ArticleScientific reports2020
HPV-EM: an accurate HPV detection and genotyping EM algorithm.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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
9 citing papers in PubMed.
- Characterization of persistent HPV-specific activated T cells in head and neck squamous cell carcinoma.Oncoimmunology · 2026Article
- Chemoradiation Reprograms Tumor Cells and the Immune Microenvironment in Cervical Cancer.Cancer research · 2026Article
- Drug Repositioning for HPV Clade-Specific Cervicouterine Cancer Using the OCTAD Pipeline.International journal of molecular sciences · 2025Article
- Study on the clinical characteristics, persistent infection capability, and viral load of human papillomavirus type 82 single infection.Virology journal · 2025Article
- A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights.Nature communications · 2024Article
- Geny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes.Frontiers in immunology · 2024Article
- Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma.Nature genetics · 2023Article
- Novel canonical and non-canonical viral antigens extend current targets for immunotherapy of HPV-driven cervical cancer.iScience · 2023Article
- Development of an HPV Genotype Detection Platform Based on Aggregation-Induced Emission (AIE) and Flow-Through Hybridization Technologies.Molecules (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Accurate HPV genotyping is crucial in facilitating epidemiology studies, vaccine trials, and HPV-related cancer research. Contemporary HPV genotyping assays only detect < 25% of all known HPV genotypes and are not accurate for low-risk or mixed HPV genotypes. Current genomic HPV genotyping algorithms use a simple read-alignment and filtering strategy that has difficulty handling repeats and homology sequences. Therefore, we have developed an optimized expectation-maximization algorithm, designated HPV-EM, to address the ambiguities caused by repetitive sequencing reads. HPV-EM achieved 97-100% accuracy when benchmarked using cell line data and TCGA cervical cancer data. We also validated HPV-EM using DNA tiling data on an institutional cervical cancer cohort (96.5% accuracy). Using HPV-EM, we demonstrated HPV genotypic differences in recurrence and patient outcomes in cervical and head and neck cancers.
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Registered trials
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