LQN204 Molecular Genomics


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Unit Outline: Semester 1 2025, Online

Unit code:LQN204
Credit points:12
Coordinator:Michael Gabbett | michael.gabbett@qut.edu.au
Disclaimer - Offer of some units is subject to viability, and information in these Unit Outlines is subject to change prior to commencement of the teaching period.

Overview

This unit provides high-level training in human molecular diagnostic genomics covering the knowledge in genomics that scientists and clinicians working in genomics need to have. This includes medical conditions that are commonly referred to clinical laboratories, genetic testing required to confirm diagnoses, and the interpretation of results.

Learning Outcomes

On successful completion of this unit you will be able to:

  1. Critically evaluate advanced molecular genomics theory as it applies to both Mendelian and non-Mendelian human diseases.
  2. Collaboratively analyse case studies of human diseases to identify and explain the molecular lesions and their underlying causes.
  3. Examine molecular genotype as it relates to disease phenotype, and vice versa.
  4. Scrutinise in detail the phenotypes of human genetic disease and critique the evidence detailing the most appropriate molecular tools to diagnose such diseases.

Content

  • Basic molecular techniques, including PCR and Southern blotting.
  • Variant curation, based upon ACMG principles.
  • The different mutation types and mechanisms leading to these disorders and genotype-phenotype relationships.
  • 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.
  • The effect of X inactivation in disease manifestation in X-linked recessive conditions and the process of X inactivation.
  • Basic genetic epidemiology, including the principle of Hardy-Weinberg equilibrium and calculation of carrier risks using Bayes theorem.
  • The principles of prenatal screening and testing
  • The differences between diagnostic and carrier testing.

The clinical phenotype and identification of the genes for:
a. common autosomal dominant disorders
b. common autosomal recessive disorders including, inborn errors of metabolism.
c. common mitochondrial disorders.
d. common triplet repeat disorders, including the significance of normal, intermediate and affected ranges for the trinucleotide repeat disorders.
e. common X-linked conditions
f. common cancer conditions
g. imprinting disorders and uniparental disomy involving chromosomes containing imprinted genes.

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 learning 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. 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 Canvas site.

Assessment

Overview

There are two summative assessment items in LQN204. Assessment 1 consists of a project in which students are assigned into small groups to curate a specific genomic variant. Each student will then be asked to critique the poster written by another group.

Assessment 2 is a portfolio of your theoretical knowledge, based on questions asked in relation to your coursework notes.

Unit Grading Scheme

7- point scale

Assessment Tasks

Assessment: Variant Curation Poster

 

Part 1: 40% (Due date: End Week 7) In this authentic assessment piece, you are placed into a small working group. Each group is assigned a genomic variant. Your task is to work as a group and assign a pathogenicity score (class 1 to 5) to the variant. You are to present your findings and reasoning behind your conclusion (referencing lines of evidence used) in a poster format  (eg, a PowerPoint slide). Upload your poster to both Padlet and to Canvas. Each member of the group will receive the same grade. The use of generative artificial intelligence (AI) may be used to produce data for this poster, but the group must include a paragraph appraising how AI helped or hindered the project.
 
Part 2: 10% (Due date: End Week 9) Once uploaded, each student will critique one of your classmate's posters. Your critique will be anonymised.

This assignment is eligible for the 48-hour late submission period and assignment extensions.

Weight: 50
Length: approximately 1000 words
Individual/Group: Individual and group
Due (indicative): Week 9
Related Unit learning outcomes: 1, 2

Assessment: Portfolio

In this assessment piece, you will submit a portfolio based on answers to questions relating to the content presented throughout the unit. All submissions will be interrogated through TurnitIn to detect evidence of potential student collusion.

This assignment is eligible for the 48-hour late submission period and assignment extensions.

Weight: 50
Length: Up to 3000 words
Individual/Group: Individual
Due (indicative): Week 13
Related Unit learning outcomes: 3, 4

Academic Integrity

Academic integrity is a commitment to undertaking academic work and assessment in a manner that is ethical, fair, honest, respectful and accountable.

The Academic Integrity Policy sets out the range of conduct that can be a failure to maintain the standards of academic integrity. This includes, cheating in exams, plagiarism, self-plagiarism, collusion and contract cheating. It also includes providing fraudulent or altered documentation in support of an academic concession application, for example an assignment extension or a deferred exam.

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.

Breaching QUT’s Academic Integrity Policy or engaging in conduct that may defeat or compromise the purpose of assessment can lead to a finding of student misconduct (Code of Conduct – Student) and result in the imposition of penalties under the Management of Student Misconduct Policy, 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.

Course Learning Outcomes

This unit is designed to support your development of the following course/study area learning outcomes.

LS72 Graduate Diploma in Diagnostic Genomics

  1. Apply scientific knowledge and skills, focused on current genomic trends in practice and research, utilising digital capabilities.
    Relates to: ULO1, ULO2, ULO3
  2. Critically evaluate scientific findings and locate solutions to solve complex genomics problems, employing high order cognitive skills, clinical reasoning, and reflective practice.
    Relates to: ULO2, ULO3, ULO4
  3. Develop and apply professional oral and written communication skills that inform effective collaboration and digital interactions with colleagues and other stakeholders across the medical and scientific contexts.
    Relates to: ULO4
  4. Practise within a framework of personal accountability, collegiality and ethical judgment, while valuing cultural safety and sensitivity in professional practice, clinical decision-making and research.
    Relates to: ULO4

LS81 Master of Diagnostic Genomics

  1. Apply scientific knowledge and skills, focused on current genomic trends in practice and research, utilising digital capabilities.
    Relates to: ULO1, ULO2, ULO3
  2. Critically evaluate scientific findings and locate solutions to solve complex genomics problems, employing high order cognitive skills, clinical reasoning, and reflective practice.
    Relates to: ULO2, ULO3, ULO4, Variant Curation Poster
  3. Develop and apply professional oral and written communication skills that inform effective collaboration and digital interactions with colleagues and other stakeholders across the medical and scientific contexts.
    Relates to: ULO4, Variant Curation Poster, Portfolio
  4. Practise within a framework of personal accountability, collegiality and ethical judgement, drawing upon Indigenous perspectives, cultural safety and sensitivity in professional practice, clinical decision-making and research.
    Relates to: ULO4, Portfolio