Evidence summary: tumour RNA fusion detection workflows: attributes.value

Stable ID: metadata-correction-qa-20261012-d74ed516e7fa2d4e0516

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attributes.value

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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 tenth 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. 2025), 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.

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

Crossref record for 10.3343/alm.2025.0300 (volume 46, issue 3, pages 257-269, print 2026-05-01); Lin et al. 2026 dataset records (mean 1.4 M and 11.2 M reads)

review

method: automated-source-review; method note: Compared previous_value with origin/main e79f7a5 and value with the working tree byte for byte; confirmed against Crossref (10.3343/alm.2025.0300: volume 46, issue 3, pages 257-269, online 2025-10-16, print 2026-05-01) that the volume and print year is 2026, matching how the store cites other sources published online in one year and in print the next (You et al. 2026, Dalla-Torre et al. 2025); confirmed the depth ratio against the Lin et al. 2026 full-text XML (SHA-256 matches the source record), which reports means of 11.2 and 1.4 million reads, a ratio of 8.0.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that made the change; no human review claimed; date: 2026-10-12; note: Correct the citation year for Kim et al. (Ann Lab Med 2026;46(3):257-269, published online 2025-10-16) and the Lin depth ratio (1.4 M against 11.2 M mean reads is about one eighth, not one tenth). Historical releases retain the previous value. Independent review 2026-10-12: correct as made.

• subject: Evidence summary: tumour RNA fusion detection workflows