Melbourne Genomics Health Alliance (Melbourne Genomics)

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.