Course Content

CORE MODULES

Core 1 – Fundamentals in Human Genetics and Genomics

This module will introduce and teach fundamental principles in human genetics and genomics, providing a platform of knowledge for the rest of the course and enabling students to understand the basis of inheritance, variation and link with disease. Teaching will be contextualised to allow appreciation of the key discoveries and advances in the past, present and likely future of the genomic era and exemplified by those involving Oxford researchers.

Core 2 – Genomics of Rare and Inherited Diseases

This module will introduce the disease phenotypes and molecular basis of common and rare inherited disease. It will cover genetic mapping strategies, techniques and approaches to identify causal genes and variants, and their interpretation in the context of disease. This will be complemented by an emphasis on the role of genomic medicine in precision medicine, case studies from clinical practice, as well as ethical and societal implications.

Core 3 – Omic Technologies and their Application to Genomic Medicine

This module will introduce current -omics technologies and their application to understand genome biology and disease in a research and clinical setting. The focus will be on wet-lab methods and principles underlying DNA sequencing and assays for profiling the genome at various levels.

Core 4 - Bioinformatics and Statistics for Genomic Data Interpretation

This module will equip students with a strong theoretical understanding and practical ability in bioinformatics and statistics for genomic data analysis. The module will use computational sessions focussed on real-world data examples to develop practical abilities and reinforce concepts. Throughout, we will emphasise best-practice approaches to programming, data handling, analysis and interpretation, with a focus on drawing scientifically appropriate conclusions from underlying data.

ELECTIVE MODULES

Elective A1 – Molecular Pathology and Precision Medicine

This module will introduce molecular pathology and how this is being informed and developed through genomics and related -omic technologies to allow better understanding of the basis of disease, the development of precision medicine approaches and novel therapies. A particular focus will be application to cancer, the impact of germline and somatic mutations, determination of risk, development of tailored therapeutics for individual use; to immunobiology and infectious disease; and to pharmacogenomics. Application to derive a molecular classification of disease, discover disease mechanisms and quantify individual risk; stratification of patients in trials and for interventions and screening; use to discover novel biomarkers and therapeutics.

Elective A2 – Advanced Quantitative Methods (Bioinformatics & Statistics)

This module is designed for students wishing to gain a deeper knowledge and understanding of quantitative methods used in bioinformatic and statistical analysis of large scale and high dimensional -omic datasets. The content will equip students with the skills to be able to work in a high-performance computing workspace to execute scripts and pipelines. In-depth topics will include whole genome sequence analysis; RNA sequencing analysis; integrative multi-omic analysis and the use of workflow languages for pipelining.

Elective A3 – Genome Engineering and Gene-Based Therapeutics

This module will provide in depth content on the development and current applications of genome engineering. Mechanistic basis of programmable nucleases including ZFNs, TALENs and CRISPR/Cas9. Application in model systems and human cells to understand genome function and biology. Use of gene editing and gene-based therapeutics for human disease including haematological and retinal disease, cardiomyopathies. Challenges to implementation. Ethics and societal implications.

Elective A4 – Single-cell and Spatial Omics for Precision Medicine

This module will focus on the use of single cell technologies to achieve unprecedented resolution at a cellular and tissue level for functional genomic and related -omic assays. Students will learn about the development of different experimental platforms, analysis pipelines and application of single cell RNAseq, epigenomics, proteomics, and immune cell repertoire profiling. Use of single cell approaches to understand tissue heterogeneity and identify molecular features correlated with clinical outcomes. Application in microbiology, neurobiology, cancer, and developmental biology.

Elective B1 – Genomics in Clinical Practice

This module will provide more advanced learning in the clinical application of genomic medicine, focused on students are health care practitioners. The content of the module will focus on practical experience of working with genomic data for diagnostic purposes, including whole genome sequencing for rare disease and cancer. There will be further content on informed consent for genetic testing, genetic counselling, advanced bioinformatic approaches and tools including for variant identification and interpretation and managing clinical workflows.

Elective B2 – Applications of Genomics in Therapeutics, Vaccinology and Industry

This module will focus on the translational use of genomics in drug development, vaccinology, and other industrial settings. The content will focus on the theory and application of pharmacogenomics to individualise drug therapy to the individual patient; the use of genetic and genomic data for drug target identification and prioritisation; application of genomics to enable patient stratification in clinical trials; rapid development of vaccines; targeted therapy and precision medicine. Students will learn about the process of drug development, clinical trials and factors impacting successful outcomes together with opportunities for academic-pharma partnerships, cross-disciplinary working, and collaborations. There will be a strong emphasis on inviting guest speakers from industry partners and highlighting relevant case studies for discussion.

RESEARCH PROJECT

The final term will focus on a research project undertaken for a twelve to fourteen week period. Approximately 30 projects will be offered by academic research groups and affiliated clinical supervisors in Oxford, as well as industry placements where possible. Students can select projects from the official list on offer but requests for alternative projects can be submitted for consideration. You will have a named supervisor with experience in supervision of postgraduate students. You will produce a written dissertation based on your research project of 10,000-12,000 words.

ACADEMIC AND RESEARCH SKILLS

This module will run throughout the course helping you develop skills in academic writing, scientific communication and good research practice, alongside topics such as career support. It will also include bespoke computational and statistics training as a foundation for the core module ‘Bioinformatics, Statistics and Data Interpretation in Genomic Analysis’.

TEACHING FORMAT

Modules will comprise a mix of lectures, small-group tutorials, structured learning, individual and group-based assignments, practical wet-lab and computational sessions and independent learning. You will be expected to spend approximately 30-40 hours studying per week, with the balance of contact teaching hours and self-directed learning being approximately equal. In the first term, a student-focussed seminar series will feature expert guest speakers discussing cutting-edge research in genomic medicine and its clinical application.