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MRC DiMeN Doctoral Training Partnership: Machine learning to predict disease course in newly diagnosed chronic lymphocytic leukaemia (CLL) patients


   MRC DiMeN Doctoral Training Partnership

  Prof James Allan, , , Dr Amir Enshaei  Friday, January 14, 2022  Competition Funded PhD Project (Students Worldwide)

Newcastle United Kingdom Artificial Intelligence Bioinformatics Cancer Biology Data Science Epidemiology Genomics Human Genetics Immunology Machine Learning Molecular Genetics

About the Project

Chronic lymphocytic leukaemia (CLL) is the most common leukaemia in people of European ancestry with more than 10 new cases per day in the UK alone. CLL has a highly heterogeneous clinical course and most patients are diagnosed with early stage asymptomatic disease that does not initially require treatment. Some patients live with asymptomatic disease for several years while others progress quickly requiring treatment. CLL is inherently incurable and a significant cause of mortality and morbidity, including high risk of recurrent infections.

CLL therapy has been transformed by highly effective and well tolerated B-cell receptor signalling pathway inhibitors (BCRi) which improve patient outcomes for those with advanced disease. Given the success in treating symptomatic CLL, focus has recently shifted towards addressing whether pre-emptive treatment can improve outcomes for patients with early-stage asymptomatic disease but at high-risk of progressing. Preliminary results from the German CLL12 trial report remarkable improvements in outcomes for high-risk CLL patients treated early with the BCRi ibrutinib, where time to death was 4-5 times longer in high-risk patients treated early. Despite this success, current prognostication models are inadequate and identify only a minority of high-risk patients.

The aim of this project is to develop accurate prognostication models for early-stage CLL in order to identify high-risk patients who might benefit from earlier treatment. To this end, we recently published a genome-wide association study utilising early-stage CLL cases and identified two common germline genetic variants that significantly associate (P ≤ 5 x 10-8) with high-risk CLL (Lin et al, 2021). These variants have prognostic value equivalent to established clinical markers and provide proof of concept that the incorporation of germline genetic markers can significantly improve prognostication models for the majority of CLL patients.

We have recently expanded our CLL cohort to approximately 2000 patients with a median follow-up of 15 years that includes data on infections and bleeding events as well as death. In addition to identifying new germline genetic variants predicting high-risk disease, this project will use machine learning to identify leukaemia-specific insertions and deletions (somatic alterations) from high-density array data already generated by our group. This project will also provide an opportunity to functionally interrogate novel somatic alternations using cell-based models.

Critically, this will be the first study to incorporate patient germline and leukaemia somatic genetic data along with established clinical markers for accurate prognostication in early-stage CLL patients. Implementation of the resulting model into clinical practise is predicted to improve outcomes for the tens of thousands of patients living with CLL and could also lead to similar approaches being adopted to improve prognostication in other cancers.

This project is based in the laboratory of Professor James Allan at the Newcastle University Centre for Cancer (https://twitter.com/nu_cancer) in collaboration with the Hull York Medical School (David Allsup) and Southampton University (Andrew Collins).

https://www.ncl.ac.uk/medical-sciences/people/profile/jamesallan.html

https://www.hyms.ac.uk/about/people/david-allsup

https://www.southampton.ac.uk/medicine/about/staff/arc.page

https://www.ncl.ac.uk/medical-sciences/people/profile/amirenshaei.html

https://www.ncl.ac.uk/cancer/

https://www.ncl.ac.uk/medical-sciences/research/research-themes/genomics-informatics/

Benefits of being in the DiMeN DTP:

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle, York and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards

Further information on the programme and how to apply can be found on our website:

http://www.dimen.org.uk/how-to-apply/application-overview


Funding Notes

Studentships are fully funded by the Medical Research Council (MRC) for 4yrs. Funding will cover UK tuition fees, stipend and project costs as standard. We also aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will be awarded to exceptional candidates only, due to the competitive nature of this scheme. Please read additional guidance here: View Website
Studentships commence: 1st October 2022
Good luck!

References

https://cllsociety.org/2019/11/eha-2019-dr-peter-hillmen-on-watch-and-wait-versus-early-ibrutinib-in-cll-chronic-lymphocytic-leukemia/
Lin W-Y, Fordham SE, Sunter NJ, Elstob C, Rahman T, Willmore E, Shepherd C, Strathdee G, Mainou-Fowler T, Piddock R, Mearns H, Barrow T, Houlston RS, Marr H, Wallis J, Summerfield G, Marshall S, Pettitt A, Pepper C, Fegan C, Forconi F, Dyer MJS, Jayne S, Sellors A, Schuh A, Robbe P, Oscier D, Bailey J, Rais S, Bentley A, Cawkwell L, Evans P, Hillmen P, Pratt G, Allsup DJ, Allan JM (2021) Genome-wide association study identifies risk loci for progressive chronic lymphocytic leukemia. Nature Communications, 12: 665. doi: 10.1038/s41467-020-20822-9.

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