Diagnosis and quantification of subtype admixture in pancreatic cancer tumours with machine learning methods (Ref FHMS - FF - 22 BIO)

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a five-year survivability of less than five percent [1]. Therefore, rapid diagnosis and precise treatment are essential for improved prognosis. PDAC subtyping enables personalized diagnosis and individualised treatment. Currently, there are two established pancreatic tumour subtypes (Classic and Basal) and ongoing debate regarding others [1]. However, recent single-cell RNA-Seq (scRNA-Seq) analyses have challenged this consensus [2]. scRNA-Seq uncovered that PDAC tumours consist of an admixture of cells from basal and classic subtypes and identified hybrid intermediate transitional cell-types that co-express both profiles. Therefore, the current diagnosis paradigm based on discrete homogeneous subtypes is inaccurate, which may frustrate treatment. 

In this PhD, you will investigate novel methodology for subtype admixture analysis based on mixtures of continuous latent factors. You will explore tumour gene expression profiles, cell-type composition and markers of the tumour micro-environment to characterize tumours and stratify patients. Your research will contribute to improvements in diagnosis, therapeutic targets and prognosis.

The project will be conducted at the University of Surrey, under the supervision of Drs. Alexessander Couto Alves, Adam Frampton, and Lisiane Meira within the Surrey Artificial Intelligence Institute, the Bioinformatics Core Facility, the Oncology group, with access to other core facilities at the University of Surrey. The student will benefit from computing and research resources from AI Institute. At the Oncology group the student will benefit from a vibrant and collegial environment with technical and bioinformatics expertise and infrastructure to provide training and support.

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Entry requirements

Open to UK and international students with the project starting in October 2023. Note that a maximum of 30% of the studentships will be offered to international students.

You will need to meet the minimum entry requirements for our PhD programme https://www.surrey.ac.uk/postgraduate/biosciences-and-medicine-phd#entry.

How to apply

Applicants are strongly encouraged to contact the relevant principal supervisor(s) to discuss the project(s) before submitting their application.

Applications should be submitted via the [https://www.surrey.ac.uk/postgraduate/biosciences-and-medicine-phd programme page (N.B. Please select the October 2023 start date when applying).

You may opt to apply for a single project or for 2 of these Faculty-funded studentship projects

When completing your application, in place of a research proposal, please provide a brief motivational document (1 page maximum) which specifies:

• the reference numbers(s) for the project or two projects you are applying for 
• the project title(s) and principal supervisor name(s) 
• if applying for two projects, please also indicate your order of preference for the projects
• an explanation of your motivations for wanting to study for a PhD 
• an explanation of your reasons for selecting the project(s) you have chosen

Additionally, to complete a full application, you MUST also email a copy of your CV and 1-page motivational document directly to the relevant project principal supervisor of each project you apply for. Due to short turnaround times for applicant shortlisting, failure to do this may mean that your application is not considered.

Please note that online interviews for shortlisted applicants are expected to take place during the week commencing 30th January.