Clinical PhD Programme

Clinical PhD fellowships are available for medically qualified applicants who exhibit academic excellence and the potential to pursue a career in academic medicine.

The application process for the 2022 intake of the Wellcome Sanger Institute’s Clinical PhD Programme will open towards the end of October 2021.


The Wellcome Sanger Institute Clinical PhD Programme is a 3-year programme, run in partnership with the Cambridge Wellcome PhD Programme for Clinicians. The University of East Anglia is also a partner in the programme.

Up to seven fellowships are available each year, two of which are funded by the Institute. To be eligible to apply for the two Sanger Institute fellowships you must be medically qualified (individuals qualified in veterinary medicine can apply for the remaining fellowships). Although veterinary graduates are not eligible for a Sanger Institute fellowship, they can undertake research at the Sanger Institute supervised either solely or jointly by a Sanger faculty member, whilst supported by another fellowship from the programme. The two Sanger Institute fellowships are open to overseas applicants, and if successful you will be required to obtain General Medical Council registration. It is anticipated that most applicants will have already commenced their specialist training, but this is not essential. The most important criteria we are looking for are academic excellence and the potential to pursue a career in academic medicine. Salaries are maintained in accordance with recognised UK clinical academic scales.

Before starting their PhD, successful applicants are offered up to 3 months funding to enable them to meet potential supervisors from the Sanger Institute and the departments/institutes of the University of Cambridge and the University of East Anglia, and undertake one or more mini-projects within their broad area of interest. This allows them to make an informed choice of PhD project and supervisor.

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

Those clinicians that 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 Cambridge Wellcome PhD Programme for Clinicians. In addition, the Director of the Programme arranges ‘clinical’ mentoring for the students. All Sanger Institute clinicians on the programme hold honorary contracts at Addenbrooke’s Hospital in order to maintain their clinical links.

The progress of our clinical PhD students is monitored by assessment of their first year report and by thesis committee meetings, which take place every six months. Also within the first few months of their PhD, in common with the other students on the Cambridge Wellcome PhD Programme for Clinicians, 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, before being submitted to Wellcome.

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 at the forefront of experimental, computational and translational genomic research. Our Faculty members use large-scale genomic tools to investigate important global health problems such as cancer, malaria and infectious disease. Please visit our potential supervisors page for information on Faculty members and their research areas.

Examples of potential PhD projects include:

  • Exploring synthetic lethality for cancer drug discovery – Dr David Adams
  • Using single-cell genomics and DNA sequencing to identify novel drug targets for inflammatory bowel disease – Dr Carl Anderson
  • Understanding brain development and disease using spatial transcriptomics – Dr Omer Bayraktar
  • Finding the origins of human cancer – Dr Sam Behjati
  • Using functional genomics to understand patient heterogeneity within disease and in response to treatment – Dr Emma Davenport
  • Oncology drug target discovery using functional genomics – Dr Mathew Garnett
  • Developmental immune programmes in tissue morphogenesis and disease – Prof Muzz Haniffa
  • Informing therapeutic strategies for neurodevelopmental disorders through experimental perturbation of gene regulation in cellular models – Dr Matt Hurles
  • Functional and metagenomic analysis of human intestinal microbiome during health and irritable bowel syndrome – Dr Trevor Lawley
  • Using single cell genomics to investigate malaria transmission in Africa – Dr Mara Lawniczak
  • Understanding the effect of ageing on human oocytes using multi-omics approaches – Dr Raheleh Rahbari
  • Deciphering immunity using single cell genomics – Dr Sarah Teichmann
  • Comparing human B cell repertoires induced by oral vaccination or by natural infection: towards the development of therapeutic antibodies – Prof Nick Thomson and Prof Steve Baker
  • Women’s health genomics – 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 (external 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 every six months.

The thesis committee, which consists of the principal supervisor, the co-supervisor (external 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

Sanger Institute
eSCAMPS 2015 committee

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

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

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 Cambridge Wellcome PhD Programme for Clinicians. 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 £1000 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: – this webpage is currently being updated

In brief, applications must be made via the University of Cambridge Postgraduate Admissions on-line applicant portal – this link will be made live towards the end of October.

Applicants are shortlisted and interviewed by a selection panel consisting of the Programme Director, Deputy Director, a Director of another Wellcome Clinical PhD Programme, a representative from the Sanger Institute, representatives from the University of East Anglia and the University of Cambridge Department of Veterinary Medicine and a selection of ‘theme leads’ for the programme – the make-up of the selection panel for recruitment of the 2022 intake will be confirmed shortly.

The application process for the 2022 intake of the Institute’s Clinical PhD Programme will open towards the end of October 2021 and the closing date is likely to be in early January.

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 Infectious Diseases and Microbiology, Addenbrooke’s Hospital, Cambridge.

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.
Current position: Group Leader, Sanger Institute and Wellcome Intermediate Clinical Fellow, University of Cambridge.

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 Connecting Science and Public Engagement 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 outcome 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 students come from low and middle income countries such as Malawi, Uganda, Kenya, Mexico, Colombia, China, Vietnam, Pakistan and Bangladesh. 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.

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 Graduate Programme Office.