GENOMIC DATA REPORT

About the report:

A review of the Australian genomic data landscape

The collection, management and exchange of genomic data into healthcare delivery is critical to supporting better person-centred care, driving value to the health system and to building a thriving research ecosystem.

The delivery of mature genomics information management which supports the integration of genomics into mainstream health care requires a comprehensive and collaborative approach.

The genomics industry has an important role in delivering this maturity and ensuring that value is derived for all stakeholders.

As a united voice for the genomics industry, InGeNA has undertaken a review of the Australian genomic data landscape to identify the challenges and opportunities evidence regarding the management, governance, sharing and use of genomic data to support better outcomes for all Australians.

Engagement with stakeholders from industry, healthcare, research and consumers indicated three consistent themes, being a need for clarity in how the sector communicates, certainty about regulatory and compliance matters, and the importance of standards adoption to support the application of genomics to realise the value for people, the healthcare sector and the research community.

Genomic data in Australia

An industry perspective on clarity, certainty and standardisation

 

Genomic Data in Australia, the first industry-led report on data sharing and the challenges facing governance around genomic data, is published by the Industry Genomics Network Alliance (InGeNA). If, for any reason, you have trouble downloading the report, please email us for a direct link.

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David Bunker

David Bunker

InGeNA Chair

“There is a need for Australia to adopt a national approach to managing genomic data to benefit both clinical genomics and genomics research that meets community expectations confidentiality and security.

Finding a balance that meets the needs for all will require coordination across Commonwealth and state and territory governments, the community, research funders and institutions, commercial partners and private healthcare organisations.”

Monica Ferrie

Monica Ferrie

CEO, Genetic Support Network of Victoria

“Data is the foundation on which all genomic advancement is based. The genetic, undiagnosed, rare disease and cancer community understands this.

We need to improve public trust because we want our data collected, stored, used and shared securely and in ways that protect us. We want that data used to learn more about rare diseases, to develop treatments, to create natural histories, to change the trajectory for children, adults and families, to save lives.”

Executive summary

The collection, management and exchange of genomic data into healthcare delivery is critical to supporting better person-centred care, driving value to the health system and to building a thriving research ecosystem. The delivery of mature genomics information management which supports the integration of genomics into mainstream health care requires a comprehensive and collaborative approach.

The genomics industry has an important role in delivering this maturity and ensuring that value is derived for all stakeholders. With the establishment of the Industry Genomics Network Alliance (InGeNA) in 2020, it is now appropriate to examine industry’s role in leveraging the value of genomic data to support better health outcomes for Australians.

Engagement with stakeholders from industry, healthcare, research and consumers indicated three consistent themes, being a need for clarity in how the sector communicates, certainty about regulatory and compliance matters, and the importance of standards adoption to support the application of genomics to realise the value for people, the healthcare sector and the research community.

As a united voice for the genomics industry, InGeNA has undertaken a review of the Australian genomic data landscape to identify the challenges and opportunities evidence regarding the management, governance, sharing and use of genomic data to support better outcomes for all Australians. This report then considers the role that InGeNA can play in supporting the delivery of this potential.

By establishing shared positions regarding how genomic data is shared, managed and used in Australia, InGeNA can engage with governments at all levels, and with professional bodies, consumer groups, research groups and the broader healthcare sector to support and encourage the appropriate use of genomic data in Australia without the perception of self-interest that any one organisation may attract. Indeed, the very diversity of interests among the InGeNA membership ensures that a balanced and positive position can be found across a range of topics.

This report is intended primarily as an input to planning for InGeNA. However, it should also serve as a useful guide to the value industry can bring to public health, research and the broader sector.

Case Studies

Examples of the positive use of genomics data and data sharing at a person or population level can provide useful to understand different aspects of genomic data implementation. These case studies each demonstrate an issue that is important to the genomics industry.

Case Study 1 Innovation & Genomic Profiling in Australia by OMICO

Founded in 2019, Omico is an Australian non-profit, incorporated national cancer network, funded by government, industry and the community, Omico’s aims create a sustainable ecosystem enabling research-led cancer care by providing precision oncology based on genomic medicine. Omico has built a nationwide network of research and treatment centres that facilitate, support and promote clinical trials in genomic cancer medicine [144], [145].

