ArticleThe Journal of molecular diagnostics : JMD2011
Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue.
Article in The Journal of molecular diagnostics : JMD, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
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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
65 citing papers in PubMed, 122 citations in OpenAlex.
- Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers.PloS one · 2015Trial
- Long-read target enrichment sequencing for rAAV integration site analysis in engineered clones with targeted viral insertion.Molecular therapy. Nucleic acids · 2026Article
- Interlocking host and viral cis-regulatory networks drive Merkel cell carcinoma.The Journal of clinical investigation · 2025Article
- Genomic Signatures of Poor Prognosis in Merkel Cell Carcinoma: A Single-Institution Prospective Study.Molecular cancer research : MCR · 2025Article
- Evaluation of a Probe-Based Enrichment Protocol for Nanopore Sequencing of Zoonotic Viruses.Viruses · 2025Article
- Comparison and cross-validation of long-read and short-read target-enrichment sequencing methods to assess AAV vector integration into host genome.Molecular therapy. Methods & clinical development · 2024Article
- Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.Nucleic acids research · 2024Article
- Unraveling the role of hepatitis B virus DNA integration in B-cell lymphomagenesis.British journal of cancer · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Possible association between polyomaviruses and gastrointestinal complications: a narrative review.Gastroenterology and hepatology from bed to bench · 2024Review
- Comparing molecular and computational approaches for detecting viral integration of AAV gene therapy constructs.Molecular therapy. Methods & clinical development · 2023Article
- Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology.Diagnostics (Basel, Switzerland) · 2022Review
- Article
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Genome Sequencing from Post-Mortem Formalin-Fixed, Paraffin-Embedded Lung Tissues.The Journal of molecular diagnostics : JMD · 2021Article
- Article
- Virus-positive Merkel Cell Carcinoma Is an Independent Prognostic Group with Distinct Predictive Biomarkers.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Analysis of HPV Integrations in Mexican Pre-Tumoral Cervical Lesions Reveal Centromere-Enriched Breakpoints and Abundant Unspecific HPV Regions.International journal of molecular sciences · 2021Article
- A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data.Briefings in bioinformatics · 2021Article
- High Throughput Sequencing for the Detection and Characterization of RNA Viruses.Frontiers in microbiology · 2021Review
5 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although next-generation sequencing (NGS) has been the domain of large genome centers, it is quickly becoming more accessible to general pathology laboratories. In addition to finding single-base changes, NGS allows for the detection of larger structural variants, including insertions/deletions, translocations, and viral insertions. We describe the use of targeted NGS on DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissue, and show that the short read lengths of NGS are ideally suited to fragmented DNA obtained from FFPE tissue. Further, we describe a novel method for performing hybrid-capture target enrichment using PCR-generated capture probes. As a model, we captured the 5.3-kb Merkel cell polyomavirus (MCPyV) genome in FFPE cases of Merkel cell carcinoma using inexpensive, PCR-derived capture probes, and achieved up to 37,000-fold coverage of the MCPyV genome without prior virus-specific PCR amplification. This depth of coverage made it possible to reproducibly detect viral genome deletions and insertion sites anywhere within the human genome. Out of four cases sequenced, we identified the 5' insertion sites in four of four cases and the 3' sites in three of four cases. These findings demonstrate the potential for an inexpensive gene targeting and NGS method that can be easily adapted for use with FFPE tissue to identify large structural rearrangements, opening up the possibility for further discovery from archival tissue.
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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.