatric acute leukaemia patients (Kim et al. 2026), an Arriba workflow with manual review detected 40 of 48 conventionally detected fusions (sensitivity 83.3%) and called fusions in 21.4% of 56 conventionally negative results; these count against specificity, although the authors describe several as well-known recurrent fusions and confirmed one by RT-PCR and Sanger sequencing. These are cell lines, simulations and leukaemia samples: no linked comparison covers solid-tumour specimens, FFPE tissue or novel-fusion discovery, only Kim et al. score against orthogonal clinical assays, none reports interval estimates, and none establishes clinical performance.
- source locator
- amp-oncology-rna-20261007-source-pmc8642973: Seraseq and NCH results; rna-fusion-20261009-source-tamura2026-supplementary: Supplementary Tables 3 and 5; rna-fusion-20261009-source-tamura2026: Methods and Author contributions; rna-fusion-20261009-source-lin2026: Tables 3 and 6, Results; rna-fusion-longread-20261011-source-dorney2026: see claims.csv of its batch; rna-fusion-longread-20261011-source-dorney2026-repository: see claims.csv of its batch; rna-fusion-leukaemia-20261011-source-kim2025: see claims.csv of its batch
- review
- method: source-hash-verification; independent-cell-check; automated-source-review; reviewer: claude; reviewer note: Claude research agent reviewer-onc-2, independent of the extractor uc-oncology who drafted the summary proposal; the reviewer corrected the text; no human review claimed; reviewed at: 2026-10-11T23:30:00Z; note: Reviewer's approved text applied verbatim; every number traced to stored source_checked results. Descriptive summary only; no execution, human scientific review or clinical validation. See docs/reviews/use-cases/tumour-rna-fusion-detection-2026-10-11.md.
- pins
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