CHICAGO (GenomeWeb) – The Melbourne Genomics Health Alliance, an organization tasked with implementing clinical genomics programs in Australia's state of Victoria, has been rolling out its GenoVic clinical informatics platform to several users over the past few months.
According to Kate Birch, program manager for data and technology at the Parkville, Victoria-based alliance, Victorian Clinical Genetics Services, the first user of the GenoVic clinical genomics platform. will wrap up parallel testing any day now and switch off its old, in-house clinical information system. Monash Health and the Royal Melbourne Hospital are "actively implementing" GenoVic, and another two are developing plans to adopt the statewide platform by the end of 2019.
The launch of GenoVic in mid-2018 represented a milestone for Melbourne Genomics. Created in late 2014 and funded largely with a A$25 million ($17.8 million) grant from the government of Victoria, the organization is responsible for implementing clinical genomics programs, such as whole-exome sequencing for diagnosing rare diseases, genetic immunology, and precision cancer care across Australia's second most-populous state. Its membership now includes 10 healthcare and biomedical research organizations, though not all will start using GenoVic, as some do not have clinical genomics laboratories, Birch explained.
The primary purpose of GenoVic is to support genomics in clinical practice. "Our system is absolutely clinical genomic delivery-focused. We support clinical delivery first and then research access second to that," Birch said.
For the initial rollout of GenoVic, Melbourne Genomics installed the DNAnexus genome informatics platform for bioinformatics and Agilent's Alissa Interpret for variant interpretation in an Amazon Web Services-hosted cloud environment. The organization has added its own middleware to coordinate workflows between the different technologies.
The alliance is also building a statewide data repository to support various forms of biomedical analytics.
A key benefit of GenoVic is that it stores clinically generated genomic data in a way that any Melbourne Genomics member can access the information for research. "Patients are consented not just to the [molecular] test but to the sharing of data for research purposes, so we can share that data in a way that's compliant with that consent with all our other research-focused members," Birch said.
However, Birch noted that the alliance found that bioinformaticians do not want to share whole pipelines but prefer to share components of pipelines.As a result, Melbourne Genomics changed its bioinformatics strategy in the last couple of years to add "plug-and-play" capabilities for various bioinformatics components that have gone into GenoVic. "We've changed the way we think about supporting the bioinformatics across our members," she said.
In addition, Melbourne Genomics found that the vendor landscape was less mature than expected, leading to the combination of DNAnexus and Alissa Interpret. "Because clinical genomics is still really coming online globally, the vendor products weren't as far advanced as we had hoped," Birch said.
Rather than buying an end-to-end system, Melbourne Genomics recognized that different vendors had different specialties in different areas, so it purchased from multiple suppliers and put GenoVic together.
Another wrinkle in the implementation was the fact that some of the largest hospitals in Victoria were still bringing up their electronic health records systems. "IT departments are busy, and [there is the] challenge of bringing a new technology in because you're not the thing that's broken. You're the thing that's coming over the horizon," Birch said.
In Australia, health IT policy has largely been made at the state level. While Queensland, the massive northeastern state that includes Brisbane, Cairns, and Gold Coast, picked Cerner to install EHRs at all its hospitals several years ago, Victoria gave each hospital more autonomy, which has resulted in installations of Epic Systems, Allscripts Healthcare Solutions, Cerner, and a few other EHRs. Further complicating the work of Melbourne Genomics, each institution has had its own implementation schedule, and EHRs from different vendors are not always interoperable.
For the most part, large-scale clinical genomics has not made its way into doctor's offices or even standalone cancer centers among Melbourne Genomics members. But the organization is starting to think about how it can support clinic-based and consumer-focused genomics, including 23andMe-type test results that patients bring in, according to Birch.
Melbourne Genomics also is trying to figure out its role within the context of the Australian Genomics Health Futures Mission, for which the Australian federal government appropriated A$500 million over a 10-year period that started July 2018. This program is part of a broader A$1.3 billion national Health and Medical Industry Growth Plan aimed at improving health outcomes of more than 200,000 Australians.
The Australian Health Futures Mission will include a series of studies to tackle rare diseases and cancers, clinical trials to allow patients early access to test drugs, co-investing with philanthropic and business interests, and a community dialogue to understand the privacy, legal, social, and familial impacts of genomic medicine.
The mission's first genomics project — known as Mackenzie's Mission — will use A$20 million for a preconception carrier screening trial for rare and debilitating birth disorders, including spinal muscular atrophy, fragile X syndrome, and cystic fibrosis. Birch said that a testing center in Melbourne will be one of the two initial sites for Mackenzie's Mission.
For the most part, though, the Australian Health Futures Mission is still working its way through the bureaucratic governance process on how to allocate such a large pot of money.
"While that is happening, we're in those conversations saying, 'These are the lessons that we've learned from doing this clinically to make sure that what we've done can help guide that national agenda,'" Birch said.