AMED3003: Semester 2, 2024

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Units AMED3003 Semester 2 2024 [Normal day]

Unit outline_

AMED3003: Diagnostics and Biomarkers

Semester 2, 2024 [Normal day] - Westmead, Sydney

Overview

Diagnostic sciences have evolved at a rapid pace and provide the cornerstone of our health care system. Effective diagnostic assays enable the identification of people who have, or are at risk of, a disease, and guide their treatment. Research into the pathophysiology of disease underpins the discovery of novel biomarkers and in turn, the development of revolutionary diagnostic assays that make use of state-of-the-art molecular and cellular methods. In this unit you will explore a diverse range of diagnostic tests and gain valuable practical experience in a number of core diagnostic methodologies, many of which are currently used in hospital laboratories. Together we will also cover the regulatory, social, and ethical aspects of the use of biomarkers and diagnostic tests and explore the pathways to their translation into clinical practice. By undertaking this unit, you will develop your understanding of diagnostic assays and biomarkers and acquire the skills needed to embark on a career in diagnostic sciences.

Unit details and rules

Academic unit	Department of Medical Sciences
Credit points	6
Prerequisites ?	12cp from (IMMU2101 or MEDS2004 or MIMI2002 or MIMI2902 or PHSI2005 or PHSI2905 or PHSI2006 or PHSI2906 or PHSI2007 or PHSI2907 or MEDS2001 or PCOL2011 or PCOL2021 or MEDS2002 or BCMB2001 or BCMB2901 or MEDS2003) or [BMED2401 and 6cp from (BMED2402 or BMED2403 or BMED2404 or BMED2405 or BMED2406)]
Corequisites ?	None
Prohibitions ?	AMED3903
Assumed knowledge ?	None
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Kavitha Gowrishankar, kavitha.gowrishankar@sydney.edu.au
Lecturer(s)	Fabienne Brilot-Turville, fabienne.brilot@sydney.edu.au
	Kavitha Gowrishankar, kavitha.gowrishankar@sydney.edu.au
	Michaela Yuen, michaela.yuen@sydney.edu.au

Assessment

The census date for this unit availability is 2 September 2024

Details
Criteria

Type	Description	Weight	Due	Length
Supervised exam ?	Exam SAQs, critical thinking, data analysis	30%	Formal exam period	1 hour
Outcomes assessed:
Tutorial quiz	Quiz and participation (workshops) Short Quiz (MCQ) at the end of most workshops and practicals	10%	Multiple weeks	10 minutes for each quiz
Outcomes assessed:
Assignment	Assignment 2: POSTER Data analysis and graphing, critical evaluation of diagnostic assay	30%	Week 08 Due date: 16 Sep 2024 at 23:59	~600 words poster format
Outcomes assessed:
Presentation	Assignment 1: Schematic and oral presentation Schematic (week5) and oral presentation-individual-during workshop (week11)	30%	Week 11	Oral presentation of ~6min
Outcomes assessed:

Assessment summary

Tutorial quizzes and participation – short quiz at most workshops and participation for some workshops – individual assesment (10% of final)
Assignment 1: Schematic and Oral presentation – individual assessment (30% of final)
Assignment 2: Poster generation on Practical: report, data analysis graphing and interpretation, discussion, critical thinking – individual assessment (30% of final)
Open Book Exam – SAQs, critical thinking, data analysis – individual

Further details can be found on the unit’s Canvas page.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (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.

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.

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.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

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	UoS introduction, lecture on basics of biomarkers and introduction to schematic presentation	Workshop (2.5 hr)
Week 02	Biomarkers in Parkinson's disease	Workshop (2.5 hr)
Week 03	Imaging based diagnostics	Workshop (2.5 hr)
Week 03	Laboratory practical 1 -ELISA	Practical (5 hr)
Week 04	Neuroimaging: role of Artificial Intelligence in diagnosis	Workshop (2.5 hr)
Week 05	Disease surveillance and pathogen variants: Genomics based diagnosis	Workshop (2.5 hr)
Week 06	Laboratory practical 2 - Flow Cytometry	Practical (5 hr)
Week 06	Diagnosis of SMA: Gene copy number evaluation using qPCR	Workshop (2.5 hr)
Week 07	Flow cytometry based diagnosis of autoimmune disorders	Workshop (2.5 hr)
Week 08	Gold standard, sensitivity and specificity	Workshop (2.5 hr)
Week 09	Normal range determinations and diagnosis of haematological disorders	Workshop (2.5 hr)
Week 10	Bad biomarkers and unorthodox testing	Workshop (2.5 hr)
Week 11	Oral presentations	Workshop (2.5 hr)
Week 12	Method validation from biomarker to diagnostic and regulatory framework	Workshop (2.5 hr)
Week 13	Revision exercises for final exam	Workshop (2.5 hr)

Attendance and class requirements

Attendance:

AMED3003/3903 UoS are not based on an “on-demand” learning and as such workshop content will not be recorded. Workshops are interactive where a high level of participation is expected to get the most of this kind of teaching. Many workshops include exercises and data analysis, and results are discussed with the class. Each topic is unique and will be covered by an expert academic and only offered once in the semester.

