Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026)
Number of the 34 previously reported Huh7 fusions recovered by any caller on each sequencing library type.
Overview
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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
3 evaluations · 3 results. Different protocols are not a single leaderboard.
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)
Sorted by True positives (known Huh7 fusions recovered of 34, union of callers) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | True positives (known Huh7 fusions recovered of 34, union of callers) |
|---|---|
| Union of six long-read callers on PacBio Kinnex (Dorney et al. 2026)Evaluation | 20 (best in column) |
| Union of six long-read callers on ONT PCR-cDNA (Dorney et al. 2026)Evaluation | 17 |
| Union of JAFFA-direct, Arriba and STAR-Fusion on Illumina (Dorney et al. 2026)Evaluation | 15 |
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
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Evidence
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Evidence table
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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-protocol-huh7-known-fusions
- areas
- rna-transcriptomes
- contexts
- clinical_research
- protocol
- Known fusions recovered by the union of all six long-read callers (long-read libraries) or of JAFFA-direct, Arriba and STAR-Fusion (Illumina), calls with at least two spanning reads or pairs, both replicates.
- version
- Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2
- metric
- true-positive-count
- denominator
- 34
- 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.
- source locator
- Results paragraph quoted in the version field; Figure 4 legend (C, D)
Related records
- uses data: Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)
- assessment: Union of JAFFA-direct, Arriba and STAR-Fusion on Huh7 Illumina (Dorney et al. 2026)
- assessment: Union of six long-read callers on Huh7 ONT PCR-cDNA (Dorney et al. 2026)
- assessment: Union of six long-read callers on Huh7 PacBio Kinnex (Dorney et al. 2026)
- assessed by: Select a tumour RNA fusion-detection workflow