Analytics provider BizData has helped sequence genomes for a Western Australian lab, enabling it to speed up matching patients to stem cell donors.
Building a platform on Microsoft Azure, BizData enabled PathWest labs to automate genetic analysis of almost 4,000 files -- 250GB worth of data -- of potential stem or organ donors.
According to BizData, the Microsoft partner first assessed the lab’s on-premises pipeline and then validated its pipeline on different GPU and compute resources on Azure.
“Finally, we worked together over several weeks to run multiple tests to validate the quality and accuracy of the results, by comparing them to new and historical analysis results obtained with their on-premises manual data analysis pipeline,” BizData research and advanced computing director Felipe Ayora said.
The lab developed a data analysis pipeline to perform high resolution genotyping using the cloud-based platform, which uses a single molecule sequencing device known as the MinION from Oxford Nanopore Technologies.
Data files from the MinION platform are automatically sent to the Azure-based Loome software, developed by BizData, which orchestrates the analysis pipeline and expedites processing.
According to PathWest, the platform has fully automated the analysis process, halving the amount of time it takes to complete.
The data is said to be encrypted in transit and at rest, while also remaining in Australia to “maximise security and privacy”.
According to senior scientist at the Department of Immunology Dr Dianne De Santis, PathWest can now provide a high-resolution (HLA) genotyping result of a donor organ in just four hours, calling it a world first.
“High resolution typing of donors at the point of recruitment provides more information about the donor type to the clinician and transplant team, therefore eliminating potential unknown mismatches during the donor selection process and allows patients to proceed to transplant quickly, an important factor in the patients’ overall clinical outcome,” she said.