Genomics and Precision Medicine

Unit outlines will be available through Find a unit outline two weeks before the first day of teaching for 1000-level and 5000-level units, or one week before the first day of teaching for all other units.
 

Genomics and Precision Medicine

Master of Medicine (Genomics and Precision Medicine)

Students must complete 48 credit points, including:
(a) 12 credit points of compulsory units of study; and
(b) 24 credit points of stream specific units of study; and
(c) 12 credit points of stream specific or general elective units of study.

Master of Medicine (Advanced) (Genomics and Precision Medicine)

Students must complete 60 credit points, including:
(a) 48 credit points of study as required for the Master of Medicine
(b) 12 credit points of project units of study.

Graduate Diploma in Medicine (Genomics and Precision Medicine)

Students must complete 36 credit points, including:
(a) 6 credit points of compulsory units of study; and
(b) 24 credit points of stream specific units of study; and
(c) 6 credit points of stream specific or general elective units of study.

Graduate Certificate in Medicine (Genomics and Precision Medicine)

Students must complete 24 credit points, including:
(a) 24 credit points of stream specific units of study.

Compulsory units

Compulsory unit - Graduate Diploma

CEPI5100 Introduction to Clinical Epidemiology

Credit points: 6 Teacher/Coordinator: Dr Fiona Stanaway Session: Intensive July,Semester 1,Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Prohibitions: PUBH5010 Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Normal (lecture/lab/tutorial) day, Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
This online unit with an optional face-to-face component introduces the concept of clinical epidemiology and provides students with core skills in clinical epidemiology at an introductory level. Topics covered include asking and answering clinical questions; basic and accessible literature searching techniques; study designs used in clinical epidemiological research; confounding and effect modification; sources of bias; interpretation of results including odds ratios, relative risks, confidence intervals and p values; applicability of results to individual patients; critical appraisal of clinical epidemiological research literature used to answer questions of therapy (RCTs and systematic reviews), harm, prognosis, diagnosis and screening; applicability of results to individual patients; and evidence-based use of health resources.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units

Compulsory units - Master of Medicine, Master of Medicine (Advanced)

CEPI5100 Introduction to Clinical Epidemiology

Credit points: 6 Teacher/Coordinator: Dr Fiona Stanaway Session: Intensive July,Semester 1,Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Prohibitions: PUBH5010 Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Normal (lecture/lab/tutorial) day, Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
This online unit with an optional face-to-face component introduces the concept of clinical epidemiology and provides students with core skills in clinical epidemiology at an introductory level. Topics covered include asking and answering clinical questions; basic and accessible literature searching techniques; study designs used in clinical epidemiological research; confounding and effect modification; sources of bias; interpretation of results including odds ratios, relative risks, confidence intervals and p values; applicability of results to individual patients; critical appraisal of clinical epidemiological research literature used to answer questions of therapy (RCTs and systematic reviews), harm, prognosis, diagnosis and screening; applicability of results to individual patients; and evidence-based use of health resources.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
GMED5005 Ethics and Evidence in Genomics

Credit points: 6 Teacher/Coordinator: Dr Ingrid Sinnerbrink, Dr Alan Ma, Dr Gladys Ho Session: Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Corequisites: CEPI5100 and 18 credit points of stream specific (GMED5001, GMED5002, GMED5003, WARC5001, CEPI5312) Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
This is the capstone unit of the Genomics and Precision Medicine Master's degree and it aims to develop the ethical and critical thinking needed to inform best clinical practice in Genomic Medicine. It is divided into two parts: an introduction to key ethical concepts and methods of ethical analysis relevant to health care practice and research, and an overview of evidence. Students will critically appraise the evidence base related to an area of practice in their workplace or a clinical guideline. This will require the development of a clinical question, a literature review, then an appraisal of the literature and application of evidence to individual patient care. Learning modules will include how to carry out a literature review, an example of how clinical practice and guidelines have changed based on changing evidence and review, and further refinement of clinical epidemiology and critical appraisal skills developed in CEPI5100 Introduction to Clinical Epidemiology.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units

