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Omics Techniques and their Application to Genomic Medicine ONLINE

Module description

This module will cover the methods and technologies of genomics and  while placing epigenomics, proteomics and metabolomics in context. We will cover their application and interpretation in key areas such as cancer, rare inherited diseases and infectious diseases. Omics technologies are the backbone of genomics research, and are becoming more common in clinical practise. Knowledge gained from this module will enable you to better understand how contemporary biomedical data is arrived at and how it is used in the context of personalised medicine.

Module aims - intentions of the module

This module explores the state of the art genomics techniques as a holistic systems approach to disease diagnosis and treatment. Specifically, we will cover DNA sequencing (e.g. targeted approaches, whole exome and whole genome sequencing) and RNA sequencing, using highly parallel techniques together with current technologies routinely used to investigate genomic variation and evaluate pathogenicity of variants in the clinical setting. This module will also cover the use of array based methodologies and RNA sequencing in estimating levels of mRNA, protein expression, micro RNAs and long non–coding RNAs, and provide a comprehensive introduction to epigenomics, metabolomics and proteomics, and their role in the functional interpretation of genomic data and discovery of disease biomarkers. Finally, an introduction to the bioinformatics approaches required for the analysis of genomic data will be given, including strategies employed to evaluate pathogenicity of variants for clinical reporting, which will form a sequel to the data governance covered in the ‘Introduction to Human Genetics and Genomics’ module, and a prequel to the ‘Bioinformatics, Interpretation, Statistics and Data Quality Assurance’ module.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

• 1. Describe and critically evaluate a range of current up-to-date genomic technologies.
• 2. Develop and demonstrate insight into the application of omics techniques to a diverse range of clinical settings
• 3. Explain how to select appropriate technology platforms for applications in medical genomics either for research or medical diagnostic purposes
• 4. Critically appraise approaches to the bioinformatics analysis and interpretation of omics data.

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

• 5. Critically evaluate the different omics technologies and platforms, their application to genomic medicine and the impact of personalised medicine.

ILO: Personal and key skills

On successfully completing the module you will be able to...

• 6. Critically reflect on personal practice and make connections between known and unknown areas, to allow for personal development, adaptation and change.
• 7. Respond to innovation and new technologies and be able to evaluate these in the context of best practice and the need for improved service delivery and/or improved research performance.
• 8. Communicate accurately and effectively with peers, tutors and the public.

Syllabus plan

Whilst the module's precise content may vary from year to year, an example of an overall structure is as follows:

• Basis of genotyping and detection of genetic variation: whole exome and whole genome sequencing including library preparation methods, sequencing chemistries and platforms.
• Brief overview of methodologies for detecting single nucleotide variants (SNV), small insertions and deletions (INDELs), copy number variants (CNV) or rearrangements. Methodologies will include Sanger sequencing, MLPA, QF-PCR and microarray.
• Genomic testing strategies such as gene-focused, multiple genes or whole genome/exome. Testing strategies for detection of sequence, copy number or rearrangements.
• Additional techniques: RNA expression profiling (expression array) and RNA sequencing, metabolomics, proteomics and epigenomics.
• Overview of bioinformatics approaches to the analysis of genomic data.
• Approaches to the evaluation of pathogenicity of variants in the context of an NHS clinical report.

Learning activities and teaching methods (given in hours of study time)

Details of learning activities and teaching methods

Formative assessment

Summative assessment (% of credit)

Details of summative assessment

Details of re-assessment (where required by referral or deferral)

Re-assessment notes

Please refer to the TQA section on Referral/Deferral: http://as.exeter.ac.uk/academic-policy-standards/tqa-manual/aph/consequenceoffailure/

Indicative learning resources - Basic reading

• Read, A. and Donnai, D. (2015). New clinical genetics. Bloxham, Oxfordshire: Scion.
• Turnpenny, P. and Ellard, S. (2012). Emery's elements of medical genetics. Philadelphia: Elsevier/Churchill Livingstone. (electronic access through University of Exeter library)
• Strachan, T., Read, A. and Strachan, T. (2011). Human molecular genetics 4. New York: Garland Science.
• Strachan, T., Goodship, J. and Chinnery, P. (2015). Genetics and genomics in medicine. New York: Garland Science.

Indicative learning resources - Web based and electronic resources

– http://vle.exeter.ac.uk/course/view.php?id=6140

Henry Stewart Talks -  The Genetic Basis of Neurological Disorders:

https://hstalks.com/playlist/908/the-genetic-basis-of-neurological-disorders/?biosci

Key words search

Sanger sequencing,  MLPA, RNAseq, Proteomics, microbiome, metabolomics, , microarray, bioinformatics, next-generation sequencing, expression profiling