BMS327 Unit Information 2021 s1 PDF

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Diagnostic Genomics Unit guide semester 1 2021...

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BMS327 DIAGNOSTIC GENOMICS Unit Information Semester 1, 2021 This information should be read in conjunction with the online learning materials which can be found on your MyUnits page.

Unit Coordinator Dr Shane Colley College of Science, Health, Engineering and Education Medical, Molecular and Forensic Sciences

Unit Email: [email protected]

© Published by Murdoch University, Perth, Western Australia, 2021.

This publication is copyright. Except as permitted by the Copyright Act, no part of it may, in any form or by any electronic, mechanical, photocopying, recording or any other means be reproduced, stored in a retrieval system or be broadcast or transmitted without the prior written permission of the publisher.

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BMS327 Murdoch University

Contents Unit information Information about the unit Contact details How to study this unit Academic Support and Advice Resources for the unit Study schedule Assessment

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This unit was originally written in July 2017 by Dr Quintin Hughes, Assoc. Prof. Murray Adams and Assoc. Prof. Wayne Greene, with additional valuable input from senior scientists based at the Diagnostic Genomics Unit (PathWest), QEII.

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Information about the unit Welcome to BMS327 Diagnostic Genomics.

Unit description Diagnostic genomics is a rapidly developing discipline within clinical pathology focused on determining the genetic basis of phenotypes and disease diagnosis through examination of patient genomes and their products. This includes prenatal genetic testing, genetic disease diagnosis and screening, pharmacogenetic assessment, cancer diagnosis and prognostication. Current platforms and tools used in molecular diagnostic laboratories to identify genetic mutations and gene variants including next generation DNA sequencing will be covered in this unit, with a focus on interpretation and reporting.

Unit Prerequisite BIO282 Molecular Biology

Learning outcomes for the unit On completion of this unit, students will be able to demonstrate the following learning outcomes and skills: 1. Knowledge: The student will demonstrate an understanding of the principles and applications involved in identifying a range of genetic states and disorders, utilising a range of diagnostic techniques. 2. Communication: Students will be able to report constitutional, somatic, healthy and pathological genetic variants using standardised nomenclature. The student will need to demonstrate an ability to generate, understand, compile and report genetic pathology information. 3. Problem solving skills: The student will demonstrate an ability to assimilate data from multiple sources of genetic investigation with patient histories to formulate diagnoses and treatment strategies. 4. Social responsibility: Students will contemplate fundamental ethical considerations required when dealing with patient genetic information.

Graduate attributes developed in the unit This unit will contribute to the development of the following Graduate Attributes: • • •

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Communication Critical and creative thinking Laboratory based skills

• Independent and lifelong learning • Ethics

BMS327 Murdoch University

What you need to know Generic information which students need to know is available at Murdoch University’s “myMurdoch Support & Advice” web page: http://our.murdoch.edu.au/Educational-technologies/What-you-need-to-know/ The information provided covers: • Student code of conduct • Assessment Policy • Academic Integrity • Links to information about: Examinations; Non-discriminatory language; Student appeals; Student complaints; Conscientious objection and assessment policy • Determination of grades from components/marks • Information for equity students.

Contact details Unit Coordinator’s contact details:

Dr Shane Colley College of Science, Health, Engineering and Education Medical, Molecular and Forensic Sciences Room: 250.2.018 (Building 250) Phone: +61 8 9360 6391 Email: [email protected] For queries about your enrolment in this unit, or if you need information about the University in general, please contact The Student Centre on 1300 687 3624. Technical help For technical difficulties with accessing the online unit or running software in University computing labs, contact the IT Service Desk: Email: [email protected] Phone: 9360 2000

BMS327 LMS site The Unit’s LMS page is a major channel of communication for staff and students. Please ensure you check it regularly for announcements and other Unit information. All matters of a personal nature should be raised privately with the Unit Coordinator or Student Advisors. For any specific or individual concerns regarding the Unit or your participation in it, please contact the Unit Coordinator directly via [email protected], or in person (Room 2.018, Building 250). Please include the unit code (BMS327) in the email subject line and your student number in the text of your email.

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How to study this unit Diagnostic Genomics is a three credit point unit. Previously, students were required to attend five to six hours of scheduled activities, consisting of up to 3 one hour lectures and a threehour laboratory practical each week. Under current COVID circumstances, lectures will not be presented in person. Instead, lectures will be presented as a blend of Live on Line sessions (Tuesdays at 10:30 via BlackBoard Collaborate hosted on LMS) and recordings from previous years accessible through ECHO. These should be reviewed in the order presented below. The lectures provide theoretical content of the unit and support the practical program. Collaborate session icon on LMS:

The laboratory practical sessions expand upon the theoretical content presented in lectures and provide hands on skills required in a diagnostic genomics laboratory. Participation in the laboratory practicals and resultant laboratory reports account for 20% of the Unit’s overall mark.

