LQN301 Cancer 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: | LQN301 |
|---|---|
| Credit points: | 12 |
| Timetable | Details in HiQ, if available |
| Availabilities |
|
| Domestic tuition unit fee | $3,744 |
| International unit fee | $5,148 |
Unit Outline: Semester 1 2025, Online
| Unit code: | LQN301 |
|---|---|
| Credit points: | 12 |
| Coordinator: | Pamela Pollock | pamela.pollock@qut.edu.au |
Overview
This unit examines both the somatic and germline genomic lesions behind cancer initiation, progression and resistance to therapies. Clinicians, biomedical scientists and those working in diagnostic laboratories need to understand the genetic basis of cancer including the role of hereditary cancer predisposition syndromes and the varied genomic changes that can occur somatically. An understanding of the utility of cancer genomic testing in classifying and diagnosing cancer, the separate roles of this testing for predicting prognosis and as predictive biomarkers for precision oncology therapies and in monitoring disease progression will also be explored.
Learning Outcomes
On successful completion of this unit you will be able to:
- Evaluate details of the genetic basis of cancer, including the most common cancer predisposition syndromes and how penetrance can be affected by environmental risk factors and specify the role of genomics in familial cancer diagnosis, surveillance and treatment and/or management.
- Analyse common genomic aberrations in cancer and how their drive cancer initiation, progression and metastasis through the lens of the known cancer hallmarks and why some combination therapies are more effective at preventing recurrence than others.
- Critically examine how cancer genomics can be used for molecular risk stratification (identification of prognostic biomarkers) and matching precision oncology treatments to those patients most likely to benefit (via predictive biomarkers).
- Critically analyse how diagnostic genomics can identify both intrinsic and acquired mechanisms of resistance to various cancer therapies, the pros and cons of different testing platforms and detection via tumour biopsies versus liquid biopsy of circulating free DNA.
Content
- The many varied "hallmarks of cancer" underlying initiation and cancer progression.
- Overview of the cell cycle and DNA repair mechanisms and how common aberrations drive different hallmarks
- Principles of the mechanisms of cancer evolution (the common types of changes in the genome which result in the development of cancer)
- Established familial cancer predisposition syndromes such as Retinoblastoma, Lynch syndrome, Familial Adenomatous Polyposis, Li Fraumeni syndrome, Hereditary Breast and Ovarian Cancer (BRCA1/2), Multiple Endocrine Neoplasia, von-Hippel Lindau, and their associated genetic lesions
- Use of genomic data in the routine diagnosis, classification, prognostication, and disease monitoring in malignancy
- Molecular classification of Cancer in general and its role in predicting prognosis and response to therapy as well as detailed explanation of how molecular classification is currently being applied in the context of a single cancer.
- Known environmental risk factors including biological, chemical and physical/environmental and the link between known common mutagens and specific mutational and in/del profiles including distinguishing shared risk factors from familial cancer predisposition risk
- Somatic cancer detection approaches currently used in diagnostic laboratories including whole exam sequencing (WES), mRNA sequencing to detect fusion genes, total RNA sequencing to detect lncRNAs and miRNAs, whole genome sequencing and single cell RNAseq and the detection of methylated DNA
- Common Methods of variant detection including the complexity of interpreting variants of unknown significance (VUS) and driver mutations in tumours with a high mutational burden
- Identification of robust and reliable web-based and literature resources for analysis, interpretation, and implications of genetic changes in cancer with respect to precision oncology using targeted therapies.
- Principles of personalised treatment of cancer; seminal examples of established companion diagnostics / co-dependent gene-drug interactions (e.g. kinase inhibitors such as imatinib and BCR-ABL1 gene fusion; HER2 and herceptin, BRAF and debrafinib)
- Common mechanisms of resistance to traditional chemotherapies as well as those commonly seen in patients treated with tyrosine kinase inhibitors and the role of genomics in detecting resistance and informing the subsequent line/s of therapy
- Immuno-oncology and the increasing role of immune checkpoint inhibitors as well as the role of genomic testing as a predictive marker to IO therapies in some cancer types
- Genomic predictive biomarkers and clinical trial design e.g. Umbrella trials, Basket trials and the introduction of adaptive clinical trial design
- Molecular Tumour Boards (MTBs) as a multidisciplinary group of experts to personalise cancer diagnosis for precision therapy (eg oncologist, radiologist, molecular pathologist, bioinformatician, cancer geneticist, molecular biologist/translational scientist, pharmacologist) and their different implementations in different countries
- Genetic/genomic methods used to investigate cancers
- Emerging cancer genomics technologies currently in clinical trials and how their wider implementation may change how diagnostic, prognostic and predictive biomarkers are utilised to improve the survival of cancer patients.
Learning Approaches
This unit is designed to introduce you to the core concepts of cancer genomics. The online delivery is through Canvas, which offers an asynchronous learning environment and allows you to access work through lectures, materials and research/activity-based exercises at your own pace. The unit is developed around the principles of adult learning, theory and practice and facilitated through open learning guidelines.
