ArticleScientific reports2019
TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration.
Article in Scientific reports, 2019. 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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Who cites it
20 citing papers in PubMed.
- Mock Samples That Mimic Human Cervicovaginal Samples to Accelerate the Development and Evaluation of Assays for High-Risk HPV for Cervical Cancer Screening.Journal of medical virology · 2026Article
- Therapeutic Landscape of HPV-Associated Cancers: From Mechanisms and Conventional Approaches to Future Innovations.Cancers · 2026Review
- Scalable long-read nanopore HPV16 amplicon-based whole-genome sequencing.Scientific reports · 2025Article
- Genotype distribution and molecular characterization of HPV in the Peruvian amazon: insights into prevalence, lineage diversity, and viral integration.Scientific reports · 2025Article
- GENOMICON-Seq enables realistic simulation of amplicon and exome sequencing for low-frequency mutation detection.Scientific reports · 2025Article
- Intratype variants and high genotypic diversity of human papillomavirus with polymorphisms in the antigenic hypervariable loops of the L1 protein from women living with human immunodeficiency virus in Northeastern Brazil.Journal of medical microbiology · 2025Article
- A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics.International journal of molecular sciences · 2024Review
- Article
- Single-tube four-target lateral flow assay detects human papillomavirus types associated with majority of cervical cancers.Analytical biochemistry · 2024Article
- HPV DNA Integration at Actionable Cancer-Related Genes Loci in HPV-Associated Carcinomas.Cancers · 2024Article
- A novel tailed primer nucleic acid test for detection of HPV 16, 18 and 45 DNA at the point of care.Scientific reports · 2023Article
- Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome biology · 2023Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- TaME-seq2: tagmentation-assisted multiplex PCR enrichment sequencing for viral genomic profiling.Virology journal · 2023Article
- Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny.Tumour virus research · 2022Article
- HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study.Infectious agents and cancer · 2022Article
- PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing.BMC bioinformatics · 2020Article
- Pathology of HPV-Associated Head and Neck Carcinomas: Recent Data and Perspectives for the Development of Specific Tumor Markers.Frontiers in oncology · 2020Review
- High Levels of Within-Host Variations of Human Papillomavirus 16Frontiers in microbiology · 2020Article
- Next-generation sequencing in routine clinical microbiology and infectious diseases: an ESGMD-ESGEM ESCMID postgraduate course.New microbes and new infectionsArticle
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
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