ArticleBMC genomics2020
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed, 53 citations in OpenAlex.
- Review
- Characteristics of fusion genes in breast cancer.Cancer cell international · 2026Review
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- Filtering of artificial chimeric reads generated by ligation preparation method of nanopore sequencing.iScience · 2026Article
- Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia.The Journal of molecular diagnostics : JMD · 2026Article
- Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.Nature communications · 2026Article
- Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas.bioRxiv : the preprint server for biology · 2026Article
- Fusion gene discovery in single cells from high throughput long read single cell transcriptomes.bioRxiv : the preprint server for biology · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- A de novo assembly based fusion gene detection concept based on DNA-seq data of 100 Ewing sarcoma cases.Briefings in bioinformatics · 2026Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- PACLseq: A Standalone Diagnostic Method for Ph-Like Acute Lymphoblastic Leukemia Using Nanopore Sequencing.MedComm · 2025Article
- Whole transcriptome analysis identifiesCancer pathogenesis and therapy · 2025Article
- Combining panel-based and whole-transcriptome-based gene fusion detection by long-read sequencing.Cell reports methods · 2025Article
- Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- Real-time genomic characterization of pediatric acute leukemia using adaptive sampling.Leukemia · 2025Article
- Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution.Genome research · 2025Article
- Review
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundLong-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors.
resultsIn this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data. We evaluated LongGF on tens of simulated long-read RNA-seq datasets, and demonstrated its superior performance in gene fusion detection. We also tested LongGF on a Nanopore direct mRNA sequencing dataset and a PacBio sequencing dataset generated on a mixture of 10 cancer cell lines, and found that LongGF achieved better performance to detect known gene fusions over existing computational tools. Furthermore, we tested LongGF on a Nanopore cDNA sequencing dataset on acute myeloid leukemia, and pinpointed the exact location of a translocation (previously known in cytogenetic resolution) in base resolution, which was further validated by Sanger sequencing.
conclusionsIn summary, LongGF will greatly facilitate the discovery of candidate gene fusion events from long-read RNA-Seq data, especially in cancer samples. LongGF is implemented in C++ and is available at https://github.com/WGLab/LongGF .
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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.