Development of Next Generation Sequencing (NGS) as a diagnostic tool for microbiology diagnostic screening

New genomics technologies for investigating pathogen emergence and the microbiological safety of blood transfusion and transplant

To apply, you will need to contact [Email Address Removed] in the first instance. He will then provide details of how to apply to the relevant DPhil programme at Oxford.

A fully funded studentship is offered at the University of Oxford a project within the area of virus genomics and new diagnostic detection technologies and their application towards blood and transplant safety and pandemic preparedness. The student will work within a large research unit funded by the National Institute for Health Research (NIHR) that is focussed towards harnessing new screening technologies for transfusion transmitted infections by NHS Blood and Transplant services

The Research Unit comprises a large team of academics, clinical laboratory scientists and PhD students in Oxford and in University College London, along with support and administrative staff and resource development. This infrastructure will support a final roster of nine PhD students working in Oxford, UCL, NHSBT and UK Health Security Agency.

The student will work in the following project area:

Development of Next Generation Sequencing (NGS) as a diagnostic tool for microbiology diagnostic screening.

The development of highly sensitive NGS methods represents a major opportunity to greatly enhance the effectiveness and breadth of targeted screening of blood donors for transfusion-transmitted infectious agents. In the project, we will explore the potential of new methodologies and enhancements in sample extraction, target enrichment, library construction and bioinformatics capabilities to drive sensitivity and specificity of HTS to or below those of PCR and other targeted molecular methods. NGS technologies enhance donor/linking in the investigation of transfusion-transmitted bacterial or viral infections. 

Methodological improvements may further include the use of CRISPR Cas9 or Cas13 constructs for nucleic acid editing/degradation as highly specific sensors for pathogens, able to find target sequences in dsDNA and RNA with single copy sensitivity and complete specificity. Coupled to a point-of-care diagnostic infrastructure, such methods have the potential to realise the remarkable possibility of immediate and effective donor NAT and confirmation/genomic characterisation within blood donor centres or in hospital settings for organ donors.

Training Opportunities offered in the studentships

• Laboratory: Experience in NGS library construction and Illumina and Nanopore sequencing methodologies; RNA/DNA capture methods including the application of CRISPR-Cas constructs
• Bioinformatics: Acquisition of expertise in standard and new developed sequence data processing pathways for assembly and analysis of read data
• Standard HBV diagnostics, sample handling, PCR, serological assays.
• Next generation sequencing methods and associated bioinformatics analysis of read data.
• Molecular methods for virus detection and screening
• Detection methods of T cell immune reactivity to HBV
• Participation in the clinical investigation of donors with occult HBV and its natural history.
• Shared working with other PhD/MPhil students in the wider programme investigating a range of other aspects of transfusion-related microbiology
• Programmes of presentations, seminars and attendance at national and international scientific meeting to present research findings
• Working within a combined University / NHSBT environment, the latter providing knowledge of how a large scale, healthcare-based service provider works and delivers to patients and the donor community.