Clinical PhD Programme

Clinical PhD fellowships are available for clinical health professionals with an aptitude for research and the potential to become future leaders in genomics, biomedicine and healthcare science.

The application process for the 2025 intake of the Wellcome Sanger Institute Clinical PhD Programme is now closed. The closing date was Tuesday 5th November 2024 (23:59 GMT). Interviews will be held in early January 2025 – exact dates to be confirmed.

Successful candidates will need to have started their PhD by the end of 2025.

Overview

The Wellcome Sanger Institute Clinical PhD Programme is a 3-year programme, run in partnership with the PhD Programme for Health Professionals at the Universities of Cambridge and East Anglia.

The PhD Programme for Health Professionals aims to provide high-quality research training to clinical health professionals with an aptitude for research, to enable them to become future leaders in medical and healthcare science.

The Programme offers training opportunities with world-leading researchers in outstanding environments, spanning basic science, translational medicine, and interdisciplinary, behavioural and applied health research. All we are looking for in our trainees is the pursuit of research excellence, hard work and the will to make a difference to health.

Up to seven fellowships are available each year, two of which are funded by the Sanger Institute. To be eligible to hold one of these fellowships, you must be qualified in clinical, dental or veterinary medicine, or be a non-medical health professional, and be registered with a national professional regulatory body in the UK. In addition, medical, dental and veterinary applicants must be in a training grade (i.e., not a Consultant, University Faculty or equivalent position). Non-medical health professionals may be at different stages in their clinical careers, but should possess sufficient relevant research experience to be able to take advantage of this unique opportunity. They also would not be expected to be University Faculty or equivalent position. Salaries are maintained in accordance with recognised UK clinical scales.

It is important to note that fellowships supported by the Universities of Cambridge and East Anglia are only open to health professionals in clinical training in the UK, whereas Sanger Institute funded fellowships are open to health professionals in clinical training both in the UK and overseas. However, all successful candidates must be registered with the appropriate national professional regulatory body in the UK prior to commencement of the fellowship.

For medical graduates who do not hold academic clinical fellowships (ACFs) and non-medical health professionals, there is the opportunity to undertake a three-month pre-doctoral research placement. During this time, you can undertake mini-projects with research groups in your areas of interest, thereby enabling you to make an informed choice of PhD project and supervisor(s).

For more information about research opportunities at the Sanger Institute, please see some examples of Potential PhD projects below.

Those health professionals who choose to carry out their PhD at the Sanger Institute are expected to attend training courses in transferable and general research skills, participate in the students’ journal club, present their work regularly and attend seminars. They also have to present their work annually at a Summer Symposium held jointly with the other students on the PhD Programme for Health Professionals. In addition, the Directors of the Programme arrange ‘clinical’ mentoring for all Programme students. Students on the Programme are able to hold honorary contracts at Addenbrooke’s Hospital in order to maintain their clinical links.

Within the first few months of their PhD, in common with the other students on the PhD Programme for Health Professionals, our clinical students have to prepare a research proposal for their project in the form of a ‘Project Grant Application’. This is discussed with a panel of leading academics connected with the Programme. Student progress is monitored by assessment of their first year report and by thesis committee meetings, which take place at least once per year.

For information on how to make an application to our Clinical PhD Programme please go to the How to apply section below.

To see what some of our former clinical PhD students have achieved during their time at the Institute, and since, please go to the Case studies section below.

University of Cambridge affiliation

Students at the Wellcome Sanger Institute are awarded a University of Cambridge PhD degree.

The Wellcome Sanger Institute was granted affiliation with the University of Cambridge as a ‘University Partner Institution’ in 1995. All postgraduate students at the Institute are registered with the University and are members of a Cambridge College. This allows our students to take an active part in the University’s academic and social life and brings many benefits such as access to events/courses run by University departments and the Postgraduate School of Life Sciences, and access to University facilities such as the library and the careers service.

Potential PhD projects

The Wellcome Sanger Institute is a world leader in genomics research. Our Faculty apply and explore genomic technologies at scale to advance understanding of biology and improve health. Making discoveries not easily made elsewhere, our research delivers insights across health, disease, evolution and pathogen biology. We take on the challenges of applying our research to the real world, where we aim to bring benefit to people and society.  Please visit our potential supervisors page for information on Faculty members and their research areas.

