PhD Studentship - MRC Integrative Toxicology Training Partnership (ITTP)
Project Title: Characterising clonal dynamics of somatic mutations in vivo for early prediction of carcinogenicity using advanced error corrected next generation sequencing
Supervisor: Dr Alex Cagan
Department: Department of Genetics, University of Cambridge
Industrial Partner: GSK
Somatic mutations drive cancer and may underlie many chronic diseases - yet current safety testing struggles to detect the earliest signals of carcinogenic risk. This PhD project aims to transform how we evaluate the potential for new drugs and chemicals to cause cancer, by tracking somatic mutations and clonal expansions in rodent tissues using cutting-edge, ultra-accurate error-corrected sequencing (ecNGS).
Working at the interface of evolutionary genomics and toxicology, the student will generate high-resolution maps of mutation burden and cancer driver mutation (CDM) dynamics in response to carcinogenic exposure. By integrating new computational and experimental approaches (e.g. Laser capture microdissection and ecNGS), and accessing samples and expertise through GSK's Investigative Toxicology group, the student will help develop a novel framework for early carcinogenicity prediction. This project offers the rare opportunity to translate high-resolution molecular data into practical tools for non-clinical drug safety and regulatory science. This has the potential to revolutionise our ability to detect and understand the carcinogenic impact of chemical compounds.
Based in the Department of Genetics at the University of Cambridge and co-supervised by GSK, the student will receive hands-on training in ecNGS library prep, experimental toxicology, and bioinformatics. The student will also gain experience in working with industry partners, contributing to translational research in regulatory genomics and drug development.
The MRC Integrative Toxicology Training Partnership (ITTP) is a national PhD training programme for capacity building in Toxicology and related disciplines.
The safe development of new drugs, materials, chemicals and consumer products along with the assessment of risk from environmental exposure requires the integration of cutting-edge science with traditional toxicology. The ITTP provides a training platform to enable this and aims to bring together academia, industry and government agencies to provide the required expertise.
ITTP students attend a once yearly residential toxicology training course, have access to the MRC Toxicology Unit's Masterclass seminar series and attend toxicology and laboratory training in their host institutions.
We are looking for a motivated student with a strong background in genomics, molecular biology, or bioinformatics. This interdisciplinary project would suit someone interested in cancer biology, somatic evolution, toxicology, or the development of predictive models of disease. The ideal candidate will have strong analytical and collaborative skills, with the ability to work independently in a supportive research environment.
Research Associate - Pathogen Dynamics Unit (Fixed Term)
The Pathogen Dynamics Unit, located within the Department of Genetics at the University of Cambridge is looking for one full-time postdoctoral Research Associate to work on projects relating to how we can use pathogen genomes and the structure of UK society to understand the emergence and spread of infectious diseases.
The Pathogen Dynamics Unit at the University of Cambridge consists of 15-20 researchers at different stages of their career using mathematical and computational research to help our understanding of how pathogens spread in populations, assess control efforts and support policy making. We work closely with an established network of collaborators across laboratories, field-based epidemiologists, hospitals and public health agencies.
The position will be based in Cambridge and will be supervised by Professor Henrik Salje in a collaborative project with researchers at the University of Lancaster and the UK Health Security Agency (UKHSA). The project will consist of the analysis of SARS-CoV-2 genomes and contact tracing data collected as part of the COVID-19 response. The project will use phylogenetic and mathematical modelling approaches to understand the structure of UK society, and the implications of how we interact with each other leads to infectious disease spread. The finding from this work will help guide future pandemic preparedness.
The applicant will have strong quantitative skills, including applied to pathogen genomic data. The project will require the development of computationally intensive models and therefore applicants should have experience in coding and a good understanding of probability, likelihoods and Bayesian analysis. We are also seeking individuals with a strong interest in public health.
Key Responsibilities:
- Develop models that integrate different data types (e.g., serology, epidemiological data, genomic data, demography) to understand the dynamics of pathogens
- Write-up findings in manuscripts
- Work with study partners
- Present findings at conferences, external and internal meetings
- Be an active member of the Pathogen Dynamics Unit, including contributing to wider group discussions
- Supervision of students/Interns working in support of the research group
Fixed-term: The funds for this post are available for 12 months in the first instance.