Genomics and Precision Medicine

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: Semester 1,Semester 2 Classes: Offered online (no fixed-time webinars) and face-to-face (daytime tutorials) Prohibitions: PUBH5010 Assessment: Completion of online quizzes (15%), tutorial participation (10%), assignment 1 (15%), assignment 2 (60%) Mode of delivery: Normal (lecture/lab/tutorial) day, Online
Note: It is recommended that this is completed as soon as possible after enrolment into your first unit of study.
This unit 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
Online readings and resources to be provided on the eLearning website.

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

CEPI5100 Introduction to Clinical Epidemiology

Credit points: 6 Teacher/Coordinator: Dr Fiona Stanaway Session: Semester 1,Semester 2 Classes: Offered online (no fixed-time webinars) and face-to-face (daytime tutorials) Prohibitions: PUBH5010 Assessment: Completion of online quizzes (15%), tutorial participation (10%), assignment 1 (15%), assignment 2 (60%) Mode of delivery: Normal (lecture/lab/tutorial) day, Online
Note: It is recommended that this is completed as soon as possible after enrolment into your first unit of study.
This unit 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
Online readings and resources to be provided on the eLearning website.
GMED5005 Ethics and Evidence in Genomics

Credit points: 6 Session: Semester 2 Classes: weekly online lectures, discussion groups (from week 5) Corequisites: CEPI5100 and 18 credit points of stream specific (GMED5001, GMED5002, GMED5003, WARC5001, CEPI5312) Assessment: 1x 1000-1200 word ethics assignment (20%); 4x ethics discussion board tasks (10%); 5x evidence based medicine written assignments (70%) Mode of delivery: Online
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. 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
Online readings

Stream Specific units

GMED5001 Genomics in Clinical Practice

Credit points: 6 Teacher/Coordinator: Dr Ingrid Sinnerbrink Session: Semester 1 Classes: online lectures and case discussions Assessment: online quizzes (10%), 4 x 400 ¿ 500 word case-based discussion forums (30%), generation and peer review of assessment items (20%), final exam (40%) Mode of delivery: Online
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
Strachan, T and Read, A. Human Molecular Genetics (4th Edition). Garland Science.
GMED5002 Genomics, Omics and Medical Applications

Credit points: 6 Teacher/Coordinator: Dr Gladys Ho Session: Semester 1 Classes: Dr Gladys Ho 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: online quizzes (10%), 4x 400-500 word case based discussion forums (30%), generation and peer review of assessment items (20%), , final exam (40%) Mode of delivery: Online
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.
Textbooks
Strachan, T and Read, A. Human Molecular Genetics (4th Edition). Garland Science.
GMED5003 Advanced Genomics in Clinical Practice

Credit points: 6 Teacher/Coordinator: Dr Ingrid Sinnerbrink Session: Semester 2 Classes: Online lectures and case discussions 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: Online quizzes (10%), 4x 400-500 word case-based discussion forums (30%); generation and peer review of assessment items (20%), final exam (40%) Mode of delivery: Online
Major advances 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 areas such as neurology, nephrology, cardiology, ophthalmology, haematology, immunology, hepatology, rheumatology, respiratory medicine and metabolic, diseases. New diagnostic and management approaches incorporating genomics knowledge will be discussed, with particular reference to disease and system-specific factors. Students will gain a sophisticated knowledge and understanding of the integration of genomic and disease-specific clinical knowledge for optimum management. Case based 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 and limitations of precision pharmacological and genetic therapies.
Textbooks
Strachan, T and Read, A. Human Molecular Genetics (4th Edition). Garland Science
CEPI5312 Diagnostic and Screening Tests (1 and 2)

Credit points: 6 Teacher/Coordinator: Dr Katy Bell Session: Semester 2 Classes: 1 x 2 hour synchronous seminar or asynchronous online tutorial/week for 12 weeks Prerequisites: PUBH5010 or CEPI5100 Prohibitions: PUBH5208 or CEPI5202 or CEPI5311 Assessment: Class discussion/presentations (40%) and two written assignments (60%) Mode of delivery: Normal (lecture/lab/tutorial) day, Online
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, principles and use of evidence in making decisions about population screening, and overdiagnosis. It will then move to more advanced topics including: application of test results to individual patients, place of tests in diagnostic pathways, impact of tests on patient outcome, tests with continuous outcome, receiver-operator characteristic curves, systematic review of diagnostic tests, predictive models, and monitoring/surveillance. 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
Course readings will be provided.
WARC5001 Research Translation, Impact and Evaluation

