GMED5002: Semester 1, 2024

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Units GMED5002 Semester 1 2024 [Online]

Unit of study_

GMED5002: Genomics, Omics and Medical Applications

Semester 1, 2024 [Online] - Western Clinical School, Westmead

Overview

Recent technological advances in genetics and genomics have had a significant impact on medical care. This unit provides an introduction to the detection of genetic variation in the context of human disease and an overview of bioinformatics techniques and approaches for the analysis of genomic and other omic data. Technologies include types of deep resequencing including whole exome and whole genome sequencing the library preparation methods and sequencing chemistries and platforms. Methodologies and applications to diseases discussed include detection of base substitutions and splicing variants copy number variants and other structural variants. An understanding of which methodologies to be used to detect different types of genetic variants will be developed. An experiential-learning approach with clinical cases will be used to illustrate the importance of integrating phenotypic data genomic information and variant interpretation for accurate diagnosis. You will discuss techniques to prioritise variant pathogenicity and the application of new technologies in gene editing as well as omic technologies including transcriptomics proteomics and metabolomics and their current and future application to medical care.

Unit details and rules

Unit code	GMED5002
Academic unit	Genomic Medicine
Credit points	6
Prohibitions ?	None
Prerequisites ?	None
Corequisites ?	None
Assumed knowledge ?	This unit assumes knowledge equivalent to GMED5001. It is strongly recommended that students who lack a good working knowledge of genomics complete GMED5001 before enrolling in this unit or take it concurrently with GMED5001
Available to study abroad and exchange students	No

Teaching staff

Coordinator	Gladys Ho, gladys.ho@sydney.edu.au
Tutor(s)	Emma Hackett, emma.hackett@sydney.edu.au
	Katrina Fisk, katrina.fisk@sydney.edu.au
	Alan Ma, alan.ma@sydney.edu.au
	Robyn Jamieson, robyn.jamieson@sydney.edu.au

Type	Description	Weight	Due	Length
Supervised exam ?	Final Exam MCQs and SAQs	40%	Formal exam period	1 hour
Outcomes assessed:
Online task	Discussion Boards 2x Graded Discussion Boards. More details on Canvas.	30%	Multiple weeks	2x 450-500 words plus replies to peers
Outcomes assessed:
Small test	Quizzes MCQs and SAQs	15%	Multiple weeks	5x 30 minute quizzes
Outcomes assessed:
Online task	Peerwise See Canvas for details	15%	Week 08 Due date: 21 Apr 2024 at 23:59	1x cycle
Outcomes assessed:

Assessment summary

Quizzes: Students are to complete 5 graded quizzes
Peerwise: Students must author 5 questions, critique 3 questions and answer 10 questions.
Discussion Boards: Each discussion board will have a clinical scenario followed by some questions. Students must provide answers with references.
Final Exam: The exam will be 1 hour in duration and contain a mixture of MCQs and SAQs.

Detailed information for each assessment can be found on Canvas.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2021 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name	Mark range	Description
High distinction	85 - 100
Distinction	75 - 84
Credit	65 - 74
Pass	50 - 64
Fail	0 - 49	When you don’t meet the learning outcomes of the unit to a satisfactory standard.

For more information see sydney.edu.au/students/guide-to-grades.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

Deduction of 5% of the maximum mark for each calendar day after the due date.
After ten calendar days late, a mark of zero will be awarded.

This unit has an exception to the standard University policy or supplementary information has been provided by the unit coordinator. This information is displayed below:

Please note, for this unit of study (GMED5002) the late submission penalty will be 5% of the maximum awardable mark for each calendar day after the due date for 10 calendar days only. This is to ensure that timely feedback is provided to students. If the assessment is submitted more than 10 calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

Learning support

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Support for students

The Support for Students Policy 2023 reflects the University’s commitment to supporting students in their academic journey and making the University safe for students. It is important that you read and understand this policy so that you are familiar with the range of support services available to you and understand how to engage with them.

The University uses email as its primary source of communication with students who need support under the Support for Students Policy 2023. Make sure you check your University email regularly and respond to any communications received from the University.