Stream Specific units

GMED5001 Genomics in Clinical Practice

Credit points: 6 Teacher/Coordinator: Dr Ingrid Sinnerbrink and Dr Gladys Ho Session: Semester 1 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Recent major advances in understanding of the human genome and the relationship between genetic variation and disease have changed clinical practice. This unit provides contemporary knowledge of genetic disease, diagnosis, genomic testing, prognosis, management, inheritance and impact across a range of chromosomal, single gene and heterogeneous genetic conditions. You will study common conditions, such as intellectual disability, inherited cancer, and paediatric and adult-onset disorders, as well as genomic mechanisms and genetic variations which lead to human disease. A case based approach will be used to develop skills in interpretation of clinical, family history and genomic test results to formulate an appropriate diagnosis and accurate genetic risk information. Ethical issues in genomic medicine will also be considered. Advances in treatments for genetic diseases will be explored, along with possible uses and limitations of new technologies, including genome editing approaches. The RACP Clinical Genetics Advanced Training Committee has approved this unit to fulfill the Genetics University Course Requirement for advanced training in Clinical Genetics. It is suitable for all practitioners who require a working knowledge of genomics in clinical practice.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
GMED5002 Genomics, Omics and Medical Applications

Credit points: 6 Teacher/Coordinator: Refer to the unit of study outline https://www.sydney.edu.au/units Session: Semester 1 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units 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 Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
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 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
GMED5003 Advanced Genomics in Clinical Practice

Credit points: 6 Teacher/Coordinator: Dr Alan Ma and Dr Ingrid Sinnerbrink Session: Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assumed knowledge: This unit of study 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. Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Major advances and mainstreaming in genomics are impacting all specialty areas of medicine, leading to new approaches in diagnosis and management across a large range of conditions. This unit provides contemporary knowledge of these advances in many key subspecialty areas such as neurology, nephrology, cardiology, ophthalmology, and paediatric genomics.
This unit is for the advanced level non-genetics professional, aimed at providing the skills and understanding to be able to implement genomics in their own field of medicine, and understand the latest trends and approaches to genomic medicine. Students will gain a sophisticated knowledge and understanding of the integration of genomic and disease-specific clinical knowledge for optimum management, in a multidisciplinary approach with genetic counselling, bioinformatics, and molecular genetics. Case based multidisciplinary approaches will be used to develop skills to analyse the genetic and genomic literature in the context of disease-specific features and the clinical situation, to provide the most appropriate and timely diagnostic and genetic risk information for patients and families.
System and disease-specific advances in management of genetic conditions will be a focus including use of precision pharmacological and genetic therapies. There will also be an emphasis on the counselling and ethical issues of genomics, with input from consumer groups, education, health policy, and indigenous genomics experts.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
GMED5004 Cancer Genomics

Credit points: 6 Teacher/Coordinator: Refer to the unit of study outline https://www.sydney.edu.au/units Session: Semester 1 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Advances in genomics are impacting on many aspects of the diagnosis and management of cancer. This unit provides understanding of molecular mechanisms of oncogenesis, with particular reference to familial cancer conditions. It provides contemporary knowledge of familial cancer syndromes including their characteristic patterns of presentation, epidemiology, underlying causative genetic pathology and preventative management approaches. Case - based approaches will be used for the development of in-depth knowledge of familial breast, ovarian, bowel and endocrine malignancies. Other familial cancer syndromes explored will include the neurofibromatoses, and conditions such as Li-Fraumeni and Von Hippel Lindau syndromes. Review of other genetic conditions in which cancer risk is increased will be undertaken. Ethical issues in cancer genomics will be considered as well as advances in precision medicine applicable to familial cancer.
CEPI5312 Diagnostic and Screening Tests (1 and 2)

Credit points: 6 Teacher/Coordinator: Assoc Prof Katy Bell and Dr Emily He Session: Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Prerequisites: PUBH5010 or CEPI5100 Prohibitions: PUBH5208 and CEPI5202 and CEPI5311 Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Normal (lecture/lab/tutorial) day, Online
Note: Department permission required for enrolment
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
This unit of study introduces the student to basic concepts behind diagnostic and screening tests, including: test accuracy, sources of bias in test evaluation, critical appraisal of test evaluation studies, application of test results to individual patients, place of tests in diagnostic pathways, impact of tests on patient outcomes, principles and use of evidence in population screening, overdiagnosis, systematic review of diagnostic tests and meta-analysis. After completing this unit of study, the student should have a comprehensive understanding of contemporary issues and the methodology underlying, diagnostic and screening test evaluation and application.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
WARC5001 Research Translation, Impact and Evaluation

