Cloud-based bioinformatics platform fast-tracking genomic analysis
Researchers at the University of Melbourne Centre for Cancer Research (UMCCR) have established a reliable, scalable and fast bioinformatics platform to analyse the genomic data of hundreds of cancer patients.
Picture: Associate Professor Oliver Hofmann's (front, second from right) Genomics Platform Group, based at the University of Melbourne Centre for Cancer Research
This new cloud-computing based platform will allow the UMCCR team to analyse the data of large numbers of patients in parallel and drastically reduce the time taken to analyse genetic sequencing data from 72 hours to 12 hours.
The platform has been established as part of the recently announced Cancer of Unmet Need Initiative, led by Professor Sean Grimmond at the UMCCR, which aims to make cutting-edge genomic sequencing available to Victorian’s with rare and less common cancers.
It will be generating massive datasets of patient information, mapping their entire genome – as opposed to a single panel of DNA – to provide improved diagnosis and more targeted and effective treatments.
Rapid analysis is required for these datasets, to provide clinicians with a clearer idea of what they are dealing with therefore informing prompt treatment change and better chances for a positive response.
To cope with the expected number of patient data sets, Associate Professor Oliver Hofmann’s Genomics Platform Group is working closely with Illumina, one of the world’s leading biotech companies, on the newly developed Illumina Analytics Platform (IAP).
Associate Professor Hofmann said that by developing systems that reduce the time taken to sequence patient data and improve reliability, the group hopes to speed up efforts to make rare and less common cancers more manageable for patients.
"This partnership with Illumina has given us early access to a new and exciting computing platform, allowing us to fast-track rollout for cancer patients who have been failed by traditional therapies.
"Our Genomics Platform Group has been able to leverage IAP to port our analytical processes to a commercial cloud environment without having to build all solutions from scratch.
"With the Illumina Analytics Platform, we can easily contribute our own analysis and get it up and running with a few lines of code, leveraging the speed and quality of Illumina's existing DRAGEN technology without having to host and maintain our own computational infrastructure."
Jessica Gordon, Senior Director of Software Engineering at Illumina, said that the new Illumina Analytics Platform is a major step in simplifying operations and allowing for the most efficient, accurate analysis.
"We at Illumina have been transforming our software and informatics portfolio into an integrated platform that provides a common framework on which we can build our own solutions, but also allows for others to build theirs in the cloud.
"Security and data privacy are a top priority for the Illumina Analytics Platform, which is compliant with HIPAA, GDPR and adheres to best practices like ISO27001."
The Illumina Analytics Platform was developed in line with Global Alliance for Genomic Health (GA4GH) community standards, allowing researchers to make their workflows and procedures reusable and reproducible. The UMCCR aims to share developed best practices with researchers worldwide, to support similar precision medicine efforts and related positive impact for patients with challenging cancers.