LQN202 Genomics Analysis
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: | LQN202 |
|---|---|
| Equivalent(s): | LQZ202 |
| 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 2 2024, Online
| Unit code: | LQN202 |
|---|---|
| Credit points: | 12 |
| Equivalent: | LQZ202 |
| Coordinator: | Fiona Rae | f.rae@qut.edu.au |
Overview
Genomic scientists need to understand the application of array technology and massively parallel sequencing. In addition, they need to understand the tools available to assist with variant interpretation and classification. Clinicians requesting and receiving results of genetic tests increasingly need to understand variant classification in order to advise and manage patients.
Learning Outcomes
On successful completion of this unit you will be able to:
- Describe the theoretical assumptions of methodologies designed to identify causative variants and polymorphisms associated with common disease.
- Evaluate the different types of array, long read and massively parallel sequencing technologies, their methodologies and their ability to detect coding or expression aberrations.
- Analyse data from a genomic experiments, addressing the significance of findings.
- Generate scientific reports interpreting the results of array and massively parallel sequencing technologies.
Content
- Key statistical concepts including quantitative research methodologies, p-value, false discovery rate, type I error, power, association etc.
- Heritability of simple and complex traits in relation to disease
- Key polymorphic concepts including variants, mutations, SNP, CNV, haplotype, genotype
- Comparative genomic hybridisation, genotyping and expression array technologies
- Genome-wide association study arrays and diagnostic SNP arrays (both for linkage and mutation detection)
- How SNPs and CNVs are measured and detected using diagnostic arrays
- The processing of MPS data including the demultiplexing of samples, alignment of sequence data, variant calling data annotation (minor allele frequency, mutational consequence using in silico prediction tools), using variant web-based databases to determine the presence of the variant in control and disease populations
- Interpreting novel sequence variants using in silico analysis (Polyphen, SIFT, Align-GVGD, splice prediction algorithms), population frequency databases (EXAC, ESP6500, 1000 genomes), variant databases, published literature and how to classify variants using the ACMG/AMP Class 1-5 system of pathogenicity
- Biological pathways analysis using gene variant data
Learning Approaches
This unit is designed to introduce you to the core concepts of genomics analysis. 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 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 genomics analysis 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 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 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 three formal assessment items in LQN202. Assessment 1 is a problem-solving task for you to synthesise the knowledge gained during this unit and translate it into an experimental analysis. Assessment 2 is a written research paper which allows you to plan and write a research paper on an undiagnosed disease and critically evaluate the literature on different high-throughput genomic technologies to investigate the best mode of investigation. Assessment 3 is a workbook comprising of answers to questions based on the content of the unit over the semester.
Unit Grading Scheme
7- point scale
Assessment Tasks
Assessment: Problem Solving Task
In this assessment, you will be given a variant which has been identified using whole-exome sequencing in a known disease-associated gene. You will need to use in silico analysis, control and variant databases, along with the published literature to classify the pathogenicity of the variant using the ACMG-AMP guidelines.
This is an assignment for the purposes of an extension.
Assessment: Research Paper
This assessment is based upon a case of an undiagnosed genetic disease. You will be asked to write a research paper reviewing the merits of using either array technology or massively parallel sequencing, and the probability of identifying a diagnosis using each technology.
This is an assignment for the purposes of an extension.
Assessment: Workbook
The class will be provided with a series of problem-based discussion questions providing you with the opportunity to apply the content of the unit over the course of the semester.
This is an assignment for the purposes of an extension.
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.