Unless otherwise indicated, students are expected to attend a minimum of 80% of timetabled activities for a unit of study, unless granted exemption by the Associate Dean.

For some units of study the minimum attendance requirement, as specified in the relevant table of units or the unit of study outline, may be greater than 80%.

The Associate Dean may determine that a student has failed a unit of study because of inadequate attendance.

Requirements:

An electronic BYO device that you can type on (e.g. laptop).

Access to Illustrator software : Adobe Creative Cloud is available on campus - Library or Learning Hubs (https://www.sydney.edu.au/students/study-spaces.html). You can

book pods or computers in our learning hubs . Bookings can be made for up to four hours, twice a day, 8am to 9pm Monday to Friday.

Adobe Creative Cloud is also available on laptops that can be rented in Building K on Westmead campus.

Adobe Creative Cloud is also available on desktops in the Westmead Hospital Library on Westmead campus.

Alternatively, Adobe Creative Cloud is available for $45 for 1 year license offer at https://sydney.edu.au/epay. Please allow several days to receive the license.

Access to Prism GraphPad software (free download via USYD ICT website). Free access will be based on student enrollment in AMED3003 and 3903. The access to the software will be given to students for the duration of the semester.

Access to EndNote software (free download via USYD ICT).

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.

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. investigate the biological processes underlying the discovery of viable biomarkers that lead to the diagnosis of disease
LO2. evaluate the characteristics of biomarkers that make them suitable for use as diagnostic tools
LO3. compare and contrast the key tests that are used to diagnose and track the course of disease
LO4. demonstrate competence in a variety of clinical diagnostic techniques
LO5. assess data from key technologies and design strategies to improve outcomes
LO6. analyse the development of advanced diagnostic technologies and critique the scientific basis for their application
LO7. create a translational pathway for a biomarker or a diagnostic assay
LO8. apply quality assurance and audit tools as well as national regulatory and ethical standards in the application of medical sciences to the clinical environment.

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.

The content has been updated from the previous year based on USS feedback. New modules covering imaging based diagnostics have been included this year. In addition, use of emerging AI diagnostics in neurology have also been included. Redundant practicals (PCR and ELISA) have been removed and a new practical (flow cytometry) has been added/ This is also based on the final exam responses where the students struggled to understand flow cytometry concepts that were taught in the workshops. Introduction of the new flow practicals is expected to help with understanding workshop teaching. Student feedback indicated PCR technique is being covered in several units and not particualrly relevant or beneficial to the understanding of this unit. Instead, a new workshop module has been added with a specific focus on utilising qPCR data/analysis for diagnosis of Spinal Muscular Atophy, where the genomics based diagnostics will be taught with a real world application. Focus will be on content, information and not artistic representation for marking asignments and scoring rubrics have been modified accordingly, to test the learning outcomes more accurately. Requirement for Adobe Illustrator as the tool for image/schematic generation has been removed and a list of alternate online tools will be offered to the students. The change of style of oral presentation from the previous pecha kucha to a more conventional presentation has been adopted to better prepare the students for future honours degree and/or other degree related requirements. This was also decided based on student feedback. The timing of assessment submission has also been altered, based on student feedback which indicated not enough time was provided for Assessment 2, (2weeks turn around previously) which is based on a practical. Taking the feedback on board, ELISA practical has been scheduled for week 3 itself and the poster assessment based on that is now due on week 8, giving all students sufficient time to prepare and submit. The changes have been discussed with and approved by AMED coordinator Prof Byrne and academic planning adviser Dr Cameron.

Additional information

Other requirements for this unit include:

Laptop
Lab coat and closed-toe shoes for laboratory practicals - look in lab list
GraphPad Prism and EndNote to be downloaded on students’ laptop (access via USYD).
Access to Adobe Illustrator software

More information can be found on Canvas.

Science student portal:

Work, health and safety

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

No eating or drinking is allowed in any laboratory under any circumstances
A laboratory coat and closed-toe shoes are mandatory
Follow safety instructions in your manual and posted in laboratories
REN wet lab induction and mandatory training before practicals
In case of fire, follow instructions posted outside the laboratory door
First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

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

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

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