Liquid biopsy for the detection of breast cancer cell-free DNA (cfDNA): extracellular vesicles, cancer genomics and nanopore-based genetic analysis

About the research

Breast cancer, and in particular triple-negative breast cancer (TNBC), is an aggressive disease with limited treatment options and poor outcomes when diagnosed at an advanced stage. The main focus of the lab is to investigate a newly identified oncogene and potential biomarker (GCH1) using an omics–liquid biopsy approach, exploring whether its related metabolites and cfDNA can be detected in tumour cell models, extracellular vesicles, mouse xenograft plasma, and plasma from patients with breast cancer.

A student joining the lab would gain experience across a multidisciplinary programme combining cancer biology, liquid biopsy development, cancer genomics, nanopore and long-read sequencing, droplet digital PCR, and genetic and metabolomic analysis. Research opportunities include cell culture, DNA and cfDNA extraction, PCR and droplet digital PCR, extracellular vesicle isolation, variant and genomic analysis, immunoblotting, genome editing, and the interpretation of genomic, molecular, metabolic and translational biomarker data.

The project is based in the Nuffield Division of Clinical Laboratory Sciences within the Radcliffe Department of Medicine, University of Oxford, and involves collaboration with researchers in breast cancer biology, extracellular vesicles, patient plasma resources, and translational oncology. It offers an excellent opportunity to develop expertise in liquid biopsy, GCH1 cancer genomics, nanopore sequencing, genetic analysis, and biomarker discovery within a clinically relevant cancer research programme, and to contribute to publications, conference presentations, and the development of diagnostic applications.

Additional supervision will be provided by Dr Alexandra Noble, NDM Experimental Medicine, University of Oxford

The Panel Group Funding Scheme studentship provides funds for fees up to the Overseas rate and a stipend of no less than £21.5K per year for four years.

Please refer to the Courses open for studentships for information about making an application to this studentship.

Deadline for applications: 24 July, 12 noon

Training Opportunities

The student will receive hands-on training in liquid biopsy and cfDNA workflows, including DNA and cfDNA extraction, PCR and droplet digital PCR, and cell-free DNA analysis. They will develop expertise in cancer genomics and genetic/variant analysis, nanopore and other long-read sequencing and the analysis of sequencing data, extracellular vesicle isolation and characterisation, intracellular and metabolomic analysis, and core wet-laboratory techniques such as cell culture, immunoblotting and genome editing. Training in bioinformatics and the statistical analysis of cancer genomics data will also be provided, alongside the development of scientific writing and presentation skills through publications and conference presentations.

Students are encouraged to attend the MRC Weatherall Institute of Molecular Medicine DPhil Course, which takes place in the autumn of their first year. Running over several days, this course helps students to develop basic research and presentation skills, as well as introducing them to a wide range of scientific techniques and principles, ensuring that students have the opportunity to build a broad-based understanding of differing research methodologies. 

Generic skills training is offered through the Medical Sciences Division's Skills Training Programme. This programme offers a comprehensive range of courses covering many important areas of researcher development: knowledge and intellectual abilities, personal effectiveness, research governance and organisation, and engagement, influence, and impact. Students are actively encouraged to take advantage of the training opportunities available to them.

As well as the specific training detailed above, students will have access to a wide range of seminars and training opportunities through the many research institutes and centres based in Oxford.

The Department has a successful mentoring scheme, open to graduate students, which provides an additional possible channel for personal and professional development outside the regular supervisory framework. We hold an Athena SWAN Silver Award in recognition of our efforts to build a happy and rewarding environment where all staff and students are supported to achieve their full potential.

Publications