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Omics Techniques and their Application to Genomic Medicine

Module description

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, 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, including strategies employed to evaluate pathogenicity of variants for clinical reporting, which together with 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 RNA sequencing in estimating levels of RNA and its applications in genomic medicine, and provide a comprehensive introduction to epigenomics, metabolomics and proteomics, which are important for the functional interpretation of genomic data and discovery of disease biomarkers.

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 mRNA, 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,  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 sequencing, metabolomics, proteomics techniques and epigenomics.
•  Overview of bioinformatics approaches to the analysis of genomic data.
• Approaches to evaluate pathogenicity of variants

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.F. and Donnai, D. (2021). New clinical genetics. Fourth edition. Banbury: Scion.
• Turnpenny, P.D., Ellard, S. and Cleaver, R. (2022). Emery's elements of medical genetics and genomics. Sixteenth edition. Philadelphia, PA: Elsevier.
• Strachan, T., and Read, A.P.  (2019). Human molecular genetics. Fifth edition. Boca Raton, Florida: CRC Press.
• Strachan, T., Lucassen, A. and Strachan, T. (2023). Genetics and genomics in medicine. Second edition. Boca Raton: CRC Press.

Indicative learning resources - Web based and electronic resources

https://ele.exeter.ac.uk/course/view.php?id=9099

Key words search

Next-generation sequencing, RNAseq, Proteomics, microbiome, metabolomics,  bioinformatics, expression profiling