PGEN5001: Semester 2, 2021

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Units PGEN5001 Semester 2 2021 [Normal day]

Unit of study_

PGEN5001: Pathogen Genomics

Semester 2, 2021 [Normal day] - Remote

Overview

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.

Unit details and rules

Unit code	PGEN5001
Academic unit	Genomic Medicine
Credit points	6
Prohibitions ?	None
Prerequisites ?	None
Corequisites ?	None
Assumed knowledge ?	Basic understanding of microbiology or medical microbiology and genetics.
Available to study abroad and exchange students	No

Teaching staff

Coordinator	Vitali Sintchenko, vitali.sintchenko@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Open book)	Final exam extended answer questions	50%	Formal exam period	1.5 hours
Outcomes assessed:
Presentation	Journal club presentation More detailed information in canvas	10%	Week 05	15 min
Outcomes assessed:
Assignment	Group assignment/report and presentation More detailed information in canvas	20%	Week 10	Week 5 - Week 10
Outcomes assessed:
Assignment	Paper review/written assessment More detailed information in canvas	20%	Week 12	1000 words
Outcomes assessed:
= group assignment ? = Type C final exam ?

Assessment summary

Assessment	Weighting	Due date
Final exam	50%	Exam period
Journal club presentation	10%	Wk 5
Group assignment/report and presentation	20%	Wk 10
Paper review/written assignment	20%	Wk12

Assessment criteria

Result name	Mark range	Description
High distinction	85-100	Exceptional
Distinction	75-84	Excellent application of the knowledge acquired
Credit	65-74	A clear understanding of the learning outcomes and application of these.
Pass	50-64	Minimum understanding of the learning outcomes to pass the unit
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:

Late penalties apply from the day after the published due date (two marks (out of 100) per day)

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.

Learning support

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.

Weekly schedule

WK	Topic	Learning activity
Week 01	Lecture: Pathogen genomics, introduction to the course	Online class (1 hr)
	Lecture: Microbial genomes, units of analysis, core and accessory genomes	Online class (1 hr)
	Seminar: Genome mapping, alignment and assembly	Online class (2.5 hr)
Week 02	Lecture: High-throughput sequencing methods	Online class (1 hr)
	Lecture: Genome polymorphisms and recombinations	Online class (1 hr)
	Practical 1: Genomic nucleic acid extraction, sequencing library preparation and short read sequencing	Online class (3 hr)
Week 03	Lecture: Genomic markers of virulence in viruses and bacteria	Online class (1 hr)
	Practical 2: Identification of the taxonomic position of viruses and bacteria from genomic data	Online class (1 hr)
	Practical 2: Identification of the taxonomic position of viruses and bacteria from genomic data	Online class (2.5 hr)
Week 04	Lecture: Genomic mechanisms of emergence of pathogens	Online class (1 hr)
	Lecture: Genome-wide association studies for discovery of mechanisms of virulence and resistance	Online class (1 hr)
	Practical 3: Detection of genes for virulence assessment	Online class (3 hr)
Week 05	Lecture: Phylogenomics of pathogens	Online class (1 hr)
	Practical 4: Estimation of phylogenetic relationships between genomes	Online class (1.5 hr)
	Self-directed learning: Journal Club Presentations due Sunday 27 September	Independent study (2.5 hr)
Week 06	Lecture: In silico testing for drug resistance	Online class (1 hr)
	Lecture: Plasmid-mediated antibiotic resistance	Online class (1 hr)
	Seminar: Critical review of AMR databases	Seminar (1 hr)
	Practical 5: Detection of mutations and inference of antibiotic resistance	Online class (1.5 hr)
Week 07	Lecture: Pathogen discovery	Online class (1 hr)
	Lecture: Culture-independent sequencing for pathogen detection and microbiome assessment	Online class (1 hr)
	Seminar: RNAseq workflow for meta-transcriptomics	Seminar (1 hr)
Week 08	Lecture: Genomics-guided public health surveillance	Online class (1 hr)
	Lecture: Genomics for outbreak investigations	Online class (1 hr)
	Practical 6: Deciphering an outbreak of tuberculosis and approximation of transmission pathways from genomic data	Online class (2.5 hr)
Week 09	Lecture: Genomic surveillance during COVID-19 pandemic	Online class (1 hr)
	Lecture: Integration of genomic, epidemiological and clinical data	Online class (1 hr)
	Site visit: Visit of the NSW Public Health Pathogen Genomics Laboratory, NSW Health Pathology, Westmead Hospital	Field trip (2 hr)
Week 10	Lecture: Transcriptomics for study of different approaches to virulence and microbial growth	Online class (1 hr)
	Lecture: Transcriptome reconstruction and profiling for next generation risk assessment	Online class (1 hr)
	Self-directed learning: Group project presentations & reports	Independent study (3 hr)
Week 11	Lecture: Genomics of host-pathogen interactions	Online class (1 hr)
	Lecture: Bioethics of data governance and secondary analyses	Online class (1 hr)
	Seminar: Visualisation of multi-dimensional genomic and clinical data	Seminar (1 hr)
	Seminar: Diagnostics engineered from microbial sequences	Seminar (1.5 hr)
Week 12	Lecture: Proteome profiling and analysis of regulatory networks	Online class (1 hr)
	Lecture: Evolution of genomes and proteomes under vaccine pressure	Online class (1 hr)
	Seminar: Genomic data governance in the era of cloud computing	Seminar (1 hr)
	Tutorial: Vaccine redesign and epitope prediction	Tutorial (1.5 hr)

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.

Required readings

available on Canvas

Learning outcomes

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.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. Understand sequencing data and relevant quality metrics
LO2. Taxonomically classify microorganisms using short read sequencing data
LO3. Identify variation in viral, bacterial and metagenomics data
LO4. Generate and examine phylogenetic trees based on nucleotide polymorphisms and core genomes
LO5. Perform genome mapping, assembly and annotation using different resources
LO6. Interpret genomic data from an outbreak investigation
LO7. Determine relevant drug resistance genes and mutations
LO8. Understand main approaches for genome data visualisation
LO9. Recognise challenges and identify solutions for pathogen genomic data gathering, analysis, governance and reporting

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
Learning outcomes

Responding to student feedback

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

This is the first time this unit has been offered

Additional information

OLEO5502-Introduction to Pathogen Genomics

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.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Disclaimer

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