ArticleBMC genomics2017
Deep sequencing of HPV E6/E7 genes reveals loss of genotypic diversity and gain of clonal dominance in high-grade intraepithelial lesions of the cervix.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Article
- Lightweight Low-Rank Adaptation Vision Transformer Framework for Cervical Cancer Detection and Cervix Type Classification.Bioengineering (Basel, Switzerland) · 2024Article
- Article
- HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics.International journal of molecular sciences · 2022Article
- Article
- Article
- HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench.Pathogens (Basel, Switzerland) · 2021Article
- Molecular Pap Smear: Validation of HPV Genotype and Host Methylation Profiles ofFrontiers in microbiology · 2020Article
- Molecular Detection of Bovine Papillomavirus DNA in the Placenta and Blood of Healthy Mares and Respective Foals.Veterinary sciences · 2019Article
- Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology.Frontiers in genetics · 2019Article
- Epithelial stratification shapes infection dynamics.PLoS computational biology · 2019Article
- Recent Advances on the Molecular Mechanism of Cervical Carcinogenesis Based on Systems Biology Technologies.Computational and structural biotechnology journal · 2019Review
- Variant sublineages of human papillomavirus type 16 predispose women to persistent infection characterized by a sequence analysis of the E6, L1, and LCR regions.International journal of clinical and experimental pathology · 2019Article
- The vaginal eukaryotic DNA virome and preterm birth.American journal of obstetrics and gynecology · 2018Article
- Intra-host sequence variability in human papillomavirus.Papillomavirus research (Amsterdam, Netherlands) · 2018Article
- Predictors of abnormal cytology among HPV-infected women in remote territories of French Guiana.BMC women's health · 2018Article
- Whole-Genome Sequencing and Variant Analysis of Human Papillomavirus 16 Infections.Journal of virology · 2017Article
- Article
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Authors and funding
6 authors.
Funding
Abstract
backgroundHuman papillomavirus (HPV) is the carcinogen of almost all invasive cervical cancer and a major cause of oral and other anogenital malignancies. HPV genotyping by dideoxy (Sanger) sequencing is currently the reference method of choice for clinical diagnostics. However, for samples with multiple HPV infections, genotype identification is singular and occasionally imprecise or indeterminable due to overlapping chromatograms. Our aim was to explore and compare HPV metagenomes in abnormal cervical cytology by deep sequencing for correlation with disease states.
resultsLow- and high-grade intraepithelial lesion (LSIL and HSIL) cytology samples were DNA extracted for PCR-amplification of the HPV E6/E7 genes. HPV+ samples were sequenced by dideoxy and deep methods. Deep sequencing revealed ~60% of all samples (n = 72) were multi-HPV infected. Among LSIL samples (n = 43), 27 different genotypes were found. The 3 dominant (most abundant) genotypes were: HPV-39, 11/43 (26%); -16, 9/43 (21%); and -35, 4/43 (9%). Among HSIL (n = 29), 17 HPV genotypes were identified; the 3 dominant genotypes were: HPV-16, 21/29 (72%); -35, 4/29 (14%); and -39, 3/29 (10%). Phylogenetically, type-specific E6/E7 genetic distances correlated with carcinogenic potential. Species diversity analysis between LSIL and HSIL revealed loss of HPV diversity and domination by HPV-16 in HSIL samples.
conclusionsDeep sequencing resolves HPV genotype composition within multi-infected cervical cytology. Biodiversity analysis reveals loss of diversity and gain of dominance by carcinogenic genotypes in high-grade cytology. Metagenomic profiles may therefore serve as a biomarker of disease severity and a population surveillance tool for emerging genotypes.
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