ArticlePapillomavirus research (Amsterdam, Netherlands)2015
Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection.
Article in Papillomavirus research (Amsterdam, Netherlands), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
What it found
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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
70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- 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
- STK11 Mutations and Deletions Define an Aggressive Molecular Subgroup of Cervical Adenocarcinoma.Cancer medicine · 2026Article
- Longitudinal analysis of high-risk HPV infections reveals within-host viral genome changes over time.PLoS pathogens · 2026Article
- HPV16 genetic variation provides evidence of positive natural selection driven by HLA class I.Nature communications · 2026Article
- Molecular Etiology and Clinical Significance of Discordant Human Papillomavirus Testing in p16+ Oropharyngeal Cancers.JCO precision oncology · 2026Article
- Article
- Evaluation of targeted next-generation sequencing for detection of HPV genotypes and sublineages in cervical liquid-based cytology SurePath samples from the Danish screening program.International journal of cancer · 2026Article
- Detection of partial deletions of the human papillomavirus 16 E6 gene in a subset of oropharyngeal and cervical cancers.Virus research · 2025Article
- Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing.Scientific reports · 2025Article
- Direct Comparison of Alternative Blood-Based Approaches for Early Detection and Diagnosis of HPV-Associated Head and Neck Cancers.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Identification of HPV16 Lineages in South African and Mozambican Women with Normal and Abnormal Cervical Cytology.Viruses · 2024Article
- Transoral Robotic Surgery and Human Papillomavirus Infection: Impact on Oropharyngeal Cancer Prognosis.Journal of clinical medicine · 2024Article
- Differential long-term bivalent HPV vaccine cross-protection by variants in the Costa Rica HPV vaccine trial.NPJ vaccines · 2024Article
- HPV16 Phylogenetic Variants in Anogenital and Head and Neck Cancers: State of the Art and Perspectives.Viruses · 2024Review
- HPV infection and its correlation with p53 and Bcl-2 among pregnant mothers and their infants.Virus genes · 2024Article
- Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus.Virus evolution · 2024Article
- Unveiling the multifaceted realm of human papillomavirus: a comprehensive exploration of biology, interactions, and advances in cancer management.Frontiers in immunology · 2024Review
- Outcomes and associated factors of cervical human papillomavirus infection among 608 women in Shenzhen, China, 2018-2023.Frontiers in public health · 2024Article
- Intra-Patient Genomic Variations of Human Papillomavirus Type 31 in Cervical Cancer and Precancer.Viruses · 2023Article
- TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.Virology journal · 2023Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
27 authors.
Funding
Abstract
For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current "gold standard" of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%. Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3-222,
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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.