ArticleScientific reports2016
Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 42 citations in OpenAlex.
- Advances in clonality analysis of human T-cell leukemia virus type 1-infected cells: from Southern blotting to high-throughput sequencing.Journal of clinical and experimental hematopathology : JCEH · 2025Review
- Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment.Nature microbiology · 2025Article
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- Enriching the future of public health microbiology with hybridization bait capture.Clinical microbiology reviews · 2024Review
- Viral genome sequencing methods: benefits and pitfalls of current approaches.Biochemical Society transactions · 2024Review
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Integration of Viral Genome to Human Genomic DNA in Nails of Patients with Chronic Hepatitis B Virus Infection.JMA journal · 2023Article
- Comparing molecular and computational approaches for detecting viral integration of AAV gene therapy constructs.Molecular therapy. Methods & clinical development · 2023Article
- Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping.Pathogens (Basel, Switzerland) · 2022Review
- Article
- Identification and characterization of a novel enhancer in the HTLV-1 proviral genome.Nature communications · 2022Article
- A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP.Scientific reports · 2021Article
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
- A Methodology for Assessing Tumor Clonality of Adult T Cell Leukemia/Lymphoma.Molecular therapy. Methods & clinical development · 2020Article
- A high-throughput detection method for the clonality of Human T-cell leukemia virus type-1-infected cells in vivo.International journal of hematology · 2020Article
- HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP.Retrovirology · 2019Article
- Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches.The Journal of general virology · 2019Article
- HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus.Scientific reports · 2019Article
- Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples.PLoS neglected tropical diseases · 2019Article
- Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent development and advancement of next-generation sequencing (NGS) technologies have enabled the characterization of the human genome at extremely high resolution. In the retrovirology field, NGS technologies have been applied to integration-site analysis and deep sequencing of viral genomes in combination with PCR amplification using virus-specific primers. However, virus-specific primers are not available for some epigenetic analyses, like chromatin immunoprecipitation sequencing (ChIP-seq) assays. Viral sequences are poorly detected without specific PCR amplification because proviral DNA is very scarce compared to human genomic DNA. Here, we have developed and evaluated the use of biotinylated DNA probes for the capture of viral genetic fragments from a library prepared for NGS. Our results demonstrated that viral sequence detection was hundreds or thousands of times more sensitive after enrichment, enabling us to reduce the economic burden that arises when attempting to analyze the epigenetic landscape of proviruses by NGS. In addition, the method is versatile enough to analyze proviruses that have mismatches compared to the DNA probes. Taken together, we propose that this approach is a powerful tool to clarify the mechanisms of transcriptional and epigenetic regulation of retroviral proviruses that have, until now, remained elusive.
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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.