Examples of potential PhD projects include:

  • Understanding cancer predisposition with multiplex assays of variant effect – Dr David Adams
  • Using single-cell genomics and DNA sequencing to identify novel drug targets for inflammatory bowel disease – Dr Carl Anderson
  • Mapping tissue microenvironments and cellular trajectories in glioblastoma using single cell and spatial genomics – Dr Omer Bayraktar
  • Finding the origins of human cancer – Prof Sam Behjati
  • Host pathogen interactions in chronic lung disease – Dr Josie Bryant
  • Decoding genetic epistasis to predict cell phenotypes – Dr Mathew Garnett
  • Understanding tumour cell plasticity at single cell resolution – Dr Mathew Garnett
  • Educating the developing human immune system – Prof Muzz Haniffa
  • High-throughput mutagenesis to induce skin tumours in a hair-bearing skin organoid model – Prof Muzz Haniffa and Dr David Adams
  • Dissecting pathogen genomic adaptation and host response using an inducible pluripotent skin organoid model – Prof Muzz Haniffa, Dr Ewan Harrison and Dr Josie Bryant
  • Multi-omics profiling of skin disease to build AI-based generative models – Prof Muzz Haniffa and Dr Mo Lotfollahi
  • Metagenomic sequencing for pathogen genomics and studies of the respiratory microbiome – Dr Ewan Harrison
  • Role of gut microbiome on patient response to clinical interventions – Dr Trevor Lawley
  • Using single cell genomics to investigate malaria transmission in Africa – Dr Mara Lawniczak
  • Large-scale mutagenesis of human proteins for clinical variant interpretation – Dr Ben Lehner
  • Comprehensive mapping allosteric sites in regulatory proteins using deep mutagenesis and machine learning – Dr Ben Lehner
  • Deep learning and deep synthesis for therapeutic protein design – Dr Ben Lehner
  • Understanding the links between inflammation and malignancy using machine learning powered spatial genomics – Dr Mo Lotfollahi and Dr Foad Rouhani
  • Understanding the factors that promote growth and predict behaviour in kidney cancer using spatial transcriptomics and machine learning – Dr Mo Lotfollahi and Dr Tom Mitchell
  • Predicting clinical outcomes in patients with glomerulonephritis leveraging AI and spatial biology – Dr Mo Lotfollahi and Prof Menna Clatworthy
  • Uncovering the role of somatic mutations in autoimmunity and other diseases – Dr Inigo Martincorena
  • Somatic evolution of the methylome over human ageing – Dr Jyoti Nangalia
  • Deciphering clonal trajectories to cancer and disease – Dr Jyoti Nangalia
  • Engineering and characterizing disease-relevant structural variants in a cell model – Dr Leo Parts
  • Investigating the impact of ageing on human germline cells through multi-omics analysis – Dr Raheleh Rahbari
  • Clonal dynamics and mutational landscape in cancer predisposition syndromes – Dr Raheleh Rahbari
  • Single cell immunology and women’s health – Dr Roser Vento-Tormo

Supervision and monitoring

Each student has a PhD supervisor from within the Institute’s Faculty who provides day-to-day supervision of their research. They also benefit from a co-supervisor (academic adviser), selected from the University of Cambridge, who works in a similar or complementary discipline and meets regularly with the student.

Postgraduate students at the Institute are monitored and managed by the Committee of Graduate Studies, which meets regularly, together with support from dedicated administrative personnel. Monitoring of each student’s progress is achieved through their first year report, second year thesis plan and thesis committee meetings which take place at least once per year.

The thesis committee, which consists of the principal supervisor, the co-supervisor (academic adviser) and one or two Sanger Institute Faculty members, primarily serves as a scientific advisory board for the student throughout their PhD work. Its function is to offer comments, advice and support to the student in order to ensure that the thesis can be completed in an appropriate time frame and with the best possible output. In addition to the student’s own research group, the thesis committee provides an independent forum for scientific discussion.

Students are expected to complete their research and submit their thesis within the three-year time frame of the award. At this point each student must give a formal Sanger Institute seminar.

