ArticlePloS one2016
InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 66 citations in OpenAlex.
- Characteristics of fusion genes in breast cancer.Cancer cell international · 2026Review
- Comparison of gene fusion detection algorithms reveals frequently overlooked driver fusions in hematologic malignancies.NPJ precision oncology · 2026Article
- Article
- Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution.Genome research · 2025Article
- Biglycan-driven risk stratification in ZFTA-RELA fusion supratentorial ependymomas through transcriptome profiling.Acta neuropathologica communications · 2025Article
- Architects and Partners: The Dual Roles of Non-coding RNAs in Gene Fusion Events.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Fibromyxoid aSoft Tissue Tumor With PLAG1 Fusion-The First Case in an Adult Patient.Genes, chromosomes & cancer · 2024Article
- RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data.Briefings in bioinformatics · 2024Article
- CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution.bioRxiv : the preprint server for biology · 2024Article
- SFyNCS detects oncogenic fusions involving non-coding sequences in cancer.Nucleic acids research · 2023Article
- MALAT1 functions as a transcriptional promoter of MALAT1::GLI1 fusion for truncated GLI1 protein expression in cancer.BMC cancer · 2023Article
- 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.Nature communications · 2023Article
- SFyNCS detects oncogenic fusions involving non-coding sequences in cancer.bioRxiv : the preprint server for biology · 2023Article
- Full-Length RNA Sequencing Provides Insights into Goldfish Evolution under Artificial Selection.International journal of molecular sciences · 2023Article
- Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data.BMC cancer · 2022Article
- Article
- Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens.Nature biotechnology · 2022Article
- Pan-Genomic Sequencing Reveals ActionableCancers · 2021Article
- Discovery of clinically relevant fusions in pediatric cancer.BMC genomics · 2021Article
- Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing.RNA biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found. The ability to detect gene fusions of different types, including isoform fusions and fusions involving non-coding regions, has not been thoroughly studied yet. Here, we propose a novel computational toolkit called InFusion for fusion gene detection from RNA-seq data. InFusion introduces several unique features, such as discovery of fusions involving intergenic regions, and detection of anti-sense transcription in chimeric RNAs based on strand-specificity. Our approach demonstrates superior detection accuracy on simulated data and several public RNA-seq datasets. This improved performance was also evident when evaluating data from RNA deep-sequencing of two well-established prostate cancer cell lines. InFusion identified 26 novel fusion events that were validated in vitro, including alternatively spliced gene fusion isoforms and chimeric transcripts that include intergenic regions. The toolkit is freely available to download from http:/bitbucket.org/kokonech/infusion.
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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.