Genomical FAQ - Genomical

How Genomical works

What is Genomical?

Genomical is a digital health platform for genomics. It consists of several components – some custom-built, some procured from third-party vendors – integrated into a single, modular suite of services. Genomical has a unique orchestration service that moves data through an entire test workflow, and stores data securely in the AWS cloud.

Genomical underpins the entire genomic testing process: from sequenced genome data to analysis, interpretation and clinical reports. It enables medical laboratories to store genomic data securely, access it for further analysis, and even share it in line with patients’ wishes.

Why use a common platform for genomic data management?

To eliminate costly re-sequencing and duplication of effort
To ensure genomic data is stored and accessed securely by laboratories
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 privacy and security standards. Genomical uses a security and privacy-by-design approach as opposed to bolting on security controls after the fact. Genomical 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 Genomical to facilitate the analysis and curation of targeted sequencing panels, whole exome sequencing and whole genome sequencing for inherited conditions and cancer.

How is Genomical different to other genomic testing tools?

Genomical lets you use the tools you want and run the reports you need. It doesn’t tie you to a single vendor – it interfaces with the best tools available from a range of providers. Its custom-built orchestration service brings all these tools together to create a streamlined workflow.

Genomical uses healthcare interoperability standards, meaning it can create reports that can be read by your laboratory information system. It’s been tested for integration with a range of systems used by medical laboratories.

Finally, Genomical has been shown to create efficiencies. One laboratory saved over 5 hours per testing batch by eliminating manual processes from genomic testing.

Which laboratories use Genomical?

The Victorian Clinical Genetics Service, Royal Melbourne Hospital, Australian Genome Research Facility, Monash Health, Austin Health and Alfred Health are all currently using Genomical to support accredited genomic sequencing tests.

What tools can be used with Genomical?

Genomical can interface with several best-of-breed tools currently on the market. These include AGRF’s bioinformatics services, Agilent’s Alissa Interpret, Illumina’s BaseSpace, Invitae’s ArcherDX, Australian Genomics’ Shariant, Genomics England’s PanelApp, CSIRO’s Ontoserver and Cromwell. It’s modular, meaning that tools can be added to provide new capabilities as needed.

What cloud services does Genomical use?

Genomical is deployed within the Amazon Web Services (AWS) cloud computing environment using serverless architecture enabling access to almost unlimited compute and storage while only paying for what is used. Read the AWS case study.

Implementation and support

How do I register and log into Genomical?

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 Genomical for the first time.

Genomical is accessed using a secure portal with user authentication. This portal will enable your organisation to:

Submit your data for genomic analysis
View your metric data as part of the submission
Apply your post processing pipelines orchestrated by Genomical
Review the progress of your submissions
Gain access to data previously submitted by your laboratory
Manage the users who access the portal and the functionality they can use
Review audit logs of all the events that occur within the portal by all of your organisation’s users
Share genomic data with other authorised Genomical organisations

What are the Genomical APIs and how do I use them?

Genomical’s Application Programming Interfaces (APIs) are based on the modern health information data standard, FHIR, and HL7 V2. These features enable the automated flow of data from one system to the next without user intervention, tying together key information and workflows from separate systems.

These APIs enable users to interact directly with GOS, the Genomic Orchestration Service at the heart of Genomical. Using these APIs, Genomical users can perform tasks such as creating new GOS submissions and fetching past submissions. APIs also exist to action tasks in Alissa Interpret to streamline tasks such as creating new analyses, changing configuration settings and fetching patient test reports.

To make use of Genomical’s APIs, a Genomical 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 Genomical?

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 or other preferred tool.

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 Genomical are developed in collaboration with the Genomical team. The post-processing pipelines are custom created for each organisation and are developed in an iterative manner. We are also able to support the maintenance and upgrade of these pipelines.

Can I use my preferred bioinformatics tools with Genomical?

Yes. Many different tools can be used with Genomical. We can assess and work with your preferred tool vendor to ensure that they can use our API framework.

Can I integrate my LIMS and EMR with Genomical?

Many LIMS systems have limited capability to support API integration. Our interoperability team can guide you on how to generate clinical reports in Genomical that are in a compatible format for most of the common EMRs.

What support will I get to implement Genomical?

You’ll have a Genomical project manager and implementation team. Informed by your workflow and requirements, they will design the most efficient way to get Genomical working for your organisation, and work with your team every step of the way.

Will I get ongoing support?

Yes. Our operations team provide support services and capabilities to ensure that Genomical 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 Genomical Support Portal to log service requests and track progress.

How do you do software updates?

Iterative development and continuous improvement are core to Genomical. Our team uses best practice change and release processes to deploy software updates into the Genomical production environment. This helps laboratories with their accreditation processes.

Data and security

How secure is Genomical?

Genomical is secure by design and includes the following controls:

Regular independent security assessments, together with expert security penetration testing and secure code reviews
Specialist tools that perform active monitoring and threat detection
Deployment within the Amazon Web Services (AWS) cloud computing environment, which operates to the world’s best security standards and offers industry-leading data resiliency and durability
Industry standard encryption across every aspect, including all information in transit to and from Genomical, and all information stored at rest in Genomical
Tight user controls including secure two-factor authentication (2FA) access control and detailed monitoring of data access

What data is stored in Genomical?

Genomic data files and patient and specimen information are all stored in Genomical. Your organisation remains in control of the data. Your organisation’s data is stored separately from data belonging to any other organisations who use Genomical. Strict controls are in place relating to ensure no patient-identifying information is released.

Genomical does not hold photographs, diagrams of family trees, financial information, driver licences, passports or Medicare information.