Contact/participation time Lectures: a total of 2-3 hours per week, depending on the lectures scheduled. Practicals: a total of 3 hours per week. Attendance at the practical component is compulsory.

Time commitment As this is a three-credit point unit, it is expected you will spend on average 10 hours per week for the total weeks of this teaching period (or 150 hours overall) working on this unit.

Attendance requirements You are expected to: • Review lecture recordings via Echo •

attend all laboratory practicals

•

sit both the mid-semester exam in person depending on COVID circumstances

If you are having difficulty meeting participation requirements, please contact Dr Shane Colley ([email protected]) to discuss your options.

Unit changes in response to student feedback This is the fourth year that BMS327 has been taught at Murdoch. Constructive feedback on the structure and content of the unit is welcome at any time. A unit survey is conducted during the semester. Please participate as the surveys help to improve the quality of student learning experiences and has contributed previously to the Unit’s development.

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Academic Advice and Support: Student Escalation Flowchart The chart below provides guidance on who to see to resolve or discuss any issues relating to your studies at Murdoch University. This flowchart is primarily for academic matters. Students who are experiencing issues pertaining to social, emotional, financial, or spiritual/religious issues should speak to the Student Success team at our MyAdvice locations. Questions about content covered in a tutorial/laboratory/workshop session. Any assessments marked by your tutor/demonstrator for which you would like clarification. If you have concerns about another student or your learning needs in your tutorial/laboratory/workshop.

Tutor/Demonstrator

Questions about unit content, assessment, submitting assignments, attendance or changing class times. If you are having problems with your tutor/demonstrator or an issue has not been addressed by your tutor/demonstrator to your satisfaction. Any academic issues you do not feel comfortable addressing with your tutor/demonstrator.

Unit Coordinator

If you have a concern or problem that has not been addressed by the unit coordinator such as issues regarding attendance, assignments. Any academic issues relating to progression through your degree, withdrawal from unit, or intermission. Any academic issues you are uncomfortable discussing with your unit coordinator. Any academic issues which may affect multiple units across the semester.

Academic Chair

Any academic issues that you believe have not been adequately addressed by the .Academic Chair. Any academic issue which you are not comfortable discussing with your Academic Chair.

Head of Discipline

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Resources for this unit To undertake study in this unit, you will need access to the internet and computing facilities. The following will be provided during the teaching period: • lecture materials • lecture recordings • laboratory handouts required in addition to that posted to LMS • articles in ‘My Unit Readings’ BMS327 Online Unit The online unit can be accessed from your MyUnits page. The online unit hosts resources relevant to all students, such as unit information, lecture recordings, lecture materials, laboratory worksheets and assessment instructions. The online Discussion Board may be used to ask questions of your fellow students, share information and form study groups.

Computing resources Students should have access to a personal computer, preferably a laptop. It is expected that students will have basic skills in the use of software such as Word, PowerPoint and the Excel spreadsheet package. Computer software such as Excel is used to carry out numerical calculations and statistical analyses. Murdoch University currently uses Microsoft© Office products that may be accessed by students. To access a student copy of Microsoft Office 365 ProPlus, search in ‘IT Answers’ at http://our.murdoch.edu.au/IT/Get-help-with-IT/, or contact the IT Service Desk. Computing Laboratories The main computing laboratories on campus are open for extended hours every day and are available for use by students, subject to class bookings. These labs have general software including Excel 2010. The login procedure in these labs is the same one that applies in all on-campus computing laboratories. The procedure is described in your enrolment materials and on notices in the labs. Calculator You will find a basic or scientific calculator useful in this unit for occasional routine calculations and in the final examination. More sophisticated calculators are not required and will not be permitted in the examination.

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Study schedule - Lectures There are 3 x 1 hour lectures scheduled per week for this unit. Given the current COVID situation, lectures will not be presented Face to Face. Rather, a live-online lecture is to be given on Tuesdays from 10:30am and will be accessible via LMS. A recording of these lectures and those from previous years covering the remainder of the course will be available via ECHO on LMS four student to review at their own pace.