Training opportunities

eSCAMPS 2023 Committee

Students on the Clinical PhD Programme are encouraged to attend training courses in transferable and general research skills such as:

  • Health and safety
  • Postgraduate lecture series (approx 30 lectures by Sanger Faculty members)
  • Computational skills
  • Bioinformatics
  • Next generation sequencing
  • Statistics
  • Research integrity, reproducible research and ethics
  • Presentation skills
  • Scientific writing skills
  • Communication and public engagement

A wide range of courses are also run on site for which students are eligible. As members of the University of Cambridge, students have access to lecture courses run by University departments, courses run by the Postgraduate School of Life Sciences and to University facilities such as the library and the careers service. There is also an excellent library on site at the Institute.

There is a fortnightly journal club which all students, except those in their final year, are expected to attend, and students are expected to participate in the programme of journal clubs and research talks within their own research division.

There is a very active academic seminar programme on site. Also students have the opportunity to meet and have informal discussions over lunch with speakers in our Distinguished Lecture Series. In addition, relevant seminar programmes within the University are widely advertised, and students are encouraged to attend.

All clinical PhD students have the opportunity to present their work regularly to their group. They also have to present their work annually at a Summer Symposium held jointly with the other students on the PhD Programme for Health Professionals. In the final year, once students have submitted their thesis, they are required to present their work at a Sanger Institute seminar. In addition, students are encouraged to present their work at both national and international scientific meetings, and we provide up to £1500 per year to enable them to attend such meetings.

Students at the Institute are encouraged to organise their own events such as the EBI-Sanger Cambridge PhD Symposium (eSCAMPS). This meeting brings together students from the whole Cambridge area and gives them the opportunity to present their work to their peers and listen to a number of world renowned keynote speakers. Organising such a meeting (liaising with speakers, seeking sponsorship, managing logistical arrangements etc) allows the students involved to develop their networking, communication and management skills.

How to apply

For more information about the Programme, and details on how to apply, go to: PhD Programme for Health Professionals at the Universities of Cambridge and East Anglia.

In brief, applications must be made via the University of Cambridge Postgraduate Admissions on-line applicant portal.

The application process for the 2025 intake of the Institute’s Clinical PhD Programme and the PhD Programme for Health Professionals at the Universities of Cambridge and East Anglia is now closed. The application closing date was Tuesday 5th November 2024 (23:59 GMT).

Applicants will be shortlisted and interviewed by a selection panel consisting of the Programme Directors, Faculty members from the University of East Anglia, University of Cambridge Department of Veterinary Medicine and Wellcome Sanger Institute, and also a selection of Theme Leads and Principal Investigators from the Programme. A Director of another Clinical PhD Programme may be invited to join the panel. Interviews will be held in early January 2025 – exact dates to be confirmed.

Case studies

Some of our former clinical PhD students:

Vanessa Wong (2010 intake)

PhD project: ‘Salmonella Typhi: a global perspective based on genomics’, supervised by Professor Gordon Dougan.
PhD publications: Seventeen publications, including one first author Nature Genetics paper and six additional first author publications.
Awards/prizes: Furness Prize for Science Communication, Royal College of Pathologists in 2011, Oswald Morton Essay Prize, Pharmaceutical Medicine and Research Section, Royal Society of Medicine in 2012, NIHR Cambridge BRC Research Capability Funding Clinical Research Fellowship in 2014, Gold Medal Research Award, Royal College of Pathologists in 2015, Winner of Young Investigator Award, 2016 Spring Meeting, Academy of Medical Sciences, ACT Research Award 2019.
Current position: Consultant in Microbiology and Infectious Diseases at Cambridge University Hospitals NHS Foundation Trust, and the Gastrointestinal Infections and Food Safety (One Health) Division, UKHSA, in London.

Sam Behjati (2011 intake)

PhD project: ‘Massively parallel sequencing of benign and malignant human tumours’, supervised by Professor Mike Stratton and Dr Peter Campbell.
PhD publications: 18 publications, including three first/joint first author Nature Genetics papers, one first author Nature paper and four additional joint first author papers.
Awards/prizes: Conquer Cancer Foundation ASCO Merit Award in 2014, Donald Paterson Prize, Royal College of Paediatrics and Child Health in 2015, St. Baldrick’s Foundation Robert J. Arceci Innovation Award in 2016, Science & SciLifeLab Prize for Young Scientists in Genomics and Proteomics in 2016, Dr Simon Newell Early Career Investigator of the Year (Sparks) Award, Royal College of Paediatrics and Child Health in 2019, Liddy Shriver Early Research Award, Connective Tissue Oncology Society in 2019, selected as an EMBO Young Investigator in 2020, Pezcoller Foundation-EACR Rising Star Award in 2021. Royal Society’s Francis Crick Medal and Lecture 2024 for fundamental discoveries into the developmental roots of childhood cancer.
Current position: Group Leader and Wellcome Senior Research Fellow, Sanger Institute and Honorary Consultant Paediatric Oncologist, Addenbrooke’s Hospital.

