ArticleNucleic acids research2016
Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers, 1 of them a synthesis that pooled it.
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Who cites it
102 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Korean Society for Genetic Diagnostics Guidelines for Validation of Next-Generation Sequencing-Based Somatic Variant Detection in Hematologic Malignancies.Annals of laboratory medicine · 2019Guideline
- Anchored random reverse primer sequencing for quantitative detection of novel gene fusions.Nature biomedical engineering · 2026Article
- Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies.NPJ precision oncology · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- A de novo assembly based fusion gene detection concept based on DNA-seq data of 100 Ewing sarcoma cases.Briefings in bioinformatics · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Fusions4U: a resource of validated and annotated gene fusions in 328 cancer cell lines.BMC cancer · 2025Article
- Whole transcriptome analysis identifiesCancer pathogenesis and therapy · 2025Article
- T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data.Genome biology · 2025Article
- Development and application of a whole transcriptome sequencing assay for the detection of gene fusions in clinical cancer specimens.BMC cancer · 2025Article
- Oncogenic gene fusions in cancer: from biology to therapy.Signal transduction and targeted therapy · 2025Review
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Detection of germline CNVs from gene panel data: benchmarking the state of the art.Briefings in bioinformatics · 2024Article
- Renal epithelioid angiomyolipomas overexpress TFE3 and the TFE3-regulated gene TRIM63 in the absence of TFE3 rearrangement.Virchows Archiv : an international journal of pathology · 2024Article
- Improved detection of clinically relevant fusion transcripts in cancer by machine learning classification.BMC genomics · 2023Article
- Comprehensive Molecular Characterization of Polymorphous Adenocarcinoma, Cribriform Subtype: Identifying Novel Fusions and Fusion Partners.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2023Article
- Fast and sensitive validation of fusion transcripts in whole-genome sequencing data.BMC bioinformatics · 2023Article
- Decoding Oncofusions: Unveiling Mechanisms, Clinical Impact, and Prospects for Personalized Cancer Therapies.Cancers · 2023Review
- Recent advances in cancer fusion transcript detection.Briefings in bioinformatics · 2023Review
- Novornabreak: Local Assembly for Novel Splice Junction and Fusion Transcript Detection from RNA-Seq Data.Journal of bioinformatics and systems biology : Open access · 2023Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
backgroundFusion transcripts are formed by either fusion genes (DNA level) or trans-splicing events (RNA level). They have been recognized as a promising tool for diagnosing, subtyping and treating cancers. RNA-seq has become a precise and efficient standard for genome-wide screening of such aberration events. Many fusion transcript detection algorithms have been developed for paired-end RNA-seq data but their performance has not been comprehensively evaluated to guide practitioners. In this paper, we evaluated 15 popular algorithms by their precision and recall trade-off, accuracy of supporting reads and computational cost. We further combine top-performing methods for improved ensemble detection.
resultsFifteen fusion transcript detection tools were compared using three synthetic data sets under different coverage, read length, insert size and background noise, and three real data sets with selected experimental validations. No single method dominantly performed the best but SOAPfuse generally performed well, followed by FusionCatcher and JAFFA. We further demonstrated the potential of a meta-caller algorithm by combining top performing methods to re-prioritize candidate fusion transcripts with high confidence that can be followed by experimental validation.
conclusionOur result provides insightful recommendations when applying individual tool or combining top performers to identify fusion transcript candidates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.