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Omics Techniques and their Application to Genomic Medicine

Module description

In this module you will cover areas of ‘omics’ technologies, their interpretation and application in key areas of healthcare such as cancer, rare inherited diseases and infectious diseases, as well as their application to research. A specific focus will be on the approaches supporting the ‘100,000 Genomes Project’. This core module will provide you with the underpinning knowledge to enable you to understand the taught modules which follow and to support those of you undertaking your research project utilising the ‘100,000 Genomes Project’ data sets.

Module aims - intentions of the module

This module explores the state of the art genomics techniques used for 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 in the clinical setting. This module will introduce the bioinformatics approaches required for the analysis of genomic data, which together with data governance covered in the ‘Introduction to Human Genetics and Genomics’ module will provide a solid foundation for the ‘Bioinformatics, Interpretation, Statistics and Data Quality Assurance’ module. This module will also cover the use of array based methodologies and RNA sequencing in estimating levels of protein expression, micro RNAs and long non–coding RNAs. A comprehensive introduction to epigenomics, metabolomics and proteomics, which are important for the functional interpretation of genomic data and discovery of disease biomarkers, will also be included. You will also learn about the strategies employed to evaluate pathogenicity of variants for clinical reporting.

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 other 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, pyrosequencing, ARMS, MLPA, QF-PCR and microarray.

•  Genomic testing strategies 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 techniques 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

In the event of you failing a module, you will be given a chance to resubmit the failed components that led to the overall module failure. This will normally be within six weeks of the overall module result being known, except in the case of written and/or practical examinations which may take longer to reschedule. The module result will then be capped at 50.

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.

   

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

Indicative learning resources - Web based and electronic resources

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, pyrosequencing, ARMS, MLPA, QF-PCR, microarray, bioinformatics, next-generation sequencing, expression profiling