ArticleCancer research2023
Gene Fusion Detection and Characterization in Long-Read Cancer Transcriptome Sequencing Data with FusionSeeker.
Article in Cancer research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed, 48 citations in OpenAlex.
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Review
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- 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
- Review
- Fusion gene discovery in single cells from high throughput long read single cell transcriptomes.bioRxiv : the preprint server for biology · 2026Article
- Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing.Nature communications · 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
- PACLseq: A Standalone Diagnostic Method for Ph-Like Acute Lymphoblastic Leukemia Using Nanopore Sequencing.MedComm · 2025Article
- A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector.Nature protocols · 2025Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- CircCDYL Association With hnRNPL Modulates CDYL Isoform Switching in Breast Cancer Cells.Cancer science · 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
- Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution.Genome research · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Gene fusions are prevalent in a wide array of cancer types with different frequencies. Long-read transcriptome sequencing technologies, such as PacBio, Iso-Seq, and Nanopore direct RNA sequencing, provide full-length transcript sequencing reads, which could facilitate detection of gene fusions. In this work, we developed a method, FusionSeeker, to comprehensively characterize gene fusions in long-read cancer transcriptome data and reconstruct accurate fused transcripts from raw reads. FusionSeeker identified gene fusions in both exonic and intronic regions, allowing comprehensive characterization of gene fusions in cancer transcriptomes. Fused transcript sequences were reconstructed with FusionSeeker by correcting sequencing errors in the raw reads through partial order alignment algorithm. Using these accurate transcript sequences, FusionSeeker refined gene fusion breakpoint positions and predicted breakpoints at single bp resolution. Overall, FusionSeeker will enable users to discover gene fusions accurately using long-read data, which can facilitate downstream functional analysis as well as improved cancer diagnosis and treatment. SIGNIFICANCE: FusionSeeker is a new method to discover gene fusions and reconstruct fused transcript sequences in long-read cancer transcriptome sequencing data to help identify novel gene fusions important for tumorigenesis and progression.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.