ArticleMolecular oncology2019
Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect.
Article in Molecular oncology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed, 16 citations in OpenAlex.
- Molecular and Immune Landscape of Recurrent and/or Distant Metastatic Squamous Cell Carcinoma of the Head and Neck: An EORTC/IMMUCAN Project.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Genomic and Immune Landscape of Recurrent and/or Metastatic Squamous Cell Carcinoma of the Head and Neck Progressing on Anti-PD-1 Treatment.Cancer immunology research · 2026Article
- Prevalence and biological impact of clinically relevant gene fusions in head and neck cancers.NPJ precision oncology · 2025Article
- HBV DNA integration and somatic mutations in HCC patients with HBV-HCV dual infection reveals profiles intermediate between HBV- and HCV-related HCC.Journal of biomedical science · 2025Article
- Clinical relevance and therapeutic predictive ability of hypoxia biomarkers in head and neck cancer tumour models.Molecular oncology · 2024Article
- Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes.Journal for immunotherapy of cancer · 2024Article
- Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis.Brain : a journal of neurology · 2024Article
- Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data.PLoS computational biology · 2022Article
- Whole-transcriptome sequencing-based concomitant detection of viral and human genetic determinants of cutaneous lesions.JCI insight · 2022Article
- Causes and Consequences of HPV Integration in Head and Neck Squamous Cell Carcinomas: State of the Art.Cancers · 2021Review
- VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data.Bioinformatics (Oxford, England) · 2021Article
- "Protein aggregates" contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation.Aging cell · 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
9 authors at 3 institutions in 2 countries.
Funding
Abstract
Next-generation sequencing provides an opportunity to detect viral species from RNA-seq data of human tissues, but existing computational approaches do not perform optimally on clinical samples. We developed a bioinformatic method called VirTect for detecting viruses in neoplastic human tissues using RNA-seq data. Here, we used VirTect to analyze RNA-seq data from 363 head and neck squamous cell carcinoma (HNSCC) patients and identified 22 human papillomavirus (HPV)-induced HNSCCs. These predictions were validated by manual review of pathology reports on histopathologic specimens. VirTect showed better performance in recall and accuracy compared to the two existing prediction methods, VirusFinder and VirusSeq, in identifying viral sequences from RNA-seq data. The majority of HPV carcinogenesis studies thus far have been performed on cervical cancer and generalized to HNSCC. Our results suggest that carcinogenesis of HPV-induced HNSCC and other cases of HNSCC involve different genes, so understanding the underlying molecular mechanisms will have a significant impact on therapeutic approaches and outcomes. In summary, RNA-seq together with VirTect can be an effective solution for the detection of viruses from tumor samples and can facilitate the clinicopathologic characterization of various types of cancers with broad applications for oncology.
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.