This unit of study is not available in 2021

Credit points: 6 Teacher/Coordinator: Prof Julie Redfern, Prof Clara Chow, Dr Stephanie Partridge Session: Semester 2 Classes: Online lectures, discussion forums, video tutorials Assumed knowledge: An understanding of research methodology and clinical trials is assumed. Assessment: Journal Club (30%); Discussion Boards (20%); Research Proposal (50%) Mode of delivery: Online
To optimise healthcare delivery, we need evidence-based strategies to enable research translation and to assess impact. This unit of study will teach these skills, including fostering and maintaining stakeholder engagement, pragmatic study design, cost effectiveness analysis, recognising and managing barriers and enablers to implementation, and post-research translation. Case-based discussions and preparation of a research proposal will develop the skills required to enhance impact and hasten adoption of research into routine care. This practical unit will suit students who are interested in improving their skills and knowledge in the areas of clinical or health services research and who are keen to enhance the impact of their current or future research.
Textbooks
Grol R, Wensing M and Eccles M. Improving Patient Care. The Implementation of Change in Clinical Practice. 2nd ed. Oxford: John Wiley & Sons, Incorporated (2013); Brownson RC, Colditz GA and Proctor EK. Dissemination and Implementation Research in Health: Translating Science to Practice. 2nd ed. New York, NY: Oxford University Press (2017).

General elective units

PUBH5018 Introductory Biostatistics

Credit points: 6 Teacher/Coordinator: Dr Timothy Schlub, Dr Erin Cvejic Session: Semester 1 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Normal (lecture/lab/tutorial) evening, Normal (lecture/lab/tutorial) day, Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
This unit introduces students to statistical methods relevant in medicine and health. Students will learn how to appropriately summarise and visualise data, carry out a statistical analysis, interpret p-values and confidence intervals, and present statistical findings in a scientific publication. Students will also learn how to determine the appropriate sample size when planning a research study. Students will learn how to conduct analyses using calculators and statistical software.
Specific analysis methods of this unit include: hypothesis tests for one-sample, two paired samples and two independent samples for continuous and binary data; distribution-free methods for two paired samples, two independent samples; correlation and simple linear regression; power and sample size estimation for simple studies; and introduction to multivariable regression models;.
Students who wish to continue with their statistical learning after this unit are encouraged to take PUBH5217 Biostatistics: Statistical Modelling.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
CEPI5300 Research Grants: Theory and Practice

Credit points: 6 Teacher/Coordinator: Associate Professor Germaine Wong Session: Semester 1 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Prerequisites: (PUBH5010 or CEPI5100) and PUBH5018 Prohibitions: CEPI5505 Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Normal (lecture/lab/tutorial) evening
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
In this unit of study, the student will develop his/her own research proposal, to a standard suitable for a peer-reviewed granting body. Each section of a grant proposal (Abstract, Aims, Background, Significance, Methods) will be discussed, with the student presenting and refining the corresponding section of his/her own proposal in a synchronous online workshop setting. This will be complemented by online presentations from experienced researchers on the practical aspects of clinical research. Topics include: observational studies, randomised controlled trials, diagnostic test evaluation, qualitative studies, economic evaluation, and process evaluation. The unit will conclude with a one-day, face-to-face, mandatory workshop where students will learn about budgeting, qualitative research, strategies and grant administration, research ethics and peer review of research grants.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
CEPI5215 Writing and Reviewing Medical Papers

Credit points: 6 Teacher/Coordinator: Dr Christina Abdel Shaheed Session: Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Prerequisites: (PUBH5010 or CEPI5100) Prohibitions: CEPI5214 Assumed knowledge: Some basic knowledge of summary statistic is assumed Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Online
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
This unit of study will appeal to anyone wanting to write medical papers for conferences or journals, or to improve their paper writing skills. Students will work at their own pace through 9 modules covering research integrity, medical style, abstracts, presentations and posters, constructing a paper, data visualisation, manuscript submission, responding to reviewers' comments, post-publication research dissemination, and peer- reviewing a paper. This unit aims to teach students the principles of research integrity in writing for medical journals, typical issues they may face, and link to resources to help them maintain integrity through their publishing careers. It will guide them to reliable evidence-based resources to improve their conference abstract, presentation and poster design, and manuscript style and writing. Students will learn about reporting guidelines, common pitfalls in writing and presenting research, choosing a journal, keywords, improving tables and figures for manuscripts through open source software, copyright, writing cover letters and response letters to reviewers. Students will learn about measuring research impact and ways to improve research reach, dealing with the media and press releases, using social media in dissemination, digital archiving and basic skills needed to act as a peer-reviewer. This is an online unit, but those needing to study in block mode will do online study as well as a workshop.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
PGEN5001 Pathogen Genomics

