CHICAGO (GenomeWeb) – The organization for promoting and developing genomics in the Australian state of Victoria is preparing to go live with a technology system for clinical genomics.
Within the next couple of months, the Parkville, Victoria-based Melbourne Genomics Health Alliance will bring up GenoVic, a shared clinical genomics platform for its 10 members — all healthcare and biomedical research organizations. Launched in 2014 with an A$25 million ($18.8 million) grant from the government of Victoria, Melbourne Genomics is responsible for implementation of clinical genomics programs across Australia's second most-populous state.
"This is a shared clinical genomics system for the alliance members," said Kate Birch, program manager for data and technology at Melbourne Genomics. "It will go from the clinical end of being able to automate genomic tests [and] understand what test is right for your patient, right through to issuing the report and then [offering] patient tools to help patients understand their genomic outcomes."
Member organizations have learned how to order and perform genetic tests, Birch noted, but they have not been able to do so on a large scale. "Yes, we can do a couple, but now we have to do thousands of the clinical tests, so scaling up is a problem for us," she said.
For this initial rollout of GenoVic, Melbourne Genomics is installing the DNAnexus genome informatics platform for bioinformatics and Agilent's Alissa Interpret for variant interpretation in an Amazon Web Services-hosted cloud environment. This should be online by midyear, in the early part of winter in the Southern Hemisphere.
"We believe that these tools are going to enable some of that scaling," Birch said. "Our members are already doing exomes in clinical practice, but this is going to allow them to do more and to do it faster."
Melbourne Genomics is adding its own middleware to coordinate workflows between the different technologies.
"We will actually be able to deliver an automated test from information coming off the sequencer, hitting GenoVic, running through a predetermined pipeline, hitting Alissa, and possibly even going through the first bit of filtering so then a clinical or medical scientist can come in and pick up their case and do the final bit of variant interpretation and make the report for the patient," Birch explained.
Simultaneously, the alliance continues to build a statewide data repository, with the help of AWS tools. This repository will support analytics in a form that remains in an "investigative stage," Birch said, but the hope is to make the data available for researchers to apply whatever analytics technologies they choose.
"Instead of us selecting a whole lot of analytical tools that other people might want to apply to the data, we're trying to figure out how we can open that data up in situ and provide data access that way." Birch said. "The clinical applications are kind of set, but the research applications of this data are so numerous and there are so many different tools that researchers may want to apply."
Melbourne Genomics is testing some methods with the University of Melbourne and with the Commonwealth Scientific and Industrial Research Organisation, an independent Australian federal agency that supports scientific research across the country.
One tool that Melbourne Genomics is considering is VariantSpark, a cloud-based, machine-learning algorithm under development and testing at the Commonwealth Scientific and Industrial Research Organisation, Birch indicated. "We'll be seeing if we can put that on top of the data within our repository and provide researchers with access that way," she said.
Birch hopes that GenoVic will have some diagnostic tools in place before the end of 2018. By that time, she expects two unspecified Melbourne Genomics members to be active users of the platform and another two to be in the process of joining.
"We would have a solid foundation for the storage of genomic data in GenoVic, so the repository piece would be solidified. We would have things like data life-cycle management in place and [be able to] really leverage some of that AWS cost efficiency in moving to other integrations," Birch said.
She said Melbourne Genomics Health Alliance works closely with similar groups in other Australian states. Other than the Sydney Genomics Collaborative — serving the state of New South Wales — the Victoria group is ahead of its peers on this front, so Melbourne is serving as a de facto pilot site for the rest of the country, in terms of both software tools and data repositories, according to Birch.
"We are sharing those learnings all the time with our other alliances," Birch said.
Australia does lag other developed countries in adoption of electronic health records. Not all Melbourne Genomics Health Alliance members have fully functioning EHRs yet, so integration with the genomics platform is not in the immediate plans. For now, the alliance is starting to integrate with laboratory information management systems based on variations of the Fast Healthcare Interoperability Resources (FHIR) standard developed by Health Level Seven International.
The information model for GenoVic will be "as FHIR-ready as we can be" as the standard matures and as more EHRs come online in Australia, Birch said.