Please note: there may be some adjustments to the teaching arrangements published in the course catalogue for 2020-21. Given current circumstances related to the Covid-19 pandemic it is anticipated that some usual arrangements for teaching on campus will be modified to ensure the safety and wellbeing of students and staff on campus; further adjustments may also be necessary, or beneficial, during the course of the academic year as national requirements relating to management of the pandemic are revised.

Clinical Genomics MED5425

  • Academic Session: 2022-23
  • 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

Short Description

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.

Timetable

Weeks 7-11 of semester 2

Requirements of Entry

Students should be enrolled on a relevant MSc programme at the University of Glasgow, or have relevant professional experience in genetics in order to take the course as an independent CPD unit.

Assessment

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

Course Aims

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.