Melbourne Genomics Health Alliance Uses AWS to Support Genomic Testing
Genomic medicine is a rapidly evolving field of medical science that allows healthcare professionals to examine a person’s entire DNA. This information can be used to help patients get well faster through more accurate diagnosis and more precise care. The Melbourne Genomics Health Alliance is working to make genomics a part of everyday medicine in the Australian state of Victoria. The Alliance is a collaboration of 10 leading hospitals and research organizations that are dedicated to enabling genomic medicine for every patient who needs it.
Victoria’s health system is decentralized, which means there is no single entity responsible for delivering genomic testing. Instead, there are a number of accredited clinical laboratories that can perform genomic or next-generation DNA sequencing for cancer or genetic disease. Supporting multiple laboratories is an Alliance priority in order to avoid data becoming dispersed and needless duplication of effort in systems building. The Alliance met this challenge by devising and building Genomical, a shared clinical system that facilitates the management and use of genomic sequencing data by numerous laboratories, clinicians, patients, and researchers across multiple, independent organizations.
In our first year of rollout, we’ve seen how Genomical can support the testing of patients across a wide range of rare diseases, providing greater efficiencies for five laboratories."
Dr. Natalie Thorne
Scientific Director, Genomical
A key driver in establishing Genomical was to support accredited testing laboratories to process genomic tests. “The genomic workflow is complex, involving many stages of analysis and a multidisciplinary team of experts,” says Dr. Natalie Thorne, who leads the Genomic Information Management stream. “Genomical provides a set of software tools to support the different stages of the testing process, as well as data storage and management. We believe this is the first system in the world to perform all these functions in genomics across multiple, independent organizations.”
Genomical’s software tools are coordinated by a custom-built Genomic Orchestration Service (GOS), which manages a highly automated data workflow and enables integration with laboratory information management systems. “Laboratories can select which of the available tools best suit their broader genomic testing workflows,” Dr. Thorne notes. Adds Tim Bakker, senior project manager on the Innovation and Technology Team: “Testing laboratories within the Melbourne Genomics Health Alliance have varying levels of genomic experience: some are just beginning to offer genomic tests, while others are well advanced in this space and starting to differentiate their service with more specialized offerings. With Genomical, each lab can use different tools within the system depending on their maturity in terms of both genomic testing and IT integration.”
Building Genomical on AWS
To build Genomical as a modular, flexible system, Melbourne Genomics recognized that using cloud technology would be essential, and it selected Amazon Web Services (AWS) as its cloud technology provider. It developed key Genomical components on AWS services, such as AWS Lambda for serverless compute, AWS Batch to schedule batch processing jobs, AWS Step Functions to coordinate the orchestrated workflows in GOS, Amazon Relational Database Service (Amazon RDS) for PostgreSQL for database capability, and Amazon Simple Storage Service (Amazon S3) for storing genomic data. In addition, Genomical makes use of AWS CloudFormation to automate cloud resource provisioning for rapid deployment of environments.
Cloud-based infrastructure enables Genomical to be a highly secure, modular, and scalable solution. Moreover, new tools and capabilities can be rapidly integrated with Genomical, through GOS, and incorporated into testing laboratories’ workflows.
Enabling Clinically Generated Genomic Data Sharing
As a shared system, Genomical is now generating a centralized store of clinical genomic data contributed from numerous testing laboratories. This allows for a consolidated approach to data sharing, with Alliance members using a single set of data governance agreements, policies, and processes. The model can support data access for both clinical and research use, in line with patient consent.
With GOS controlling the underlying orchestration, a user interface in Genomical can enable sharing of genomic data across Alliance members. The key building blocks are now in place to build the capability for authorized users to discover, request, and gain access to sharable genomic data in a controlled, highly secure environment. The solution also supports efficient data-sharing mechanisms with other genomics-focused organizations and initiatives in Australia and worldwide.
Scaling on Demand to Meet Data Growth
Melbourne Genomics can easily scale Genomical as more laboratories begin taking advantage of the solution. In addition, the cloud-based architecture enables new testing laboratories to be onboarded and apply Genomical as part of clinical genomic testing workflows in a matter of months.
Five laboratories in Victoria are already using Genomical to support genomic testing across different areas of healthcare. For example, Victorian Clinical Genetics Services (Murdoch Children’s Research Institute) is using Genomical to support testing for complex genetic conditions in children, and the Royal Melbourne Hospital is using it to investigate adult neurological disorders. Says Dr. Thorne: “In our first year of rollout, we’ve seen how Genomical can support the testing of patients across a wide range of rare diseases, providing greater efficiencies for five laboratories.”
To learn more, visit aws.amazon.com/health/genomics.
About Melbourne Genomics Health Alliance
Working collectively to transform healthcare, the Melbourne Genomics Health Alliance is a group of 10 leading health, research, and teaching institutions in Victoria, Australia, that seeks to show how genomics can deliver more effective medical care that is less wasteful of resources and more likely to succeed the first time.
Benefits of AWS
- Establishes a highly secure, modular, scalable, shared clinical system for genomics
- Enables labs to perform genomic testing for cancer and rare diseases
- Improves testing workflow efficiency
- Scales to support increasing demand
- Onboards new labs in months to use Genomical for genomic testing
AWS Services Used
AWS Batch enables developers, scientists, and engineers to easily and efficiently run hundreds of thousands of batch computing jobs on AWS.
AWS CloudFormation provides a common language for you to model and provision AWS and third party application resources in your cloud environment.
AWS Lambda lets you run code without provisioning or managing servers. You pay only for the compute time you consume.
Amazon Simple Storage Service (Amazon S3) is an object storage service that offers industry-leading scalability, data availability, security, and performance.
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