ArticleJournal of biomolecular techniques : JBT2016
Next-Generation Sequencing-Based HPV Genotyping Assay Validated in Formalin-Fixed, Paraffin-Embedded Oropharyngeal and Cervical Cancer Specimens.
Article in Journal of biomolecular techniques : JBT, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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Who cites it
20 citing papers in PubMed, 36 citations in OpenAlex.
- Oral HPV detection and genotyping by next-generation sequencing in a healthy Palestinian cohort: pilot study.Scientific reports · 2026Article
- Multimodal assessment of high-risk human papillomavirus in sinonasal squamous cell carcinoma.Pathology, research and practice · 2024Article
- Development of a simplified and cost-effective sample preparation method for genotyping of human papillomavirus by next-generation sequencing.Archives of virology · 2023Article
- Analysis of the Prevalence and Quantification of viral load of different human papillomavirus types in Turkish women population.Asian Pacific journal of cancer prevention : APJCP · 2022Article
- Article
- Human Papillomavirus Oral Infection: Review of Methodological Aspects and Epidemiology.Pathogens (Basel, Switzerland) · 2021Review
- Multiple HPV infections among men who have sex with men engaged in anal cancer screening in Abuja, Nigeria.Papillomavirus research (Amsterdam, Netherlands) · 2020Article
- High frequency of HPV genotypes 59, 66, 52, 51, 39 and 56 in women from Western Mexico.BMC infectious diseases · 2020Article
- Assessment of a new low-cost, PCR-based strategy for high-risk human papillomavirus DNA detection for cervical cancer prevention.BMC infectious diseases · 2019Article
- Development and validation of radiomic signatures of head and neck squamous cell carcinoma molecular features and subtypes.EBioMedicine · 2019Article
- Cross-hybridization between HPV genotypes in the Linear Array Genotyping Test confirmed by Next-Generation Sequencing.Diagnostic pathology · 2019Article
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- Article
- Recent Advances on the Molecular Mechanism of Cervical Carcinogenesis Based on Systems Biology Technologies.Computational and structural biotechnology journal · 2019Review
- Evaluation and validation of HPV real-time PCR assay for the detection of HPV DNA in oral cytobrush and FFPE samples.Scientific reports · 2018Article
- Utility of high-throughput DNA sequencing in the study of the human papillomaviruses.Virus genes · 2018Review
- Genotyping of high-risk anal human papillomavirus (HPV): ion torrent-next generation sequencing vs. linear array.Virology journal · 2017Article
- Current and Emerging Molecular Tests for Human Papillomavirus-Related Neoplasia in the Genomic Era.The Journal of molecular diagnostics : JMD · 2017Review
- Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment.Journal of clinical microbiology · 2017Article
- HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization.PloS one · 2017Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5(+)/6(+) (BSGP)5(+)/6(+). To validate genotype specificity and use in archived clinical FFPE tumor samples, we compared NGS HPV genotyping at 2 sequencing centers with typing by Roche Linear Array assay in 42 oropharyngeal and cervical cancer specimens representing 10 HPV genotypes, as well as HPV-negative cases. To demonstrate the detection of a broad range of HPV genotypes, we genotyped a cohort of 266 cervical cancers. A comparison of NGS genotyping of FFPE cancer specimens with genotyping by Linear Array showed concordant results in 34/37 samples (92%) at sequencing site 1 and 39/42 samples (93%) at sequencing site 2. Concordance between sites was 92%. Designed for use with 10 ng genomic DNA, the assay detected HPV using as little as 1.25 ng FFPE-derived genomic DNA. In 266 cervical cancer specimens, the NGS assay identified 20 different HPV genotypes, including all 13 carcinogenic genotypes. This novel NGS assay provides a sensitive and specific high-throughput method to detect and genotype HPV in a range of clinical specimens derived from FFPE with low per-sample cost.
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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.