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Postgraduate training in variant interpretation

Postgraduate training in variant interpretation

Background

The Melbourne Genomics Health Alliance members are at the forefront of introducing genomics into diagnostic laboratory and clinical practice in Australia. 

From the outset, it was clear that a tertiary education program was needed to instil literacy, skills and confidence in genomics among those who would be working in this field – including health professionals, medical scientists and policy-makers.

The University of Melbourne established a Master of Genomics and Health in 2016, with the first intake in 2017. Designed for a broad audience, the course prepares students for a future in a wide range of genomics-related areas. It complements other Master programs designed to meet the Human Genetics Society of Australasia’s (HGSA) professional certification requirements for specific disciplines (e.g. genetic counselling, diagnostic genomics).

A key skill is variant interpretation, that is, determining which DNA change (variant) is causing a patient’s condition or – in the case of cancer – is driving cancer growth and may be treatable. 

A multidisciplinary team – including clinical geneticists, medical scientists, bioinformaticians, genetic counsellors and other medical specialists – work together to interpret and agree a patient’s result. The requesting clinician needs to be able to understand the result to apply it in care. 

Project description

The objective: a workforce able to incorporate genomics into patient care.

The Master of Genomics and Health provides a means by which the current and emerging workforce can gain skills in genomics, beyond the timeframe of Melbourne Genomics’ funding. 

Development of core genomic subjects for the Master of Genomics and Health has been supported by Melbourne Genomics. Progressively, more attention has been placed by Melbourne Genomics on subjects that will provide a workforce competent in interpretation (or ‘curation’), classification and reporting of genomic variants. 

The first subject focused on variant interpretation – ‘Clinical Genome Variant Analysis 1’ – was based on content developed during continuing education workshops1 and is taught using a blended learning approach of online and face-to-face components. The learning objectives and content were designed by the Melbourne Genomics education team and Instructional Designer with The University of Melbourne’s Course Coordinator and Genomics Stream Coordinator. 

The subject comprises online modules (released during a two-week pre-reading period) followed by four half-day workshops, which include live demonstrations and hands-on application through practical variant interpretation exercises and real-world case studies. Subject assessments include quizzes, presentations and case studies.

A second variant interpretation subject – ‘Clinical Genome Variant Analysis 2’ – is currently in development and will be offered for the first time in Semester 2, 2020. 

The subjects are evaluated using both The University of Melbourne’s Student Experience Survey and a post-survey designed to assess the effectiveness of the blended learning design.

Outcomes

To date, a total of 24 students have completed the variant interpretation subject (14 in 2018 and 10 in 2019), with 13 enrolled in 2020.

Joint subjects in genomics between the Master of Genomics and Health and the Master of Genetic Counselling (also offered by The University of Melbourne) contributed to revision of the latter course.

Student evaluation found that the structure of online modules and workshops supported learning and engagement with the workshop content. 

Impact

This project has enhanced genomic capability in Victoria; recent graduates have gone on to gain roles in genomic trials, genomic data management and research. 

The project has increased variant interpretation capability and capacity in Victoria. Increased efficiency in teaching variant interpretation (through online modules) has reduced the need for face-to-face teaching. This has alleviated the teaching demand on subject matter experts, maximising their availability to laboratories.

Lessons learnt

  • Students have the option to complete a Graduate Diploma or Graduate Certificate, with the majority choosing to complete the full Master’s degree program.
  • The Master of Genomics and Health has the potential to be a pathway for training of medical scientists as variant interpreters. As well as blended learning subjects in variant interpretation, students can opt to undertake an internship in a laboratory conducting variant interpretation. 
  • Students initially reported that more content on the basics of genetics and nomenclature was needed. Students did not have the same inherent genomic literacy as medical professionals in fields peripheral to genomics. This foundation content has now been incorporated into earlier subjects in the Master of Genomics and Health.

1 See project summary, ‘Variant interpretation training through workshops