For Melbourne Genomics, work is well underway towards the delivery of the first components of Victoria’s clinical system for genomics (‘GenoVic’). The work plan for this year sees the delivery of shared analysis and curation tools, data governance and clinical tools – paving the way for further elements of the system in 2018 and 2019. […]
Assoc Prof Clara Gaff, WEHI is Executive Director for this program
|University of Melbourne||LEAD INSTITUTE|
|Walter and Eliza Hall Institute of Medical Research||LEAD INSTITUTE|
|Murdoch Childrens Research Institute||LEAD INSTITUTE|
|Austin Health||LEAD INSTITUTE|
|The Royal Children's Hospital||LEAD INSTITUTE|
|The Royal Melbourne Hospital||LEAD INSTITUTE|
|Peter MacCallum Cancer Centre||LEAD INSTITUTE|
|Monash Health||LEAD INSTITUTE|
$25m funding by Victorian Government
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A Dutch study published in Genetics in Medicine on 4 February 2016 applies a cost analysis to the early use of whole-exome sequencing in diagnosing difficult-to-diagnose patients with intellectual disability. It reported that this new technology would save an average of US$3,500 in patients who obtain a diagnosis and US$1,700 in patients who do not, by avoiding doing unnecessary tests. Since a successful pilot in 2014 led to $25m funding from the Victorian Government from 2015-2018, the team at the Melbourne Genomics produced similarly impressive figures. They have been supported in their work by our Clinical Genomics experts who have been developing the necessary analysis pipelines for the work. One of the Demonstration Project’s most notable outcomes has been a significant increase in the rate of diagnosis for rare genetic conditions of childhood: from 20 to 58 per cent.
Other achievements included:
- agreement on and adoption of common approaches to testing, data handling and patient reporting across different organisations;
- the advent of multidisciplinary teams for clinical interpretation of genomic testing analysis;
- steps toward online access to genomic data for patients and their doctors; and
- linkage of several databases from different Alliance members to expand the information available for research and clinical care.
Melbourne Bioinformatics’ Clinical Genomics experts are leading the development of clinical grade bioinformatics analysis pipelines and variant curation databases. The clinical genomics pipeline has been tested on the Australian Nectar cloud for potential roll-out to healthcare networks.
It is intended that the Melbourne Genomics findings will contribute directly to future health practices and budgets, by determining where genomics has the most benefit to offer and how it might be applied across the Victorian hospital system and involvement in further national and international efforts will ensure Australia’s health system benefits from those. Learnings from Melbourne Genomics are being shared with colleagues within the Australian Genomics Health Alliance (AGHA) and globally through the World Genomics Health Alliance.
Melbourne Bioinformatics experts who have worked on this project include:
- Bernie Pope (lead) (also working directly with AGHA)
- Gayle Philip
- Peter Georgeson
- Anthony Marty
- Juny Kesumadewi
- Michael Milton
- Mailie Gall (also working directly with AGHA)
- Ivo Fokkema (Guest from Leiden University Medical Centre, Netherlands).
Over 2016 we produced a clinical-grade variant calling pipeline and variant curation database. These tools are now deployed within accredited clinical laboratories within Victoria and have been successfully used to complete the analysis of the first phase of project flagships. We also began analysing the next phase of the project flagships, with the inclusion of a new cancer analysis pipeline. As the project moves from the pilot phase to production, we have participated in requirements analysis for the future State production platform and the review of candidate solutions.
In particular, these are some of the many and varied skills we are contributing to this project include:
- variant filtering / curation software development and configuration
- bioinformatic pipeline development
- software integration
- software development
- subject matter expertise
- cloud computing
- requirements definition and negotiation
- management of vendor resources
- relationship building with Alliance members.
University of Melbourne Master of Science (Bioinformatics) student Ms Jia An Yu, is a welcome addition to Melbourne’s Biomedical and Biosciences precinct. Jia An’s undergraduate training was in biology in China’s north east at Harbin Institute of Technology (HIT), a large multi-disciplinary, nationally-renowned university focussed on science, engineering and research. At HIT she developed an […]
25 February 2019 Following our July 2018 update, Genovic, Victoria’s shared clinical system for genomics, has now reached a further milestone. Last week Melbourne Genomics announced that GenoVic is now ready for use in clinical genomic testing. Victorian Clinical Genetics Services (VCGS) is the first laboratory to agree to use the GenoVic system as its […]
Members of the Melbourne Genomics team recently travelled to the US to share experiences with colleagues. Our own Anthony Marty, as a member of the team building the Alliance’s shared clinical data system for genomics, co-presented at the DNAnexus Connect conference in San Francisco on ‘How DNAnexus is part of a system to embed genomics […]
For the second time in two years Melbourne Bioinformatics has hosted visiting scholar, Ivo F.A.C. Fokkema, from Leiden University Medical Center in the Netherlands. Ivo leaves us this week, having spent the past three months progressing his LOVD database development project. LOVD is an online platform for storing and sharing genetic variation, as well as software for […]
News release, Thursday 3 November, 2016 Victorian Health Minister, The Hon Jill Hennessy, today announced key findings from the Demonstration Project of the Melbourne Genomics Health Alliance, which show that patients get quicker, more accurate diagnosis and more personalised care when genomic sequencing is delivered within healthcare. We found that when doctors provide genomic sequencing […]
In an ABC News Online story published over the weekend, the MGHA team told how they have now celebrated their 100th successful diagnosis. Our team’s contribution is to develop a reliable, stable data analysis platform which can successfully be consistently applied in a clinical setting. In doing so, they are helping to demonstrate how bioinformatics is transforming medicine […]