ArticleNucleic acids research2018
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes.Nature methods · 2026Article
- VISDB 2.0: A manually curated resource of viral integration sites and their regulatory maps in human diseases.Scientific data · 2026Article
- RAAVioli: A comprehensive approach to characterizing AAV vector integrations and rearrangements.Molecular therapy. Advances · 2026Article
- Extrachromosomal circular DNA: a potential clinical therapeutic target in malignant tumors.Cellular & molecular biology letters · 2026Review
- Integrated transcriptomic profiling reveals oncogenic pathways and chimeric transcripts in equine sarcoid lesions with predominant BPV1 detection.Frontiers in molecular biosciences · 2026Article
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- Epigenetic Biomarkers for Cervical Cancer Progression: A Scoping Review.International journal of molecular sciences · 2025Article
- NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.PLoS computational biology · 2025Article
- Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer.Nature communications · 2025Article
- Article
- Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers.Molecular oncology · 2024Article
- Endogenous viral elements: insights into data availability and accessibility.Virus evolution · 2024Article
- BRD4 as a potential target for human papillomaviruses associated cancer.Journal of medical virology · 2023Review
- Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome biology · 2023Article
- Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications.Genes · 2023Review
- Comparing molecular and computational approaches for detecting viral integration of AAV gene therapy constructs.Molecular therapy. Methods & clinical development · 2023Article
- HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription.Nucleic acids research · 2023Article
- Application of organoid culture from HPV18-positive small cell carcinoma of the uterine cervix for precision medicine.Cancer medicine · 2023Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- Cells with stem-like properties are associated with the development of HPV18-positive cervical cancer.Cancer science · 2023Article
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5 authors.
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Abstract
The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma. We present ViFi, a computational method that combines phylogenetic methods with reference-based read mapping to detect viral integrations. In contrast with read-based reference mapping approaches, ViFi is faster, and shows high precision and sensitivity on both simulated and biological data, even when the integrated virus is a novel strain or highly mutated. We applied ViFi to matched genomic and mRNA data from 68 cervical cancer samples from TCGA and found high concordance between the two. Surprisingly, viral integration resulted in a dramatic transcriptional upregulation in all proximal elements, including LINEs and LTRs that are not normally transcribed. This upregulation is highly correlated with the presence of a viral gene fused with a downstream human element. Moreover, genomic rearrangements suggest the formation of apparent circular extrachromosomal (ecDNA) human-viral structures. Our results suggest the presence of apparent small circular fusion viral/human ecDNA, which correlates with indiscriminate and unregulated expression of proximal genomic elements, potentially contributing to the pathogenesis of HPV-associated cervical cancers. ViFi is available at https://github.com/namphuon/ViFi.
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