ArticlePloS one2011
Sequence imputation of HPV16 genomes for genetic association studies.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 2 of them syntheses that pooled it.
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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
52 citing papers in PubMed, 2 syntheses or guidelines pooled it, 92 citations in OpenAlex.
- Lineages and sublineages of high-risk human papillomavirus types associated with cervical cancer and precancer: a systematic review and meta-analysis.Journal of the National Cancer Institute · 2025Pooled it
- Genetic association between the HIF-1α P582S polymorphism and cervical cancer risk: a meta analysis.International journal of clinical and experimental pathology · 2014Pooled it
- Genetic Variability and Prediction of T Epitopes of the HPV16 E2 Gene in Asymptomatic Women from Cajamarca, Peru.Viruses · 2025Article
- Genome-Wide Association Analyses of HPV16 and HPV18 Seropositivity Identify Susceptibility Loci for Cervical Cancer.Journal of medical virology · 2025Article
- HPV Infections-Classification, Pathogenesis, and Potential New Therapies.International journal of molecular sciences · 2024Review
- Identification and Functional Implications of the E5 Oncogene Polymorphisms of Human Papillomavirus Type 16.Tropical medicine and infectious disease · 2024Article
- Article
- Human Papillomavirus 16 Lineage A Variants Associated With Persistent Genital Infections in Men: The HPV Infection in Men (HIM) Study.The Journal of infectious diseases · 2023Article
- Decoding the Genetic and Structural Features of HPV16 E5 Oncogene in Cervical Cancer Isolates from Pakistan: A Pilot Study.Iranian biomedical journal · 2023Article
- Genetic Variability in the E6/E7 Region of Human Papillomavirus 16 in Women from Ecuador.Viruses · 2023Article
- Article
- A comprehensive review for machine learning based human papillomavirus detection in forensic identification with multiple medical samples.Frontiers in microbiology · 2023Review
- Comprehensive Viral Genotyping Reveals Prognostic Viral Phylogenetic Groups in HPV16-Associated Squamous Cell Carcinoma of the Oropharynx.Molecular cancer research : MCR · 2022Article
- Genetic diversity of E6, E7 and the long control region in human papillomavirus type 16 variants in Beijing, China.Biochemistry and biophysics reports · 2022Article
- A Straightforward HPV16 Lineage Classification Based on Machine Learning.Frontiers in artificial intelligence · 2022Article
- Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences.GigaScience · 2021Article
- Article
- Genetic and Epigenetic Variations of HPV52 in Cervical Precancer.International journal of molecular sciences · 2021Article
- Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance.Nature communications · 2020Article
- Next Generation Sequencing Assay for Detection of Circulating HPV DNA (cHPV-DNA) in Patients Undergoing Radical (Chemo)Radiotherapy in Anal Squamous Cell Carcinoma (ASCC).Frontiers in oncology · 2020Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundHuman Papillomavirus type 16 (HPV16) causes over half of all cervical cancer and some HPV16 variants are more oncogenic than others. The genetic basis for the extraordinary oncogenic properties of HPV16 compared to other HPVs is unknown. In addition, we neither know which nucleotides vary across and within HPV types and lineages, nor which of the single nucleotide polymorphisms (SNPs) determine oncogenicity.
methodsA reference set of 62 HPV16 complete genome sequences was established and used to examine patterns of evolutionary relatedness amongst variants using a pairwise identity heatmap and HPV16 phylogeny. A BLAST-based algorithm was developed to impute complete genome data from partial sequence information using the reference database. To interrogate the oncogenic risk of determined and imputed HPV16 SNPs, odds-ratios for each SNP were calculated in a case-control viral genome-wide association study (VWAS) using biopsy confirmed high-grade cervix neoplasia and self-limited HPV16 infections from Guanacaste, Costa Rica.
resultsHPV16 variants display evolutionarily stable lineages that contain conserved diagnostic SNPs. The imputation algorithm indicated that an average of 97.5±1.03% of SNPs could be accurately imputed. The VWAS revealed specific HPV16 viral SNPs associated with variant lineages and elevated odds ratios; however, individual causal SNPs could not be distinguished with certainty due to the nature of HPV evolution.
conclusionsConserved and lineage-specific SNPs can be imputed with a high degree of accuracy from limited viral polymorphic data due to the lack of recombination and the stochastic mechanism of variation accumulation in the HPV genome. However, to determine the role of novel variants or non-lineage-specific SNPs by VWAS will require direct sequence analysis. The investigation of patterns of genetic variation and the identification of diagnostic SNPs for lineages of HPV16 variants provides a valuable resource for future studies of HPV16 pathogenicity.
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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.