Clinical Genomics MED5425
- Academic Session: 2021-22
- School: School of Medicine Dentistry and Nursing
- Credits: 20
- Level: Level 5 (SCQF level 11)
- Typically Offered: Semester 2
- Available to Visiting Students: Yes
- Available to Erasmus Students: No
This course will provide an overview of the clinical applications of genomic approaches to human disorders, particularly in relation to clinical genetics, discussing the methods and capabilities of the new technologies. Tuition and hands-on experience in data analysis will be provided, including the interpretation of next generation sequencing reports.
Weeks 7-11 of semester 2
Students will analyse and interpret clinical next generation sequencing data from patient investigations and then generate a critical report of 2,000 words which presents their analysis in the context of relevant literature and provides guidance on how the information should be presented to the patient (or their family) and to the referring clinician.
Main Assessment In: April/May
The aims of this course are to facilitate an understanding of the following topics:
■ Structure and function of the human genome (e.g. enhancers, epigenetics, chromatin remodelling, non-coding regions and the ENCODE project)
■ Diagnostic analysis of the human genome (and exome and genome sequencing) - standard and high-throughput technologies
■ Clinical bioinformatics - making sense of the data ("PHREDs, PEDs and BEDs"), with practical hands-on experience in data analysis and evaluating the pathogenicity of single nucleotide variants (SNVs).
■ Terminology (e.g. PHRED scores, PED and BED files, BAM files, CRAM files, BCFs, VCFs, SNVs, CNVs, and many more)
■ Ethical aspects of whole genome analysis (including incidental findings)
■ Stratified medicine & pharmacogenomics
Intended Learning Outcomes of Course
By the end of this course students will be able to:
Structure and function of the human genome
■ Critically appraise what is known and what is not, including literature regarding transcriptional control at a distance, epigenetics and chromatin remodelling.
■ Critically discuss the purpose and implications of the ENCODE Project.
Diagnostic analysis of the human genome
■ Critically evaluate the purpose of current standard techniques (e.g. MLPA & aCGH) in comparison with the new massively parallel sequencing techniques and technologies
■ Critically discuss the capabilities and limitations of these available technologies
Bioinformatics - making sense of the data:
■ Demonstrate critical awareness of quality checks, trios and gene panel filtering ("PHREDs, PEDs and BEDs")
■ Critically discuss the evaluation of variants using online prediction algorithms, based on
■ biophysical amino acid properties (e.g. using Grantham matrix to examine molecular volume and polarity) and
■ evolutionary sequence conservation
Stratified medicine & pharmacogenomics
■ Critically discuss examples of effects of genomic variants upon:
■ drug responses and
■ adverse effects
Minimum Requirement for Award of Credits
Students must submit at least 75% by weight of the components (including examinations) of the course's summative assessment.