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Unit outline_

AMED3903: Diagnostics and Biomarkers (Advanced)

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

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 an advanced 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
? 
A WAM of 70 and a mark of 70 or above in [12cp from (IMMU2101 or MEDS2004 or MIMI2002 or MIMI2902 or PHSI2007 or PHSI2907 or MEDS2001 or PCOL2011 or PCOL2021 or MEDS2002 or BCMB2001 or BCMB2901 or MEDS2003)] or a mark of 70 or above in [BMED2401 and 6cp from (BMED2402 or BMED2403 or BMED2404 or BMED2405 or BMED2406)]
Corequisites
? 
None
Prohibitions
? 
AMED3003
Assumed knowledge
? 

None

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Kavitha Gowrishankar, kavitha.gowrishankar@sydney.edu.au
Lecturer(s) Michaela Yuen, michaela.yuen@sydney.edu.au
Kavitha Gowrishankar, kavitha.gowrishankar@sydney.edu.au
The census date for this unit availability is 2 September 2024
Type Description Weight Due Length
Supervised exam
? 
Exam
SAQs, critical thinking, data analysis
30% Formal exam period 1 hour
Outcomes assessed: LO2 LO5 LO6 LO7 LO8
Tutorial quiz Quiz and participation
Short MCQ Quiz at most workshops and practicals
10% Multiple weeks Quiz: ~10 minutes
Outcomes assessed: LO1 LO5 LO4 LO3 LO2
Creative assessment / demonstration Assignment 2: Poster presentation
Data analysis, graphing, interpretation & critical thinking and evaluation
30% Week 08
Due date: 16 Sep 2024 at 23:59
~600 words poster presentation
Outcomes assessed: LO4 LO5 LO6 LO8
Presentation Assignment 1: Oral presentation
1 oral presentation and QandA to evaluate critical thinking
30% Week 11
Due date: 15 Oct 2024 at 14:00
Oral presentation: 15min + QandA
Outcomes assessed: LO1 LO6 LO5 LO2 LO4 LO3

Assessment summary

  • Tutorial quizzes and participation – short quiz at most workshops and practicals – individual assessment (10%)
  • Assignment 1: Oral presentation and Qand A – individual assessment (30%)
  • Assignment 2: Scientific Poster Presentation based on Practical: data analysis and graphing, data representation, interpretation and discussion; critical evaluation – individual assessment (30%)
  • Final Exam – SAQs, critical thinking, data analysis – individual assessment (30%)
  • Total assessment 100%

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.

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 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:

5% late penalty per day being late

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.

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

WK Topic Learning activity Learning outcomes
Week 01 Unit of study introduction and Group work Workshop (2.5 hr) LO2 LO3 LO4
Week 02 Biomarkers in Parkinson's disease Workshop (2.5 hr) LO1 LO2 LO3 LO4
Week 03 Imaging based diagnostics Workshop (2.5 hr) LO3 LO4 LO6
Laboratory Practical 1 (Live)- ELISA Practical (5 hr) LO3 LO5 LO6 LO8
Week 04 Neuroimaging: role of Artificial Intelligence in diagnosis Workshop (2.5 hr) LO1 LO3 LO4 LO6
Week 05 Disease surveillance and pathogen variants: Genomics based diagnosis Workshop (2.5 hr) LO1 LO4 LO6
Week 06 Laboratory Practical 2 (live) - Flow Cytometry Practical (5 hr) LO1 LO4 LO5 LO6
Diagnosis of SMA: Gene copy number evaluation using qPCR Workshop (2.5 hr) LO1 LO2 LO4 LO5 LO6
Week 07 Flow cytometry based diagnosis of autoimmune disorders Workshop (2.5 hr) LO1 LO4 LO5 LO6
Week 08 Gold standard, sensitivity and specificity Workshop (2.5 hr) LO6 LO7 LO8
Week 09 Normal range determinations and diagnosis of haematological disorders Presentation (2.5 hr) LO1 LO2 LO3 LO4 LO6
Week 10 Bad biomarkers and unorthodox testing Workshop (2.5 hr) LO2 LO3 LO4 LO5 LO6
Week 11 Oral presentations Workshop (2.5 hr) LO1 LO2 LO3 LO4 LO5 LO6
Week 12 Method validation from biomarker to diagnostic and regulatory framework Workshop (2.5 hr) LO6 LO7 LO8
Week 13 Revision exercises for final exam Workshop (2.5 hr) LO2 LO3 LO4 LO5 LO6 LO7 LO8

Attendance and class requirements

Attendance:

AMED3903 UoS is not based on an “on-demand” learning. Workshops are interactive and high level of participation is needed to get the most of this kind of teaching. Many workshops include exercises and data analysis, and results are discussed with the class.

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 during Week 1-3. 

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 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.

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
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

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

This unit is taught along with AMED3003. 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. It was deemed that for the 3903 students requiring them to submit a poster will be beneficial (assignment 2, not previously done); in addition instead of two oral presentations (one short and one long), they will be assessed on one and rubric adjusted to evaluate their broader critical thinking and analysis after their presentation. Both these modifications align better for 'Advanced' students as they will test higher level of critical analysis.

Additional costs

No textbook is required. 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.

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.