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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing
Gordon M Daly1, Nick Bexfield, Judith Heaney
1Department of Veterinary Medicine, The University of Cambridge, Cambridge, United Kingdom.
Plos One
|January 5, 2012
Summary
We developed a novel virus discovery protocol for tissue samples. This method enhances viral reads and contig length, improving next-generation sequencing for virus identification.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- Virus discovery from tissue samples presents challenges due to low viral loads.
- Current methods may lack efficiency in enriching viral genetic material from complex biological matrices.
Purpose of the Study:
- To present a novel protocol for efficient virus discovery in biopsy-sized tissue samples.
- To enhance the performance of next-generation sequencing (NGS) for viral identification.
Main Methods:
- Development of a viral enrichment procedure applicable to various virus genera.
- Validation of the protocol using canine and human liver tissue samples.
- Application of Illumina next-generation sequencing (NGS) for de novo assembly.
Main Results:
- Significantly improved viral read copy number in enriched samples.
- Increased length of viral contigs generated through de novo assembly.
- Demonstrated effectiveness of the protocol in facilitating virus discovery from tissue.
Conclusions:
- The described viral enrichment protocol is effective for identifying diverse viruses in tissue samples.
- This method enhances NGS capabilities for viral discovery, offering a valuable tool for researchers.
- The protocol shows promise for applications in diagnostics and pathogen surveillance.
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