ArticleBMC medical genomics2019
Detecting virus integration sites based on multiple related sequencing data by VirTect.
Article in BMC medical genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- VISDB 2.0: A manually curated resource of viral integration sites and their regulatory maps in human diseases.Scientific data · 2026Article
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression.bioRxiv : the preprint server for biology · 2025Article
- Detection of viral contamination in cell lines using ViralCellDetector.Frontiers in microbiology · 2025Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- Whole-transcriptome sequencing-based concomitant detection of viral and human genetic determinants of cutaneous lesions.JCI insight · 2022Article
- The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.F1000Research · 2022Article
- "Protein aggregates" contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation.Aging cell · 2021Article
- Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper.PLoS computational biology · 2021Article
- ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data.BMC bioinformatics · 2021Article
- Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data.PloS one · 2021Article
- A First NGS Investigation Suggests No Association Between Viruses and Canine Cancers.Frontiers in veterinary science · 2020Article
- The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics meets medicine.BMC medical genomics · 2019Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSince tumor often has a high level of intra-tumor heterogeneity, multiple tumor samples from the same patient at different locations or different time points are often sequenced to study tumor intra-heterogeneity or tumor evolution. In virus-related tumors such as human papillomavirus- and Hepatitis B Virus-related tumors, virus genome integrations can be critical driving events. It is thus important to investigate the integration sites of the virus genomes. Currently, a few algorithms for detecting virus integration sites based on high-throughput sequencing have been developed, but their insufficient performance in their sensitivity, specificity and computational complexity hinders their applications in multiple related tumor sequencing.
resultsWe develop VirTect for detecting virus integration sites simultaneously from multiple related-sample data. This algorithm is mainly based on the joint analysis of short reads spanning breakpoints of integration sites from multiple samples. To achieve high specificity and breakpoint accuracy, a local precise sandwich alignment algorithm is used. Simulation and real data analyses show that, compared with other algorithms, VirTect is significantly more sensitive and has a similar or lower false discovery rate.
conclusionsVirTect can provide more accurate breakpoint position and is computationally much more efficient in terms both memory requirement and computational time.
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