LQN204 Molecular Genomics
To view more information for this unit, select Unit Outline from the list below. Please note the teaching period for which the Unit Outline is relevant.
| Unit code: | LQN204 |
|---|---|
| Equivalent(s): | LQZ204 |
| Credit points: | 12 |
| Timetable | Details in HiQ, if available |
| Availabilities |
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| Domestic tuition unit fee | $3,468 |
| International unit fee | $4,764 |
Unit Outline: Semester 1 2024, Online
| Unit code: | LQN204 |
|---|---|
| Credit points: | 12 |
| Equivalent: | LQZ204 |
| Coordinator: | Michael Gabbett | michael.gabbett@qut.edu.au |
Overview
Genomic scientists and clinicians working in genomics need to have knowledge of medical conditions which are commonly are referred to clinical laboratories, the genetic testing indicated and the interpretation of results.
Learning Outcomes
On successful completion of this unit you will be able to:
- Describe advanced molecular genomics theory as it applies to both Mendelian and non-Mendelian human diseases.
- Analyse case studies of diseases caused by molecular lesions in humans.
- Apply knowledge of molecular genotype to disease phenotype, and vice versa.
- Generate reports detailing phenotypes of human genetic disease and the evidence detailing the most appropriate molecular tools to diagnose such diseases.
Content
- Inheritance patterns and pedigrees for autosomal recessive, autosomal dominant and X linked recessive, X linked dominant, mitochondrial and methylation defects.
- The role of epigenetics in gene regulation e.g. methylation, chromatin remodelling, histone modification.
- The processes involved in establishment and maintenance of DNA methylation.
- The clinical phenotype and identification of the genes for:
a. Common autosomal recessive disorders including cystic fibrosis (CF), spinal muscular atrophy (SMA), congenital adrenal hyperplasia (CAH), alpha and beta thalassaemia, haemochromatosis, nonsyndromic deafness (DFNB1), inborn errors of metabolism.
b. Common mitochondrial disorders including Kearns-Sayre syndrome (KSS), chronic progressive external ophthalmoplegia (CPEO), mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS), myoclonic epilepsy with ragged-red fibres (MERRF), neurogenic weakness with ataxia and retinitis pigmentosa (NARP), or Leigh syndrome (LS).
c. Common triplet repeat disorders including Huntington disease, spinocerebellar ataxia, myotonic dystrophy, fragile X, spinal and bulbar muscular atrophy (Kennedy disease), and Friedreich Ataxia.
d. Autosomal dominant disorders including neurofibromatosis, achondroplasia, Marfan syndrome, cardiac disorders (long QT syndrome, Brugada, aortopathies, cardiomyopathies (HCM & DCM), arrhythmogenic right ventricular cardiomyopathy, catecholaminergic polymorphic ventricular tachycardia (CPVT)), Lynch syndrome, familial adenomatous polyposis, retinoblastoma.
e. Common disorders involving defects in imprinting such as Prader Willi syndrome, Angelman syndrome, Beckwith Wiedemann syndrome, Russell Silver syndrome and uniparental disomy involving chromosomes containing imprinted genes.
f. Most common X linked conditions such as Duchenne/Becker muscular dystrophy and haemophilia A. - The different mutation types and mechanisms leading to the above disorders and genotype phenotype relationships.
- The range of genetic testing available for these disorders (deletion PCR, inversion PCR, bisulphite PCR, triplet repeat primed PCR (TP-PCR), real-time PCR, Southern blotting, linkage analysis, MLPA, methylation specific MLPA, fragment analysis, high resolution melt (HRM), Sanger sequencing, microsatellite analysis and massive parallel sequencing (NGS)) and the sensitivity/ limitations of each technique for each disorder.
- The quality control requirements for each test and the involvement of external quality assurance programmes and best practice guidelines.
- The significance of normal, intermediate and affected ranges for the trinucleotide repeat disorders.
- The terms anticipation, mosaicism, reduced penetrance, variable expressivity, incomplete penetrance, imprinted genes and how each affect inheritance patterns. Appreciate how the bottleneck effect moderates inheritance and disease prevalence. Explain how heteroplasmy and homoplasmy modulate phenotype.
- The effect of X inactivation in disease manifestation in X-linked recessive conditions and the process of X inactivation.
- The principle of Hardy-Weinberg equilibrium and be able to calculate carrier risks using Bayes theorem for the disorders mentioned above.
