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Genomic Revolutions in Blood Donation Screening and Safety: Development of Next Generation Sequencing (NGS) as a diagnostic tool for microbiology diagnostic screening.

   Nuffield Department of Medicine

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  Dr Tanya Golubchik, Dr David Bonsall  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

How to apply

To apply to this project, you will need to submit an application to the DPhil in Clinical Medicine, listing this project in the 'Proposed field and title of research project' field of the application form.

A fully funded studentship is being offered for a project in Transfusion Microbiology within a large research unit recently funded by the National Institute for Health Research (NIHR).

The development of highly sensitive NGS methods represents a major opportunity to greatly enhance the effectiveness and breadth of 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.

The appointed student will work under the supervision of Dr Tanya Golubchik (Wellcome Genome Centre) and Dr David Bonsall (Big Data Institute, Oxford) in labs in the central (South Parks Road) and Old Road campuses in Oxford.

Background information. Work in the Research Unit will be focussed in several areas critical for supporting and strengthening screening capabilities for transfusion transmitted infections by NHS Blood and Transplant services

·      Technology – Developing and evaluation of new technologies in virus genome detection and associated bioinformatics in blood and organ donations.

·      Viromics - Application of next generation sequencing for microbial and viral characterisation in investigations of transmission and pathogenicity

·      Safety - Targeted investigations of identified transmission risks, such as hepatitis B virus, arboviruses and other emerging pathogens

The Research Unit will comprise a large team of clinical and laboratory scientists 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 and Public Health England.

Training Opportunities offered in the studentship.

·      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

·      Next generation sequencing methods and associated bioinformatics analysis of read data.

·      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.

Funding Notes

Funding is provided for payment of PhD registration fees for Oxford University or UCL (£9200 / year) and tax-free stipend of £18,000 / year.


López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, et al. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol. 2021;134:104691.
Harvala H, Reynolds C, Gibney Z, Derrick J, Ijaz S, Davison KL, et al. Hepatitis B infections among blood donors in England between 2009 and 2018: Is an occult hepatitis B infection a risk for blood safety? Transfusion. 2021;61(8):2402-13.
Bonsall D, Golubchik T, de Cesare M, Limbada M, Kosloff B, MacIntyre-Cockett G, et al. A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings. J Clin Microbiol. 2020;58(10).
Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, et al. SARS-CoV-2 within-host diversity and transmission. Science. 2021;372(6539):eabg0821.
Bonsall D, Gregory WF, Ip CL, Donfield S, Iles J, Ansari MA, et al. Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR. Emerg Infect Dis. 2016;22(4):671-8.
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