The aim of this module is to enable students to gain the knowledge and understanding required to critically interpret existing genomic research, and develop the skills to formulate their own research questions as well as to collect, analyse and interpret their own NHS data using a basic range of statistical and bioinformatics techniques. This is critical to the 100,000 genomes project as the main challenge for application of genomic data is in its analysis and interpretation.
Outline Of Syllabus
- Aligning genome data to reference sequence using up to date alignment programmes (e.g. BWA)
- Assessment of data quality through application of quality control measures
- How to determine the analytical sensitivity and specificity of genomic tests
- Use of tools to call sequence variants e.g. GATK, annotation of variant-call files using established databases
- Filtering strategies of variants, in context of clinical data, and using publically-available control data sets
- Use of multiple database sources, in silico tools and literature for pathogenicity evaluation, and familiarity with the statistical programmes to support this
- Principles of integration of laboratory and clinical information, and place of best-practice guidelines for indicating the clinical significance of results
- Principles of downstream functional analysis e.g. knock-outs, and other cellular model
- How to analyse genomic data to identify epigenetic and other variation that modifies phenotype
- Practice in examples of analysis of genomic data in the Training Embassy within the Genomics England Data Centre.