Related Experiment Video
Updated: Apr 5, 2026
Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
Published on: November 2, 2013
Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing
Lasse Vinner1, Tobias Mourier1, Jens Friis-Nielsen2
1Centre for GeoGenetics Natural History Museum, University of Copenhagen Østervoldgade 5-7, 1350 Copenhagen K, Denmark.
Abstract:
Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.
Insights
A new low-stringency hybridization method detects under 100 viral DNA copies in complex samples. This technique aids in discovering novel viruses, even with significant sequence variation, advancing infectious disease research.
Area of Science:
- Virology
- Genomics
- Cancer Research
Background:
- A significant portion of human cancers are linked to infectious agents, yet the origins of most remain unknown.
- Detecting viral DNA in clinical samples is challenging due to its low abundance amidst host DNA and high sequence variability among viruses.
- Existing sensitive methods like PCR are hindered by viral genome diversity.
Purpose of the Study:
- To develop and validate a sensitive method for detecting viral sequences in clinical samples, accommodating substantial sequence variation.
- To enable the enrichment and discovery of novel or distantly related viral sequences using high-throughput sequencing.
Main Methods:
- Development of a low-stringency in-solution hybridization technique.
- Application of the method to enrich and detect viral DNA from complex clinical samples.
- Utilizing high-throughput sequencing for the discovery of unknown viral sequences.
Main Results:
- The developed method demonstrated sensitivity for detecting fewer than 100 viral copies.
- Significant enrichment (orders of magnitude) of distantly related proviral sequences was achieved.
- Investigation for novel retroviruses in human B-cell lymphoma, cutaneous T-cell lymphoma, and colorectal cancer samples yielded negative results, consistent with current literature.
Conclusions:
- The low-stringency hybridization method offers a sensitive and broadly applicable approach for detecting viral sequences in complex biological materials.
- This technique facilitates the discovery of novel viral sequences and enhances the study of viral roles in diseases.
- The study successfully applied the method to screen for retroviruses in specific cancer types, confirming its utility in clinical research.
Related Concept Videos
01:51Mechanisms of Retrovirus-induced Cancers
01:51Mechanisms of Retrovirus-induced Cancers
03:18Non-LTR Retrotransposons
01:26Human Virome