LQN206 Cytogenomics
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: | LQN206 |
|---|---|
| Credit points: | 12 |
| Timetable | Details in HiQ, if available |
| Availabilities |
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| Domestic tuition unit fee | $3,744 |
| International unit fee | $5,148 |
Unit Outline: Semester 2 2025, Online
| Unit code: | LQN206 |
|---|---|
| Credit points: | 12 |
Overview
This unit provides high-level training in human cytogenomics and develops the skills to identify and appropriately investigate chromosomal abnormalities. This unit will enable scientists to apply critical thinking to interpret the clinical significance and prognosis of chromosomal abnormalities and to apply this reasoning to drive a wholistic, genome-wide approach to patient management. Clinical and research scientists working in cytogenomic laboratories will become knowledgeable of some of the germline and somatic conditions which are commonly referred to diagnostic cytogenomic laboratories and the pipelines using the technology currently employed in diagnostic cytogenomic laboratories to investigate these genomic abnormalities.
Learning Outcomes
On successful completion of this unit you will be able to:
- Compare and contrast basic and advanced cytogenetic techniques used in diagnostic and research genomic laboratories.
- Investigate cytogenomic findings, prepare interpretive assessment and apply the standardised system of nomenclature to provide diagnostic interpretation in relation to health, disease, clinical information, prognosis and therapy.
- Investigate clinical disease states as applied to abnormalities detected using cytogenomic techniques and through employment of interprofessional skills.
- Evaluate how changes to the cytogenome result in human disease, and convey outcomes in oral, written and digital format.
Content
- Identification of chromosomal abnormalities,
- Modes of derivation of chromosomal abnormalities and clinical significance and relevance.
- Prognosis of constitutional clinical syndromes and acquired malignant disease states
- Cytogenomic processing of prenatal and postnatal constitutional samples and oncology samples
- Laboratory techniques and processes including media preparation, tissue culture, sterile practices, and appropriate quality control activities
- The principles of cytogenomic workflows including the reason for each step, the effect of each step on the end result, and how to rectify processing errors (where possible)
- Banded metaphase chromosomes analysis by karyotyping and classify karyotypes using the current International System for Human Cytogenomic Nomenclature (ISCN)
- Karyotypic result interpretation including aneuploidy (whole or part of a chromosome) and structural rearrangements, with reference to the clinical referral
- The FISH procedure for metaphase and interphase preparations; interpretation of FISH results including the meaning of abnormal signal patterns and classification using ISCN; the performance and application of different probe types
- The different types of genomic microarrays and how to evaluate their performance and application
- Interpretation of microarray results including gains, losses and copy neutral loss of heterozygosity (uniparental disomy, long continuous stretches of homozygosity); and classification of microarray results using web-based resources
- Planning appropriate further testing that may be required following initial cytogenomic investigation (additional methods, tissues, family members)
- Future technologies in Cytogenomics.
Learning Approaches
This unit is designed to introduce you to the core concepts of cytogenomics. 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.
Coursework is reinforced through the application of knowledge to problem-based learning exercises. You will be encouraged to read widely and to think critically about the nature and scope of how cytogenomics relates to the field of diagnostic genomics.
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.
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 and assessment 2 will be given regarding your analytical skills, ability to identify resources, reasoning and ability to interpret and summarise your findings. Each assessment item will include 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 LQN206. Assessment 1 is a research question in which you will compare and critically evaluate the scope and application of AI tools in the preparation of cytogenomic patient reports. Draft submission and discussion will be in week 4 and completed submission in week 8. Assessment 2 comprises of 4 tasks that will be distributed over the duration of the course. These tasks will be authentic and include evaluation of real case studies, laboratory-based scenario and testing pipeline. Questions will be provided for each task for completion as written reports which provides you the opportunity to draw on the knowledge gained during the course in order to critically appraise the literature and to write a response that answers a specific cytogenomics laboratory-based scenario. The complete submission is in week 12.
Unit Grading Scheme
7- point scale
Assessment Tasks
Assessment: Research Project
Assessment 1 is a research question in which you will compare and critically evaluate the scope and application of AI tools in the reporting of chromosomal abnormalities using standardised system of nomenclature that ius used in the preparation of cytogenomic patient reports. Draft submission and discussion will be in week 4 and completed submission in week 8.
This assignment is eligible for the 48-hour late submission period and assignment extensions.
Assessment: Portfolio
There are 4 task items in this assessment of equal value. The tasks will comprise of germline and/or somatic case studies, laboratory-based scenario or investigation pipeline query. In the case study tasks you will investigate a cytogenetic abnormality and present the results using correct ISCN nomenclature, interpretation, investigation pipeline (including relevant additional genetic testing) and the clinical significance of the abnormality. You will be required to critically appraise the literature to outline the pathogenesis of the cytogenomic disease and describe the clinical consequences. The report will be in the format of a clinical patient report or case study consistent with the requirements of the professional society (HGSA) submission and/or journal format. Directed questions will be provided for the authentic laboratory scenario and investigation pipeline tasks.
This assignment is eligible for the 48-hour late submission period and assignment extensions.
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
- Apply scientific knowledge and skills, focused on current genomic trends in practice and research, utilising digital capabilities.
Relates to: ULO1, ULO2 - 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 - 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: ULO3, ULO4 - 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: ULO3, ULO4
LS81 Master of Diagnostic Genomics
- Apply scientific knowledge and skills, focused on current genomic trends in practice and research, utilising digital capabilities.
Relates to: ULO1, ULO2, Research Project - 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, Research Project, Portfolio - 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: ULO3, ULO4, Research Project, Portfolio - 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: ULO3, ULO4