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Unit of study_

CLTR5005: Biomarker Studies

Semester 2, 2021 [Online] - Camperdown/Darlington, Sydney

Identifying the right patients for the right drug at the right time is a major goal for improving patient care. Using biomarkers to help us personalise medicine is one strategy. The discovery of new biomarkers and the development of new biomarker-directed therapies raise high hopes for personalised medicine. Despite their promise, claims of clinical benefit of biomarker use still requires careful evaluation. This unit will teach candidates how to embed biomarker studies and translational research into clinical trial designs. The special skills and techniques of translational research will be highlighted in this unit. Candidates will understand the potential uses for biomarkers in clinical practice; how to use study designs relevant for biomarker evaluation and how to incorporate biomarker studies and biospecimen (tissue and blood) collection into clinical research projects. Candidates will learn the difference between prognostic, predictive and surrogate biomarkers and biostatistical considerations in their analysis. The complexities of international regulations regarding patient consent, biospecimen collection and shipment will be highlighted.

Unit details and rules

Unit code CLTR5005
Academic unit NHMRC Clinical Trials Centre
Credit points 6
Prohibitions
? 
None
Prerequisites
? 
CLTR5001 and CLTR5007
Corequisites
? 
None
Assumed knowledge
? 

None

Available to study abroad and exchange students

No

Teaching staff

Coordinator Sonia Yip, sonia.yip@sydney.edu.au
Type Description Weight Due Length
Assignment hurdle task Assignment 2
Written task
40% Formal exam period To be added by the unit coordinator.
Assignment hurdle task Quiz 1
Short answer questions
10% Week -04 To be added by the unit coordinator
Outcomes assessed: LO1 LO4 LO3 LO2
Assignment hurdle task Assignment 1
Written task
40% Week 10 To be added by the unit coordinator.
Outcomes assessed: LO1 LO13 LO12 LO11 LO10 LO9 LO8 LO7 LO6 LO5 LO4 LO3 LO2
Assignment hurdle task Quiz 2
Short answer questions
10% Week 13 To be added by the unit coordinator.
Outcomes assessed: LO10 LO16 LO15 LO14 LO13 LO12 LO11
hurdle task = hurdle task ?

Assessment summary

  • Quiz 1: Assesses material presented in module 1.
  • Quiz 2: Assesses material presented in modules 1-3 and the recommended readings.
  • Assignment 1: Assesses material presented in modules 1-3 and the recommended readings. Comprises of five short answer response questions.
  • Assignment 2: Assesses material presented in modules 1-5 and the recommended readings. Short answer responses required.

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 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:

The marker may elect to, but is not required to, provide feedback on such work delivered after ten calendar days.

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 Module 1: Basic concepts Individual study (12 hr) LO1 LO2
Week 02 Module 1: Basic concepts Individual study (12 hr) LO2 LO3
Week 03 Module 1: Basic concepts Individual study (12 hr) LO4
Week 04 Module 2: Biomarker discovery Individual study (12 hr) LO5 LO6
Week 05 Module 2: Biomarker discovery Individual study (12 hr) LO6 LO7 LO8
Week 06 Module 2: Biomarker discovery Individual study (12 hr) LO8 LO9
Week 07 Module 3: Translating discovery to clinical application - study design Individual study (12 hr) LO10 LO11
Week 08 Module 3: Translating discovery to clinical application - study design Individual study (12 hr) LO11 LO12
Week 09 Module 3: Translating discovery to clinical application - study design Individual study (12 hr) LO13
Week 10 Module 4: Statistical considerations in biomarker studies Individual study (12 hr) LO14 LO15
Week 11 Module 4: Statistical considerations in biomarker studies Individual study (12 hr) LO15 LO16
Week 12 Module 5: Practical implementation - biospecimens and laboratory analyses Individual study (12 hr) LO17 LO18 LO19
Week 13 Module 5: Practical implementation - biospecimens and laboratory analyses Individual study (12 hr) LO19 LO20 LO21

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. Module 1: Basic concepts (a) Describe the potential clinical use of biomarkers as medical tests for screening and diagnosis of disease, prognosis, prediction of treatment response, and monitoring treatment.
  • LO2. Module 1: Basic concepts (b) Identify the stages of biomarker discovery and evaluation.
  • LO3. Module 1: Basic concepts (c) Describe the common types of study designs used to demonstrate ‘proof-of-concept’ for a biomarker as a medical test, evaluate test reliability, and test accuracy.
  • LO4. Module 1: Basic concepts (d) Calculate and interpret basic measures of test accuracy (sensitivity and specificity, positive and negative predictive values, receiver operator characteristic curve).
  • LO5. Module 2: Biomarker discovery (a) Describe general approaches for biomarker discovery
  • LO6. Module 2: Biomarker discovery (b) Identify common types of biospecimens used for biomarker research
  • LO7. Module 2: Biomarker discovery (c) Describe common laboratory techniques and latest technologies
  • LO8. Module 2: Biomarker discovery (d) Describe requirements of laboratory methods and quality control procedures.
  • LO9. Module 2: Biomarker discovery (e) Describe the other major practical challenges for exploratory biomarker research.
  • LO10. Model 3: Translating discovery to clinical application – Study design (a) Describe the key design elements for treatment trials incorporating biomarkers, including trials of biomarker targeted therapies.
  • LO11. Model 3: Translating discovery to clinical application – Study design (b) Describe the advantages and disadvantages of classical, targeted and non-targeted biomarker-stratified trial designs.
  • LO12. Model 3: Translating discovery to clinical application – Study design (c) Identify the limitations of single arm studies for evaluation of a biomarker.
  • LO13. Model 3: Translating discovery to clinical application – Study design (d) Describe alternative designs to improve trial efficiency.
  • LO14. Module 4: Statistical considerations in biomarker studies (a) Interpret data from biomarker-stratified trials.
  • LO15. Module 4: Statistical considerations in biomarker studies (b) Interpret multivariable regression models to adjust for conventional clinical markers to determine the clinical value of a biomarker.
  • LO16. Module 4: Statistical considerations in biomarker studies (c) Distinguish between the prognostic and surrogate properties of a biomarker to determine when a biomarker can be used as a valid surrogate marker.
  • LO17. Module 5: Practical Implementation – Biospecimens and laboratory analyses (a) Describe ethical considerations, consent and regulatory requirements.
  • LO18. Module 5: Practical Implementation – Biospecimens and laboratory analyses (b) Describe common methods for biospecimen collection, processing, storage and retrieval
  • LO19. Module 5: Practical Implementation – Biospecimens and laboratory analyses (c) Identify key factors determining feasibility
  • LO20. Module 5: Practical Implementation – Biospecimens and laboratory analyses (d) Develop a study protocol outline for biomarker study involving biospecimens, including a handbook for biospecimen collection and processing
  • LO21. Module 5: Practical Implementation – Biospecimens and laboratory analyses (e) Understand the significance of biobanking in clinical trials

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.

No changes have been made since this unit was last offered.

Disclaimer

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