Credit points: 6 Teacher/Coordinator: Professor Vitali Sintchenko, Dr Verlaine Timms, Dr Rebecca Rockett, Dr Gabriella Scandurra Session: Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assumed knowledge: Basic understanding of microbiology or medical microbiology and genetics. Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Normal (lecture/lab/tutorial) day
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Genomics has revolutionised medicine, providing information on a scale not previously available. Pathogen Genomics is part of this revolution and the applications of this technology have provided crucial information on pathogen discovery, new drug development, control of outbreaks and antibiotic resistance. This unit of study will introduce students to analysis of bacterial and viral genomes and main applications of genomics for translational research, precision medicine and control of diseases with epidemic potential. Students will learn how DNA is sequenced in the laboratory and develop analytical skills in microbial genomics, using public databases and the University of Sydney's high­performance computing cluster. A combination of lectures delivered by domain experts and interactive practicals will provide detailed understanding of the key concepts of genomics utilized in research and clinical practice. Case studies will enable students to perform genomic analyses and apply the technological knowledge gained from the unit to examine virulence, drug resistance and evolution of pathogens with epidemic potential. This unit will equip students with knowledge and skills important for careers in biomedical research and healthcare.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units

PROJECT UNITS

Students accepted into the Master (Advanced) program must complete 12 credit points of study. Students must enrol in a minimum of 12 credit points of project units of study in order to submit their final written work
MEDF5301 Project (Advanced Masters)

Credit points: 12 Teacher/Coordinator: Students must have a University of Sydney staff member or University approved supervisor for their project. Session: Semester 1,Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Supervision
Note: Department permission required for enrolment
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Candidates will work on an independent research project in an area of specific interest relevant to their master's degree. The project may take the form of analysis of an existing data set, a systematic or integrative review of the literature, a case series, survey or other project acceptable to the project supervisor. In some streams, projects may be available for students to select. It is essential, where there is the use of patient information or recruitment of patient study subjects, that appropriate ethics approval is gained from the governing body where the project will take place. The candidate will enter into a learning contract and will be guided through the steps required to plan and execute a substantial research project and prepare a scholarly work which may be a paper for publication. A candidate must enrol in a minimum of 12 credit points of project units of study in order to submit their final written work. Approval of the project and supervisor by the Program Director must be confirmed prior to commencing the project.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
MEDF5302 Project (Advanced Masters) (Part A)

Credit points: 6 Teacher/Coordinator: Students must have a University of Sydney staff member or University approved supervisor for their project. Session: Semester 1,Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Supervision
Note: Department permission required for enrolment
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Candidates will work on an independent research project in an area of specific interest relevant to their master's degree. The project may take the form of analysis of an existing data set, a systematic or integrative review of the literature, a case series, survey or other project acceptable to the project supervisor. In some streams, projects may be available for students to select. It is essential, where there is the use of patient information or recruitment of patient study subjects, that appropriate ethics approval is gained from the governing body where the project will take place. The candidate will enter into a learning contract and will be guided through the steps required to plan and execute a substantial research project and prepare a scholarly work which may be a paper for publication. Where appropriate students will prepare a work suitable for publication. A candidate must enrol in a minimum of 12 credit points of project units of study in order to submit their final written work. Approval of the project and supervisor by the Program Director must be confirmed prior to commencing the project.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units
MEDF5303 Project (Advanced Masters) (Part B)

Credit points: 6 Teacher/Coordinator: Students must have a University of Sydney staff member or University approved supervisor for their project. Session: Semester 1,Semester 2 Classes: Refer to the unit of study outline https://www.sydney.edu.au/units Assessment: Refer to the unit of study outline https://www.sydney.edu.au/units Practical field work: Refer to the unit of study outline https://www.sydney.edu.au/units Mode of delivery: Supervision
Note: Department permission required for enrolment
Note: Refer to the unit of study outline https://www.sydney.edu.au/units
Candidates will work on an independent research project in an area of specific interest relevant to their master's degree. The project may take the form of analysis of an existing data set, a systematic or integrative review of the literature, a case series, survey or other project acceptable to the project supervisor. In some streams, projects may be available for students to select. It is essential where there is the use of patient information or recruitment of patient study subjects that appropriate ethics approval is gained from the governing body where the project will take place. The candidate will enter into a learning contract and will be guided through the steps required to plan and execute a substantial research project and prepare a scholarly work which may be a paper for publication. A candidate must enrol in a minimum of 12 credit points of project units of study in order to submit their final written work. Approval of the project and supervisor by the Program Director must be confirmed prior to commencing the project.
Textbooks
Refer to the unit of study outline https://www.sydney.edu.au/units