Genomic Technologies and Basic Informatics

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

• Critically appraise up-to-date tools for quality control of data, sequence alignment, variant calling, annotation and variant filtration to identify potentially pathogenic variants
• Acquire relevant basic computational skills and understanding of statistical methods for handling and analysing sequencing data for application in both the diagnostic and research settings
• Develop basic workflows for automated analysis of next generation sequencing (NGS) data using a graphical user interface
• Critically evaluate a range of up-to-date sequencing technologies and select appropriate techniques for genomic testing
• Interrogate major data resources of genomic sequence variation and biological pathways, (e.g. EVS, dbSNP, ClinVar, etc.), to assess the pathogenic and potential clinical significance of genome results

• Basis of genotyping and detection of genetic variation: Application of whole exome and whole genome and targeted sequencing technologies across a variety of platforms
• Genomic testing strategies as: gene focused, multiple genes, or whole genome or exome, and for detection of sequence, copy number or rearrangements
• 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
• Use of tools to call sequence variants e.g. GATK, annotation of variant-call files using established databases
• How to determine the analytical sensitivity and specificity of variant detection
• 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, and familiarity with the statistical programmes to support this
• Principles of downstream functional analysis e.g. knock-outs, knock-ins, CRISPR and other cellular models

A variety of learning and teaching methods will be adopted to promote a wide range of skills and meet the differing learning styles of the group.

Teaching will include seminars, practical demonstrations, discussions and exercises surrounding interpretation of data and clinical scenarios, and specialist lectures given by a range of academic and health care professionals. This will ensure a breadth and depth of perspective, giving a good balance between background theories and principles and practical experience.

Off-site independent learning will take place on the virtual learning environment hosted by the UoS.

Formative

This is how we’ll give you feedback as you are learning. It is not a formal test or exam.

Workshop activities

• Assessment Type: Formative
• Feedback: Individual feedback in sessions.
• Final Assessment: No
• Group Work: No

Summative

This is how we’ll formally assess what you have learned in this module.

Referral

This is how we’ll assess you if you don’t meet the criteria to pass this module.