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Unit outline_

AMED3903: Diagnostics and Biomarkers (Advanced)

Semester 2, 2021 [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 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 Fabienne Brilot-Turville, fabienne.brilot@sydney.edu.au
Lecturer(s) Fabienne Brilot-Turville, fabienne.brilot@sydney.edu.au
Type Description Weight Due Length
Tutorial quiz Quiz and participation
short Quiz at most workshops participation for some workshops
10% Multiple weeks Quiz: ~10 minutes
Outcomes assessed: LO1 LO5 LO4 LO3 LO2
Assignment Assignment 1: Illustrator schematic and oral presentation
Illustrator schematic and 1 oral presentation: individua (small group work)
30% Multiple weeks oral presentation: ~6min (Pecha Kucha)
Outcomes assessed: LO1 LO3 LO4 LO8
Assignment Assignment 2: Lab report 1
Laboratory Report: SAQs, data plotting and analysis, Illustrator schematic.
20% Week 08 ~1000 words
Outcomes assessed: LO4 LO1 LO6 LO5
Small test Small test
SAQs, critical thinking, data analysis
20% Week 13 1 hour
Outcomes assessed: LO1 LO8 LO7 LO4 LO3 LO2
Assignment Assignment 3: POSTER
Poster including data graph and analysis
20% Week 13 1 poster including texts and graphs
Outcomes assessed: LO4 LO8 LO6 LO5

Assessment summary

Detailed information for each assessment can be found on Canvas.

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.

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.

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.

WK Topic Learning activity Learning outcomes
Week 01 Unit of study introduction and Group work Workshop (2 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8
Week 02 Prenatal diagnostic and post-natal management Workshop (2 hr) LO1 LO4 LO5
Week 03 Newborn screening and Introduction to Illustrator Workshop (2 hr) LO1 LO2 LO4
Laboratory Practical 1 (online) Practical (4 hr) LO1 LO2 LO5
Week 04 Tracking disease and disease surveillance Workshop (2 hr) LO1 LO5
Week 05 Schematic representation of a concept Workshop (2 hr) LO1 LO6 LO7
Week 06 Normal range, accuracy, and precision in diagnostic Workshop (2 hr) LO5 LO7 LO8
Laboratory Practical 2 (online) Practical (4 hr) LO4 LO5 LO6
Week 07 Gold standard, sensitivity, and specificity in diagnostics Workshop (2 hr) LO5 LO6 LO8
Week 08 How to plot data and data analysis Workshop (2 hr) LO5 LO6 LO7
Week 09 Bad biomarkers and unorthodox diagnostic tests Workshop (2 hr) LO5 LO6 LO8
Week 10 Oral presentations Presentation (2 hr) LO1 LO3 LO4 LO8
Week 11 Method validation from biomarker to diagnostic and regulatory framework Workshop (2 hr) LO7 LO8
Laboratory Practical 3 (online) Practical (4 hr) LO4 LO5 LO6
Week 12 Antibody Detection and analysis Workshop (2 hr) LO5 LO6 LO8
Week 13 In-semester test Workshop (2 hr) LO1 LO2 LO3 LO4 LO7 LO8

Attendance and class requirements

Attendance:

All ZOOM sessions are synchroneous and AMED3003/3903 UoS are not based on an “on-demand” learning.

Workshop 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.

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.

- Assessment 2 (lab report 1) has been shortened, and includes a few short answer questions for students to realise the framework of what is a good Results and Discussion Sections. - an introduction session to Illustrator has been included in Week 3, so students can start to familiarize themselves with the software -some assessment dates have been placed earlier in the semester to allow better spread of the submitted work.

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.