SC: Dr Shane Colley, Lecturer in Molecular Pathology, Murdoch University; JB: Dr Jacqueline Bentel, Senior Medical Scientist, Anatomical Pathology, Fiona Stanley Hospital; MD: Dr Mark Davis, Senior Medical Scientist, Neurogenetics and Cardiac Genetics, Pathwest, QE II Hospital; RA Dr Richard Allcock, Senior Medical Scientist, MacKenzies’s Mission, Pathwest, QEII. MF: Mahony Fenn, Medical Scientist, Cytogenetics, Western Diagnostic Pathology; MR: Marnie Russell, Associate Genetic Counsellor, Genetics Services of WA; KW: Dr Karen Woodward, Department of Diagnostic Genomics, Pathwest QEII; SF: Prof. Sue Fletcher, Centre for Comparative Genomics, Murdoch University.

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Laboratory Practicals The practical component of this unit comprises 6 separate projects conducted over the semester. These will be performed in 3 hour blocks from 9.30 to 12.30 and 1:30 to 4:30 on Wednesdays of teaching weeks. Due to the requirement for extended incubations for some labs, a number of projects will be conducted in parallel as tabled below. “Wet” labs will be conducted in 250.2.107 for which you will require your lab coats. “Dry” or in silico labs will be conducted in computing facilities in 450.3.084. The laboratory component is worth 20% of the final unit grade, however, marks for each report vary depending on the time and work involved in the class.

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Assessment Assessment for this unit is conducted in accordance with Murdoch University’s Assessment Policy.

Schedule of assessment items Assessment Item

Description

Value

Aligned Learning Outcomes

Due dates

Laboratory

Laboratory Reports

20%

1-4

Continuous, see above

Mid-Semester Examination (closed book)

20%

1-4

Group

Group oral presentation

15%

1-4

Examination

End of Semester – online

45%

1-4

Examination

Week 8 (during laboratory class) Week 13 of Semester (during laboratory class) End of semester exam period

Assessment details Laboratory Reports (20%) Your laboratory mark is based on your level of preparation for and participation in the laboratory practical activities, not just attendance. To demonstrate this, students will complete short laboratory reports detailing their findings from the practical sessions. Marks will be recorded in the LMS. Unit practicals vary in length from 1-3 weeks so report submission dates will depend on when individual labs end.

Mid-semester Examination (20%) A one-hour examination will be held Week 8, during the laboratory class in 250.2.015. The exam will comprise 20 multiple choice and 10 short answer questions assessing your knowledge of information presented in lectures 1-16 and laboratories from Weeks 1-6.

Group Oral Presentation (15%) During the laboratory classes in Week 13, students will present a case report to the class in groups of four in an oral presentation lasting not more than 15 min/presentation. Powerpoint will be used to communicate the report in the group setting. A separate, 1 page assessment of the reviewed case will also be submitted by each student to assist with examining their understanding of their chosen article. Assessment will be on clarity of presentation, understanding of the scientific and clinical concepts in the report, its results and discussion.

Final Examination (45%) A two-hour examination will be held during the normal, end of semester examination period assessing all the material of the unit. It will involve both short and longer form written questions. BMS327 Murdoch University

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It will be assumed that you have access to a basic or scientific (Level 2) calculator during the examination. Venue The final exam is expected to be hosted online via LMS. Identification The University requires that all students sitting examinations show their Murdoch University Student Card, drivers licence or passport to facilitate their identification. Examine your script Students may inspect their marked examination scripts and discuss the marking with the Unit Coordinator within 14 days of the posting of results. For further information about examinations, refer to http://our.murdoch.edu.au/Student-life/Get-organised/About-exams/

Determination of the final grade To pass the unit you will need to achieve an overall mark of at least 50%. If your overall mark lies between 45 – 49% you may be awarded supplementary assessment at the discretion of the Unit Coordinator. This unit will be assessed by the following assessment components with prescribed weights: Laboratory Examination Group Presentation Examination

Laboratory Reports Mid-Semester Examination (closed book) Group Oral Presentation End of Semester Examination (closed book)

20% 20% 15% 45%

Your final mark will be the sum of the weighted scores for these components. To pass this unit you may need to achieve a pass or better (i.e., 50% of the allocated marks) on all assessment items. An overall mark greater than 50% may still result in failure of the unit. Marks may be moderated to ensure equity of marking by different staff or across assignments of different difficulty. Final marks are converted to letter grades. See in the current Assessment Policy regarding grades. You are referred to your MyMurdoch page (under either MyUnits or MyInfo) for links to useful sites covering assessment policy and grading (academic integrity, assessment policy, copyright for students, grades, and non-discriminatory language). You will also find links to the Centre for University Teaching and Learning and from there to various study support websites.

ALL THE BEST WITH YOUR STUDIES THIS SEMESTER

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