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PhD Studentship: Genomic Revolutions in Donation Screening and Safety (GRiDSS) - Characterising The Human Virome and Its Impact On Organ Transplant and Blood Transfusion Safety

UCL

Qualification Type: PhD
Location: London
Funding for: UK Students, EU Students
Funding amount: starting stipend of £18,000 per annum (including London weighting) as well as the cost of tuition fees based on UK fee status
Hours: Full Time
Placed On: 1st November 2021
Closes: 31st January 2022
 

A 3-year PhD Studentship funded by NIHR, is available in the Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street UCL Institute of Child Health. The studentship is available to start between April-October 2022 under the supervision of  Prof. Judith Breuer and Dr Sofia Morfopoulou (GOS ICH, UCL) and Dr Ines Ushiro-Lumb, NHS Blood and Transplant..

This project will investigate the presence, viral loads and transcriptional activity of viruses in a range of human tissues and organs through the use of untargeted metagenomic high throughput sequencing (HTS) methods. Bioinformatics tools for taxonomic classification and pathogen discovery (metaMix) will be applied to detect viruses in sequencing data from clinical blood and transplant specimens, including potentially unexpected pathogens. The performance of agnostic metagenomic sequencing will be compared to methods using targeted enrichment panels and both approaches will be assessed for their analytical sensitivity and specificity. Long read methods will also be evaluated. Persistent viruses in donor and archived tissues, such as human herpesviruses, adenoviruses, polyomaviruses and parvoviruses, will be further characterised by whole genome sequencing methods and transcriptome analysis. Transmission risk by organ transplantation will be investigated and bioinformatics tools for haplotype reconstruction (HaROLD) will be applied to investigate the occurrence of mixed infections in recipients after organ transplants, including HCMV and EBV with documented transmission risks.

Further details about the project can be found on the ICH website.

The student will receive a starting stipend of £18,000 per annum (including London weighting) as well as the cost of tuition fees based on UK fee status. 

Personal Specification

Applicants should have a good first degree (UK 1st class or upper 2nd class honours degree or equivalent from abroad) and a Master’s degree is desirable (or equivalent work experience) in a quantitative discipline or a biomedical sciences degree with scientific programming experience by the time of registration.

Eligibilty

This studentship covers the cost of tuition fees based on the UK (Home) rate.  Non-UK students can apply but will have to personally fund the difference between the UK (Home) rate and the overseas rate where they are not eligible for UK fee status.

NB: You will be asked about your likely fee status at the interview so we would advise you to contact the UCL Graduate Admissions Office for advice should you be unsure whether or not you meet the eligibility criteria for Home fee status.  Further information on Brexit and the definitions for fee status assessment can be found on the UCL website and also the UKCISA website (Higher Education: Definitions for fee status assessment).

Application

To apply, please send a current CV including the contact details of two professional referees as well as a cover letter to ich.iii.programme@ucl.ac.uk. Students should contact Prof. Judith Breuer (j.breuer@ucl.ac.uk) and Dr Sofia Morfopoulou (sofia.morfopoulou.10@ucl.ac.uk) to discuss their interest.

Applications also welcome from students who may be graduating in Summer 2022.

Deadline for receipt of applications: 10th December 2021

Interview date:  January 2022 (Date to be confirmed)

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