ArticleGenome research2019
A virome-wide clonal integration analysis platform for discovering cancer viral etiology.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it, 57 citations in OpenAlex.
- The association between human papillomavirus and bladder cancer: Evidence from meta-analysis and two-sample mendelian randomization.Journal of medical virology · 2023Pooled it
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- TEvarSim: A genome simulator for transposable element (TE) variants.PLoS computational biology · 2026Article
- Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma.Genome research · 2025Article
- Review
- Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy.Virologica Sinica · 2024Article
- VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.Bioinformatics (Oxford, England) · 2024Article
- The Possible Role of Pathogens and Chronic Immune Stimulation in the Development of Diffuse Large B-Cell Lymphoma.Biomedicines · 2024Review
- Elucidating the clonal relationship of esophageal second primary tumors in patients with laryngeal squamous cell carcinoma.Infectious agents and cancer · 2023Review
- Host Transcriptional Regulatory Genes and Microbiome Networks Crosstalk through Immune Receptors Establishing Normal and Tumor Multiomics Metafirm of the Oral-Gut-Lung Axis.International journal of molecular sciences · 2023Review
- Temporal and structural patterns of hepatitis B virus integrations in hepatocellular carcinoma.Journal of medical virology · 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
- Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome.Genomics & informatics · 2022Article
- Tumor Molecular and Microenvironment Characteristics in EBV-Associated Malignancies as Potential Therapeutic Targets: Focus on Gastric Cancer.Current issues in molecular biology · 2022Review
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- HPV-16 Expression and Loss of Cell Differentiation in Primary Bladder Tumors.BioMed research international · 2022Article
- Gut Virome: Role and Distribution in Health and Gastrointestinal Diseases.Frontiers in cellular and infection microbiology · 2022Review
- Urinary Tract Virome as an Urgent Target for Metagenomics.Life (Basel, Switzerland) · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Oncoviral infection is responsible for 12%-15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early-stage clonal viral integrations. To implement this strategy, we developed VIcaller, a novel platform for identifying viral integrations that are derived from any characterized viruses and shared by a large proportion of tumor cells using whole-genome sequencing (WGS) data. The sensitivity and precision were confirmed with simulated and benchmark cancer data sets. By applying this platform to cancer WGS data sets with proven or speculated viral etiology, we newly identified or confirmed clonal integrations of hepatitis B virus (HBV), human papillomavirus (HPV), Epstein-Barr virus (EBV), and BK Virus (BKV), suggesting the involvement of these viruses in early stages of tumorigenesis in affected tumors, such as HBV in
Indexed as
Identifiers
What OpenQuestion holds
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.