Here you'll find technical information about GenoVic and how it can work for you.
GenoVic is a clinical system to support the end-to-end workflow of a genomic test.
GenoVic was designed to be used across hospitals, research and academic institutions. It is modular, customisable and built to integrate with existing systems.
We can support you to onboard GenoVic in your laboratory – ensuring you can perform consistent, high-quality genomic tests, with data that can be re-analysed whenever it’s needed.
How GenoVic works
- What is GenoVic?
- Why use a shared system for genomic testing?
- What is the difference between a research system and a clinical system?
- What types of tests are supported?
- How is GenoVic different to other genomic testing tools?
- Which laboratories use GenoVic?
- What tools are currently supported by GenoVic?
- What cloud services does GenoVic use?
Onboarding and support
- How do I register and log into GenoVic?
- What are the GenoVic APIs and how do I use them?
- How do I manage bioinformatics pipelines in GenoVic?
- Can I use my preferred bioinformatics tools with GenoVic?
- Can I integrate my LIMS and EMR with GenoVic?
- What support will I get to onboard GenoVic?
- Will I get ongoing support?
- How does GenoVic manage software updates?
Data and security
“GenoVic has enabled us to store data generated from testing, ensuring it may be available for research, validation or further clinical use in the future. This was instrumental in obtaining NATA accreditation for our cancer panels, enabling us to deliver the service clinically.”Dr Vivek Rathi
Head of Genomic Laboratories, Monash Health Pathology
How GenoVic works
What is GenoVic?
GenoVic is an all-in-one genomic data solution, designed specifically for clinical use. It consists of several components – some custom-built, some procured from third-party vendors – integrated into a single, modular suite of services.
It underpins the entire genomic testing process, from taking data off the sequencing machine to analysis, interpretation and clinical reports. But it also stores genomic data and enables it to be re-analysed over a person’s lifetime.
- To eliminate costly re-sequencing and duplication of effort
- To ensure genomic data is stored and accessed securely
- To ensure data is stored in consistent and interoperable formats
- To support audit requirements for clinical labs
- To keep pace with rapidly evolving genomic technology
What’s the difference between a research system and a clinical system?
A clinical system needs to meet specific data storage requirements that enable retrieval of patient information. Clinical systems also need to be able to connect to other healthcare systems. Research systems typically do not need to meet these requirements.
Because clinical systems store identifiable information about patients, they need to meet higher security standards. GenoVic uses a security-by-design approach as opposed to bolting on security controls after the fact. GenoVic utilises highly secure, cloud-based storage through Amazon Web Services, with rigorous processes for authorised access.
What types of tests are supported?
Laboratory scientists can use GenoVic to facilitate analysis and curation of targeted sequencing panels, whole exome sequencing and whole genome sequencing for inherited conditions and cancer.
How is GenoVic different to other genomic testing tools?
In contrast to a single end-to-end vendor platform, a modular system like GenoVic can take advantage of the best tools available from a range of vendors. Its custom-built orchestration service brings all these tools together to create a streamlined workflow. GenoVic was also built and tested for integration with a range of systems used by Victorian pathology providers.
In a rapidly changing industry, GenoVic stands the test of time.
Which laboratories use GenoVic?
The Royal Melbourne Hospital, Australian Genome Research Facility, Monash Health and the Victorian Clinical Genetics Service are all currently using GenoVic to support accredited genomic sequencing tests. Austin Health is currently onboarding GenoVic.
What tools are currently supported by GenoVic?
GenoVic is a framework for multiple custom-built and best-of-breed genomic tools – including AGRF’s bioinformatics services, Agilent’s Alissa Interpret, Illumina’s BaseSpace, Invitae’s ArcherDX, Australian Genomics’ Shariant, Genomics England’s PanelApp, and Cromwell. It’s modular, meaning that tools can be added to provide new capabilities as needed.
What cloud services does GenoVic use?
GenoVic is deployed within the Amazon Web Services cloud computing environment. Read the AWS case study.
Onboarding and support
How do I register and log into GenoVic?
Once your laboratory has been onboarded and you have been verified as a legitimate user, an account will be created for you to enable you to register and log into GenoVic for the first time. For more information, please contact the GenoVic team.
What are the GenoVic APIs and how do I use them?
These APIs enable users to interact directly with GOS, the genomic orchestration service at the heart of GenoVic. GenoVic users can perform tasks such as creating new GOS submissions and fetching past submissions. APIs exist to action tasks in Alissa Interpret to streamline tasks such as creating new patients, changing configuration settings and fetching patient test reports.
To make use of GenoVic's APIs, a GenoVic user is required to have an AWS account that has been authorised to interact with GOS. Once authorised, calls to the APIs can be made from any tool or language that supports AWS v4 signing.
How do I manage bioinformatics pipelines in GenoVic?
Bioinformatics pipelines are custom created for each lab to perform any post-processing steps required, before passing the data into a third-party variant interpretation software, such as Alissa Interpret.
These post-processing steps can include transforming genomics files (e.g. VCFs) into a format supported by Alissa Interpret, performing variant annotation (e.g. using VEP) and computing quality control statistics.
The bioinformatics pipelines in GenoVic are developed in collaboration with the GenoVic team. The post-processing pipelines are custom created using a standard bioinformatics pipeline language for each organisation. This is then executed by an application called Cromwell.
We are able to support the maintenance and upgrade of these pipelines.
Can I use my preferred bioinformatics tools with GenoVic?
Yes, if your tool uses a common workflow language. We will work with your bioinformaticians to map requirements and potential risks, and test any changes to your clinical pipeline.
Can I integrate my LIMS and EMR with GenoVic?
Many LIMS systems have limited capability to support API integration. Our operations team can guide you on how to generate clinical reports in GenoVic that are in a compatible format for most of the common EMRs.
What support will I get to onboard GenoVic?
You’ll have a GenoVic project manager and dedicated team. Informed by your workflow and requirements, they will design the most efficient pathway for onboarding GenoVic. And they’ll manage the project from end to end.
Will I get ongoing support?
Yes. Our operations team provide support services and capabilities to ensure that GenoVic and its core services are available and running smoothly for our users. We also work with our users to support new functionality and improve user experience.
You can use the GenoVic Support Portal to log service requests and track progress. The portal is the primary method of communication between GenoVic users, Citadel Health (the third-party operating entity for GenoVic) and software component providers such as Agilent.
How does GenoVic manage software updates?
Iterative development and continuous improvement are core to GenoVic. Our team uses best practice change and release processes to deploy software updates into the GenoVic production environment. This helps laboratories with their accreditation processes.
Data and security
How secure is GenoVic?
GenoVic is secure by design. It has an annual independent security assessment, together with expert security penetration testing and secure code review. We have specialist services to perform active monitoring and threat detection, and security is continually reviewed and updated.
GenoVic is deployed within the Amazon Web Services (AWS) cloud computing environment. Some of the world’s most successful organisations use AWS to deliver their technology platforms, so it operates to the world’s best security standards and offers industry-leading data resiliency and durability.
GenoVic uses industry standard encryption across every aspect, including all information in transit to and from GenoVic, ensuring that data is safe from unauthorised access. There are tight user access controls and detailed monitoring of access to the system and data within GenoVic.
What data is stored in GenoVic?
Genomic data files, patient and specimen information are all stored in GenoVic. Strict controls are in place to ensure no patient identifying information is released, unless authorised.