A National Diagnostic and Research Network

Prof John Christodoulou
Murdoch Children’s Research Institute & The University of Melbourne

Prof Nigel Laing
The University of Western Australia and Harry Perkins Institute of Medical Research

Prof Hamish Scott
SA Pathology and the Centre for Cancer Biology

Variant classification is a complex process and as we become better at understanding the human genome, we have the opportunity to re-interpret existing variant classifications in light of our new knowledge. As a result, clinical variant classifications evolve. This reclassification of variants is often of great benefit as it can uncover additional diagnoses and improve test accuracy. At the same time it can have significant clinical, ethical and legal consequences. In the absence of guidelines and appropriate technical and financial support, re-classification is currently performed on an ad hoc basis, dependent on local policies and limited resources. We suspect that re-classification occurs more than we think and that we can find better ways to help laboratories and clinics prepare for and deal with the consequences of re-classification.

In order to do this, the Clinical Variant Re-classification project is looking to understand the different approaches used by Australian laboratories to manage variant re-classification and use these experiences to develop consensus recommendations on best practice for variant review, reclassification and notification for all Australian healthcare providers.

Providing the public with clear information during the consent process is essential to support decision-making before and after a genomic test, and is the foundation to legally recognised ‘informed consent’. However in Australia it is left to individual states and territories and the various genetic service providers to administer patient consent, potentially creating inconsistent experiences, outcomes and patient management.

This project was formed in 2017 with the aim to help standardise the consent process for genomic testing across the country. The project team has since collaboratively developed recommendations around clinical genomic consent in Australia, and incorporated these into a national consent form and accompanying supporting information.

The consent materials were piloted with genetic services in Queensland and Victoria in 2019, assessing the adequacy and completeness of the information included, the simplicity and clarity of the language used in the materials, and the degree to which the materials support the consent process for health professionals in the genomics community.

The finalised Australian Genomics consent form and accompanying supporting information are now available and able to be adapted at a local level.

In 2019, the Australian Health Ministers’ Advisory Council Project Reference Group on Health Genomics launched a project led by NSW Ministry of Health to ‘build on existing work to develop and promote nationally consistent templates and guidance for consent’, under Australia’s Health Genomics Policy Framework.  Australian Genomics is collaborating with this NSW-led project to share the outcomes of our work, so the learnings of our consultation and pilot can inform this process.

The national Medical Services Advisory Committee assesses applications and advises the Australian Government on whether a medical service should receive public funding. This Australian Genomics project is building capability and experience in channelling submissions through to the Medical Services Advisory Committee to support a pipeline of applications for which there is clinical and economic evidence to support genomic testing.

Our first application through this pipeline seeks reimbursement of whole exome analysis for Childhood Syndromes. This application is based on data from a successful pilot study led by Melbourne Genomics Health Alliance, which investigated the clinical effectiveness and cost-efficiencies of genomic testing as an early diagnostic test for Childhood Syndromes. In its review of this application, the Medical Services Advisory Committee has recommended the Australian Government fund whole exome analysis for Childhood Syndromes.

The Australian Genomics working group is now forming a second application, seeking subsidised genomic testing for Developmental and Epileptic Encephalopathies.

Functional genomics investigates how a variation in a person’s genotype relates to their phenotype often at a molecular or cellular level. The Australian Functional Genomics Network is a platform to strengthen the relationship between clinical teams discovering disease-causing genes in patients with researchers who can investigate the functions of those genes. These collaborations between clinical and scientific teams will help to accelerate the diagnostic process.

See more about the Australian Functional Genomics Network

In collaboration with patient support and advocacy groups, Australian Genomics is developing information materials to help patients and the public navigate the complex world of genomics and genomic testing.

This project includes a new platform – genomicsinfo.org.au – to share curated patient information materials from sources around the world, and material developed through this project.

Find these resources at genomicsinfo.org.au

Genomic pathology reports have been traditionally requested by, and written for, genetic specialists. But as genomic testing transitions to mainstream healthcare, the consumers of these reports will expand beyond specialists to non-specialist clinicians and to patients, particularly with the introduction of My Health Record.

In collaboration with a range of stakeholders, this project is developing recommendations relating to content, accessibility and the language of genomic pathology reports in the context of laboratory accreditation restrictions and requirements.

This new project aims to explore potential barriers (for example, age, geography, language, culture, socioeconomic status or other) to ethical and equitable access to genomic testing across the nation.

It is envisaged this work will touch on the activities and recruitment practices in different states, and catalogue perceptions of unmet genomic testing need. The initial focus of the project will be to undertake semi-structured interviews with representatives from across all Australian clinical genetics services to investigate clinicians’ perceptions of areas of unmet needs.

These interviews will then be analysed and areas for focused investigation will be identified.