ArticleBritish journal of cancer2015
NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome.
Article in British journal of cancer, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 69 citations in OpenAlex.
- Integrated genomic and proteomic profiling reveals insights into chemoradiation resistance in cervical cancer.Molecular oncology · 2026Article
- A Holistic Framework for Cervical Cancer Screening and Risk Stratification: Integrating Etiology, Morphology, Epigenetics, and Microecology.Cancer management and research · 2026Review
- HPVPool-Seq: a genotype-guided pooling strategy for cost-effective next-generation sequencing detection of HPV integration in cervical samples.Microbiology spectrum · 2025Article
- HPV-KITE: sequence analysis software for rapid HPV genotype detection.Briefings in bioinformatics · 2025Article
- Integrated mutational landscape analysis of poorly differentiated high-grade neuroendocrine carcinoma of the uterine cervix.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines.BMC genomics · 2024Article
- Identification of novel genomic hotspots and tumor-relevant genes via comprehensive analysis of HPV integration in Chinese patients of cervical cancer.American journal of cancer research · 2024Article
- Detection of Microorganisms in Body Fluid Samples.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Viral oncogenes, viruses, and cancer: a third-generation sequencing perspective on viral integration into the human genome.Frontiers in oncology · 2023Review
- HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study.Infectious agents and cancer · 2022Article
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- Influence of tumor mutational burden, inflammatory gene expression profile, and PD-L1 expression on response to pembrolizumab in head and neck squamous cell carcinoma.Journal for immunotherapy of cancer · 2022Article
- Genomic alterations caused by HPV integration in a cohort of Chinese endocervical adenocarcinomas.Cancer gene therapy · 2021Article
- Genomic analyses of high-grade neuroendocrine gynecological malignancies reveal a unique mutational landscape and therapeutic vulnerabilities.Molecular oncology · 2021Article
- The Prevalence of High- and Low-Risk Types of HPV in Patients with Squamous Cell Carcinoma of the Head and Neck, Patients with Chronic Tonsillitis, and Healthy Individuals Living in Poland.Diagnostics (Basel, Switzerland) · 2021Article
- A NGS-based Blood Test For the Diagnosis of Invasive HPV-associated Carcinomas with Extensive Viral Genomic Characterization.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
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- Integrative sequencing discovers an ATF1-motif enriched molecular signature that differentiates hyalinizing clear cell carcinoma from mucoepidemoid carcinoma.Oral oncology · 2021Article
- Circulating HPV DNA in the Management of Oropharyngeal and Cervical Cancers: Current Knowledge and Future Perspectives.Journal of clinical medicine · 2021Review
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundHuman papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool 'HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets.
methodsWe developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a 'quick mode' to identify presence of HPV types and an 'integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html.
resultsOn the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71.
conclusionsHPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge.
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