Learning resources and detailed information about weekly assessment and learning activities can be accessed via Canvas. It is essential that you visit your unit of study Canvas site to ensure you are up to date with all of your tasks.

If you are having difficulties completing your studies, or are feeling unsure about your progress, we are here to help. You can access the support services offered by the University at any time:

Support and Services (including health and wellbeing services, financial support and learning support)
Course planning and administration
Meet with an Academic Adviser

Weekly schedule

WK	Topic	Learning activity
Week 01	Module 1: Molecular Techniques for detecting genetic variation	Individual study (10 hr)
Week 02	Module 1: Molecular Techniques for detecting genetic variation	Individual study (10 hr)
Week 03	Module 1: Molecular Techniques for detecting genetic variation	Individual study (10 hr)
Week 04	Module 2: Copy number and structural variation	Individual study (10 hr)
Week 05	Module 2: Copy number and structural variation	Individual study (10 hr)
Week 06	Module 3: Other advanced genomic techniques	Individual study (10 hr)
Week 07	Module 4: Variant annotation, pathogenicity and interpretation	Individual study (10 hr)
Week 08	Module 4: Variant annotation, pathogenicity and interpretation	Individual study (10 hr)
Week 09	Module 5: Role of segregation testing in evaluating the pathogenicity of genetic variants	Individual study (10 hr)
Week 10	Module 6: Functional genomics	Individual study (10 hr)
Week 11	Module 6: Functional genomics	Individual study (10 hr)
Week 12	Module 7: Metabolomics	Individual study (10 hr)
Week 13	Module 8: Other Omics, pathogen genomics and cancer genomics	Individual study (10 hr)

Attendance and class requirements

This unit is run completely online.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Required readings

Specific readings will be listed on Canvas. The main text book for this unit of study is:

Strachan, T., & Read, A. (2019). Human molecular genetics (Fifth edition.). CRC Press

Learning outcomes

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. Describe different types of genomic variants and their potential impact on gene function
LO2. Explain various methods routinely used for the detection of genomic variants and identify the limitations of these methods.
LO3. Interpret the pathogenicity of genomic variants using standard classification guidelines and evaluate tools that are used for interpretation
LO4. Explain the role of segregation in the interpretation of the pathogenicity of genomic variants
LO5. Outline the importance of functional genomics and evaluate some of the functional genomic techniques that can be used to determine the pathogenicity of genomic variants
LO6. Describe the clinical utility of metabolomics and proteomics and outline their advantages and disadvantages in studying human disease
LO7. Describe the challenges for other genomic testing, e.g. pathogen genomics and cancer genomics, and the methods that are used to overcome these challenges

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1	Depth of disciplinary expertise Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.
GQ2	Critical thinking and problem solving Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.
GQ3	Oral and written communication Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.
GQ4	Information and digital literacy Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.
GQ5	Inventiveness Generating novel ideas and solutions.
GQ6	Cultural competence Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.
GQ7	Interdisciplinary effectiveness Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.
GQ8	Integrated professional, ethical, and personal identity An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.
GQ9	Influence Engaging others in a process, idea or vision.

Outcome map

Learning outcomes	Graduate qualities
Learning outcomes

Responding to student feedback

This section outlines changes made to this unit following staff and student reviews.

We value your feedback about any aspect of the unit of study and your experience as a student of Sydney Medical School. To help ensure our courses meet your needs and maintain a high standard, we welcome your feedback at any time and we ask you to complete the Mid-Semester Evaluation Survey and the unit of study Evaluation Survey at the end of the semester. You can also rate any component of the unit using our star rating system found at the bottom of many pages as you progress through the unit. Your ratings and comments are anonymous and specifying what you liked and didn’t like about any of the learning materials, assessment items, discussion forums, feedback etc will help us to target our improvement efforts. Please note that your participation in this unit of study permits de-identified information about your learning experience and interaction with learning resources to be used for the purpose of improving the student learning experience.

Additional information

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Additional costs

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Site visit guidelines

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Work, health and safety

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Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Support for students

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Site visit guidelines

Work, health and safety

Disclaimer

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