The Canvas site will provide you with learning resources including well structured online information, links to more detailed review papers (prescribed readings and recommended readings), as well as a small number of video presentations by experts in their field. You will also be able to access online knowledge check questions on each module and interact with your peers through an online discussion board.
To reinforce learning you will complete a portfolio of questions to demonstrate your breadth of understanding of the content and a separate case study discussion assignment to show your depth of understanding of precision oncology. Through these assessments, you will be encouraged to read widely and to think critically about the nature and scope of how our increasing understanding of cancer genomics can be best utilised in a diagnostic genomics laboratory to improve patient outcomes.
There will be at least two live webinars discussing the expectations around 1) the large portfolio assessment (with formative feedback provided on your discussions of the first two topics/questions) and 2) the case study assignment. Additional live discussions via zoom will be held if requested by multiple students as they work through the weekly content and answer the associated portfolio questions.
Canvas will facilitate your ongoing conversations with other students and with the unit coordinator. Guidance will be provided, through regular announcements in the Canvas site for you in terms of appropriate self-pacing of your study and completion of your formative and summative assessment items during the semester.
Feedback on Learning and Assessment
We will provide formative feedback on two questions/tasks based on the content of week 1 and week 2 to support your progress in the portfolio assessment. In addition we will provide a live zoom Q and A session in week 2/3, one week prior to the due date.
Formative feedback on the Portfolio assessment will be given regarding your ability to identify reliable resources and reference them appropriately, your analysis skills and reasoning and your ability to interpret and summarise your findings using appropriate scientific language. Areas where you can improve will be highlighted. Assessment 2 feedback will be based on how your assessment adheres to the detailed criteria sheet provided through individual comments on where you can improve and section marks for "content", "analysis and interpretation" and "overall formatting". Further feedback will be given on the final portfolio submission. Each assessment item will include individual feedback based on the assessment criteria and in additional areas for improvement across the cohort will be provided to the group through the Announcements page on the Canvas site.
Assessment
Overview
There are two summative assessment items in LQN301 and one formative assessment.
Assessment 1 will be a formative assessment where you will gain valuable feedback from the unit coordinator regarding the detail of the presented content alongside your referencing of both primary literature and review articles as well as the extent of critical analysis expected to score a high grade in the final portfolio assessment item.
Assessment 2 is a written research paper in which you are presented with the results from panel sequencing of a patient's tumour. This assessment allows you the opportunity to plan a research paper, critically evaluate the relevant literature, describe the clinical aspects of the case and the molecular consequence of the NGS panel results and based on current literature discuss how these genomic results would be used to inform the next line of therapy.
Assessment 3 is a portfolio of your answers to a series of questions, problem solving tasks and case study discussions relevant to each week's learning. Some questions will be tied to a specific module (1 or 2 weeks of content) while several others will assess your ability to synthesise content across multiple modules in order to provide a high quality response.
Should there be any questions arising from the inappropriate use of AI in these assessments, authentication of learning and verification of identity may be assessed by an online viva with the unit coordinator where you will be asked questions to assess your independent understanding of one or more topics.
Unit Grading Scheme
7- point scale
Assessment Tasks
Assessment: Formative Portfolio Assessment
In this formative assessment piece you will be presented with two questions/ problem solving tasks/ case studies representative of other portfolio assessments and given the opportunity to synthesise the knowledge gained from the content presented in the week 1 and week 2 modules and show critical analysis and appropriate referencing of both primary research articles and review articles in your responses. These will be graded using the Assessment 3 final portfolio criteria sheet and formative feedback provided as to where you could have strengthened your response to improve your grade in the different categories of "content", "critical analysis" and "overall formatting".
This assignment is eligible for the 48-hour late submission period and assignment extensions.
Assessment: Research Paper
Assessment 2 is a written research paper in which you are presented with the results from panel sequencing of a patient's tumour. This assessment allows you the opportunity to plan a research paper, critically evaluate the relevant literature, describe the clinical aspects of the case and the molecular consequence of the NGS panel results and based on current literature and clinical trial results discuss how these genomic results would be used to inform the next line of therapy.
This assignment is eligible for the 48-hour late submission period and assignment extensions.
Assessment: Cancer Genomics Portfolio
This final portfolio will include responses to a variety of problem solving tasks/case study discussions/ or set of questions to demonstrate your understanding of the content presented in this unit.
Some questions will be tied to a specific module (1 or 2 weeks of content) while several others will assess your ability to synthesise content across multiple modules in order to provide a high quality response. The aim of this portfolio is to ensure that you have a strong breadth of knowledge of the essential elements of cancer genomics and how this information is currently used or has potential to be used in the future to improve patient outcomes.
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, ULO3 - 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: ULO2, 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, ULO3, Formative Portfolio Assessment, Cancer Genomics Portfolio - 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, Formative Portfolio Assessment, Research Paper - 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: ULO2, ULO4, Formative Portfolio Assessment, Research Paper