- The process of prenatal testing for all these disorders (types of controls required, maternal cell contamination (MCC), linkage analysis).
- The differences between diagnostic and carrier testing for all these disorders.
Learning Approaches
This unit is designed to introduce you to the core concepts of molecular genomics. The online delivery is through Canvas. The unit is developed around the principles of adult learning, theory and practice and open learning guidelines. This predominantly asynchronous learning environment allows you to go through lectures, materials and exercises at your own pace.
The Canvas site will provide you with resources including pre-recorded lectures, research papers, media articles and videos. You will also be able to access online meetings, interactive exercises and online message boards. There will be at least one webinar or video-conferencing in which a concept is explained and students will be expected to solve a problem or discuss approaches to a case during the virtual class.
Canvas will facilitate your ongoing conversations with other students and with academic staff. Guidance will be provided, through regular announcements in the Canvas site for you in terms of appropriate self-pacing of your study during the semester. You will be expected to engage in online discussions and complete formative assessment tasks to consolidate your learning.
You will be encouraged to read widely and to think critically about the nature and scope of how molecular genomics relates to the field of diagnostic genomics.
Feedback on Learning and Assessment
The online webinars and discussion boards are the key places you can ask for and receive feedback on your understanding of course materials. Feedback on assessment 1 will be given regarding your analytical skills, ability to identify resources, reasoning and ability to interpret and summarise your findings. Feedback of assessment 2 occurs throughout the semester in an interactive problem-based setting. Assessment 3 feedback will be by way of a mark which reflects your theoretical knowledge. Each assessment item will include individual feedback on your progress as stated above and feedback will be offered to the group through the Announcements page on the Backboard site.
Assessment
Overview
There are three summative assessment items in LQN204. Assessment 1 consists of a written assignment which provides you with the opportunity to draw on the knowledge gained during the course in order to review the clinical features and genomic aspects of a list of genetic differential diagnoses; critically appraise the literature; and synthesise this information to recommend the best approach for testing. Assessment 2 is a portfolio of your contributions to the problem-based learning activities which occur throughout the semester. Assessment 3 is a test consisting of multiple choice, short answer and long answer questions covering the semester's content, administered online.
Unit Grading Scheme
7- point scale
Assessment Tasks
Assessment: Report
In this authentic assessment piece, you will be provided with a pathology request slip listing a number of differential genetic diagnoses. You are required to submit a written assignment which critically appraises the literature to summarise the clinical features of the conditions, explain the molecular basis of genotype-phenotype correlations, and recommend an approach to molecular testing.
Assessment task will be summative, graded on 1-7 scale.
This is an assignment for the purposes of an extension.
Relates to learning outcomes
2 and 4.
Assessment: Portfolio
In this authentic assessment piece, you will submit a portfolio of your Canvas discussions based around the problem based learning activities provided throughout the semester.
Assessment task will be summative, graded on 1-7 scale.
This is an assignment for the purposes of an extension.
Relates to learning outcomes
3 and 4.
Assessment: Examination
This written examination is aimed to ensure that all students have a coherent knowledge of the essential elements of molecular genomics needed for those who work in this field. It will consist of multiple choice, short answer and long answer questions.
Assessment task will be summative, graded on 1-7 scale.
Relates to learning outcomes
1.
Academic Integrity
Students are expected to engage in learning and assessment at QUT with honesty, transparency and fairness. Maintaining academic integrity means upholding these principles and demonstrating valuable professional capabilities based on ethical foundations.
Failure to maintain academic integrity can take many forms. It includes cheating in examinations, plagiarism, self-plagiarism, collusion, and submitting an assessment item completed by another person (e.g. contract cheating). It can also include providing your assessment to another entity, such as to a person or website.
You are encouraged to make use of QUT’s learning support services, resources and tools to assure the academic integrity of your assessment. This includes the use of text matching software that may be available to assist with self-assessing your academic integrity as part of the assessment submission process.
Further details of QUT’s approach to academic integrity are outlined in the Academic integrity policy and the Student Code of Conduct. Breaching QUT’s Academic integrity policy is regarded as student misconduct and can lead to the imposition of penalties ranging from a grade reduction to exclusion from QUT.
Resources
In addition to online lecture notes, a selection of online textbooks, journal articles, and internet resources will be made available each week through the QUT Library.
Risk Assessment Statement
There are no out of the ordinary risks associated with this unit.