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: 2 x 2hr lectures, 10 x 1hr lectures, 11 x 2hr tutorials, 2 x 1hr and 8 x 0.5hr statistical computing self directed learning tasks over 12 weeks - lectures and tutorials may be completed online Assessment: Weekly quizzes (10%), 1x4 page assignment (20%), 1x1hr online test (20%) and 1x1.5hr open-book exam (50%). For distance students it may be possible to complete the exam externally with the approval of the course coordinator. Mode of delivery: Normal (lecture/lab/tutorial) day, Normal (lecture/lab/tutorial) evening, Online
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
Course notes will be made available.
CEPI5300 Research Grants: Theory and Practice

Credit points: 6 Teacher/Coordinator: Associate Professor Germaine Wong Session: Semester 1 Classes: 11 online or face-to-face sessions and 1 face-to-face workshop (June) Prerequisites: (PUBH5010 or CEPI5100) and PUBH5018 Prohibitions: CEPI5505 Assessment: 1 x written research proposal (60%); online class presentations (30%); workshop participation (10%) Mode of delivery: Block mode, Normal (lecture/lab/tutorial) evening
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.
CEPI5215 Writing and Reviewing Medical Papers

Credit points: 6 Teacher/Coordinator: Professor Angela Webster Session: Semester 1,Semester 2 Classes: 9 self-paced modules each comprising: course notes, lecture, demonstrations, exercises, quizzes Prerequisites: (PUBH5010 or CEPI5100) Prohibitions: CEPI5214 Assumed knowledge: Some basic knowledge of summary statistic is assumed Assessment: quizzes (30%), assignment 1 (20%), assignment 2 (50%) Mode of delivery: Online
Note: Students without the pre-requisites are encouraged to contact the Unit Coordinator to discuss their motivation and experience.
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
Fayers P, Machin D. Quality of Life: The Assessment, Analysis and Reporting of Patient-reported Outcomes, 3rd Edition. 3 ed. Chichester, UK: Wiley Blackwell; 2016
PGEN5001 Pathogen Genomics

Credit points: 6 Teacher/Coordinator: Professor Vitali Sintechnko, Dr Verlaine Timms, Dr Rebecca Rockett, Dr Gabriella Scandurra Session: Semester 2 Classes: 2x1hr lec/wk and 5x1hr seminars or 6x3hr practical classes/sem Assumed knowledge: Basic understanding of microbiology or medical microbiology and genetics. Assessment: 1x 1.5hr examination (50%), group project (20%) and presentation (10%) and 1x1000 wd paper review (20%) Mode of delivery: Normal (lecture/lab/tutorial) day
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, outbreak control and antibiotic resistance. This unit of study will introduce students to bacterial genomes, how they change and how that change can be measured. Students will learn how DNA is sequenced in the laboratory and develop analytical skills in bacterial genomics, using public databases and the University of Sydney's high-performance computing cluster. Students will experience the breadth and power of pathogen genomics and its wide applications within diagnostics and research. A combination of lectures and practicals will impart knowledge and understanding of a large number of applications used in genomics today. Case studies will enable students to perform genomic analysis on unknown samples and apply the technological knowledge gained from the unit to answer biological questions. This unit will provide students with a greater appreciation for the artistry of bacterial virulence and how understanding these mechanisms can inform overall general health outcomes for humans.
Textbooks
Online readings will be provided

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: Students will be required to have regular contact with their supervisor to discuss the progress of their project. Assessment: 2000 word written project proposal (30%) and written final work of up to 10000 words, or a publication (as negotiated) (70%) Mode of delivery: Supervision
Note: Approval of the project and supervisor by the Program Director must be confirmed prior to commencing the project.
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 recruitiment 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.
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: Students will be required to have regular contact with their supervisor to discuss the progress of their project. Assessment: 2000 word written project proposal (30%) and written final work of up to 10000 words, or a publication (as negotiated) (70%) Mode of delivery: Supervision
Note: Approval of the project and supervisor by the Program Director must be confirmed prior to commencing the project.
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.
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: Students will be required to have regular contact with their supervisor to discuss the progress of their project Assessment: 2000 word written project proposal (30%) and written final work of up to 10000 words, or a publication (as negotiated) (70%) Mode of delivery: Supervision
Note: Approval of the project and supervisor by the Program Director must be confirmed prior to commencing the project.
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.