Tom McKerrell (2012 intake)

PhD project: ‘‘A Study of Myeloid Malignancies and their Pre-Clinical Evolution’ supervised by Dr George Vassiliou. Major findings include the identification of age-related clonal haemopoiesis driven by leukaemia-associated mutations in healthy individuals.
PhD publications: Six publications, including four first author publications.
Awards/prizes: Wellcome Sanger Institute Early Career Innovation Award 2014.
Current position: NIHR Academic Clinical Lecturer in Haematology, University of Cambridge.

Equality and diversity

The Wellcome Sanger Institute values the diversity of its employees, students, visitors and collaborators. The diversity of our workforce is of critical importance in drawing together the broad range of skills and experience we depend on to conduct world class science and support biomedical discovery.

We therefore believe that it is in the best interests of the Institute and those that benefit from its work to attract, retain and develop a diverse pool of talent and to provide a working environment that encourages and supports excellent performance from all who work here. We aim to achieve this by:

  • Providing equality of opportunity in recruitment, selection, training, promotion and career management
  • The elimination of unlawful discrimination
  • The promotion of diversity and equality
  • Stimulating interest in scientific careers through our Wellcome Connecting Science Engagement and Society Programme
  • Developing an Equality, Diversity and Inclusion Strategy to further embed the principles of Equality & Diversity in the work and people of the Institute and monitoring the outcomes of this

Selection of PhD Students

The Institute’s PhD programmes aspire to be equally accessible to all applicants irrespective of gender, country of origin, ethnicity, colour, religion, age, disability or factors other than academic matters. Applications are welcomed from candidates worldwide and will be considered exclusively on merit. To reduce financial and geographic barriers to admission, we provide payment of all University tuition fees along with a generous stipend/salary. Indeed many of our MPhil and PhD students come from low and middle income countries such as Kenya, Tanzania, Mexico, Brazil, Colombia, Peru, China, Vietnam, Indonesia, the Philippines, Pakistan, Bangladesh and Turkey. Also, our typical annual intake of students is roughly half male, half female.

Wherever practical the Institute will adopt a flexible approach to prevent any disadvantage that could arise for prospective PhD students from career and/or study gaps that may be due to maternity, paternity, adoption and other caring responsibilities or periods of illness or disability.

Please note that all candidates selected for the PhD Programme for Health Professionals must be registered with the appropriate national professional regulatory body in the UK prior to commencement of the fellowship.

Equality in Science

The Sanger Institute and its campus neighbour, the European Bioinformatics Institute (EBI), run an active Equality in Science Programme aimed at highlighting and addressing issues affecting the gender imbalance that occurs in the senior ranks of science. This includes consideration of work-life balance issues that affect both male and female scientists and a regular Careers Day for everyone on campus with a chance to speak with funders and learn about a range of scientific careers. The programme is also looking at issues affecting marginalised groups such as LGBT+, BME and disabled scientists.

Athena SWAN Silver Award

In April 2020 we were awarded the Athena SWAN Silver award, having been one of the first research institutes to achieve the Bronze award in April 2014.

Balancing PhD studies with family life

We recognise that for some PhD students, there will be a need to allow time and flexibility to deal with caring responsibilities (e.g. for children and/or relatives) and we want to provide a PhD programme that is supportive of these needs, whilst not compromising on giving you an excellent start to your scientific career. This includes provisions to pause studies for maternity, paternity, adoption or shared parental leave, access to our onsite nursery facilities and a flexible approach to work.

Since Sanger Institute PhD students are registered at the University of Cambridge, they are also able to access childcare services provided by the University.

If you have any queries about balancing PhD studies with family life, please contact the Postgraduate Programme Office.