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Bioinformatics, Interpretation and Data Quality Assurance in Genome Analysis

Module description

The main challenge for application of genomic data is in its analysis and interpretation. The aim of this module is to enable you to gain the knowledge and understanding required to critically interpret existing genomic research, and develop the skills to formulate your own research questions as well as to collect, analyse and interpret your own NHS data using a basic range of statistical and bioinformatics techniques.

Module aims - intentions of the module

The module will cover the fundamental principles of informatics and bioinformatics applied to clinical genomics. You will find and use major genomic and genetic data resources, software packages, in silico tools, databases and literature searches to align sequence data to the reference genome. You will also critically assess, annotate and interpret findings from genetic and genomic analyses. Theoretical sessions will be coupled with practical assignments performing analysis and annotation of predefined data sets.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

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

• 1. Apply basic computational skills and statistical methods for the handling and analysis of sequencing data for application in both diagnostic and research settings.
• 2. Demonstrate practical experience of a bioinformatics pipeline for analysing sequencing data.
• 3. Analyse the principles applied to quality control of sequencing data and filtering strategies to identify pathogenic mutations in sequencing data.

ILO: Discipline-specific skills

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

• 4. Justify and defend the place of Professional Best Practice Guidelines in the diagnostic setting for the reporting of genomic variation.
• 5. Interrogate major data sources and integrate with clinical data, to assess the pathogenic and clinical significance of the genome result.

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.
• 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:

• Aligning next-generation sequencing data to reference sequence using up to date alignment programmes (e.g. BWA).
• Assessment of data quality through application of quality control measures.
• Use of tools to call sequence variants and annotate variant-call files using established databases.
• Filtering strategies of variants, in context of clinical data, and using publicly available control data sets
• Use of multiple database sources, in silico tools and literature for pathogenicity evaluation
• Principles of integration of laboratory and clinical information, and place of best practice guidelines for indicating the clinical significance of results.

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=10168

Key words search

Alignment, data analysis, bioinformatics, sequencing, filtering