To address the key barriers to the implementation of precision medicine, Omico has:

  • created a system for organisations to engage nationally in genomic cancer medicine in a uniform manner across tertiary referral hospitals/centres
  • progressively scaled activities to test fundamental concepts such as national engagement of academic centres/research for clinical trials
  • delivered a demonstrable ROI for government through commercial engagement.

By screening up to 80,000 Australian cancer patients, Omico aims to enrol an estimated 12,000 of those patients in clinical trials to access novel therapies over the next five years. Eventually, the objective is to establish universal genomic profiling of oncology patients in Australia using a public-private consortium consisting of government, biotechnology and pharmaceutical companies, contract research organisations, investment organisations and data and analytics providers.

As a national network of cancer research and treatment centres, Omico can deliver genomic cancer medicine clinical trials. Omico’s programs seek to understand the genetic causes of cancer, and develop strategies to detect cancers at an early, curable stage for those at increased cancer risk. Omico is currently operating three programs [144]:

  • Molecular Screening & Therapeutics (MoST) study: Using genomic technology to characterise molecular changes in a patient’s cancer that may help to identify a targeted therapy.
  • Genetic Cancer Risk in the Young (RisC) study: Studying the genetic variants contributing to inherited cancer.
  • Surveillance study in Multi-Organ Cancer prone syndromes (SMOC+): Investigating and evaluating the surveillance practices used for people at high risk of multi-organ cancer.

Omico acts as a single point of entry for industry groups seeking participants in clinical trials of new or repurposed therapies, providing access to appropriate patients of biomarker directed studies. InGeNA has a MOU arrangement with Omico and several InGeNA members are industry partners with Omico in their own right.

Omico is establishing a National Genomic Medicine Platform [145] that is hoped to result in improved health benefits for patients, enhancement of the quality and capabilities of the healthcare sector, increased economic activity and the creation of skilled jobs. While targeted at oncology genomics, such a platform would be consistent with the roadmap outlined in the NAGIM Blueprint and Australian Genomics is one of Omico’s partners.

The recent announcement by global clinical research organisation George Clinical of its collaboration with Omico to harness the National Genomic Medicine Platform [146] demonstrates the value placed by leading Australian and international clinical research groups in this platform, and the importance of collaboration between government, research and industry groups.

Case study 2: Genomics as a population health response to the COVID-19 pandemic

Australia, like countries worldwide, has been impacted by the COVID-19 pandemic caused by the SARS-CoV-2 virus. However, a surprising by-product of the pandemic has been increased public visibility of genomic sequencing, with daily media reports describing how public health officials use the technique to trace sources of infection [147].

Underpinning Australia’s response to the pandemic has been a national repository of genomic sequence data for the SARS-CoV-2 virus. The system, called AusTrakka, was developed by the Communicable Diseases Genomics Network (CDGN). AusTrakka allows health authorities around Australia and New Zealand to share, store, analyse and view aggregated COVID-19 genomic data in a single secure, and private repository. Fundamental to the system is a data sharing framework [148].

This framework allows authorised public health laboratories to upload genomic sequences to AusTrakka. A phylogenetic tree is constructed from the data each night that shows how specific sequences are related, support public health officials to trace the outbreak [147].

Specific data privacy rules are embodied in the framework, allowing public health laboratories to access their own information and aggregated data from other jurisdictions. The framework also outlines the governance model for the repository and provides procedures for research data requests within Australia and internationally [148], [149].

While the AusTrakka system was developed by public health bodies rather than industry participants, it demonstrates several factors that are important when InGeNA is engaging with government groups or consumers in general. Using a single system that transcends traditional state-based restrictions on data sharing has been fundamental to the pandemic response in Australia. It has also lifted the public awareness of genomics as a disease surveillance technique and reflected positively on the science [147]. It also demonstrates that data sharing arrangements can be achieved if an appropriate value proposition is identified.

Case study 3: Clinical genomics and data sharing in Victoria

When Melbourne Genomics was established in 2016, one of the key objectives of the program was to establish a common system for clinical genomics across several public hospitals in Melbourne. Because of the independent nature of the hospital system in Victoria, the solution required the ability to keep data separate for each hospital within a common cloud storage and analysis platform [44], [150].

The system, called GenoVic, now supports genomic testing at five organisations:

  • Victorian Clinical Genetics Services
  • The Royal Melbourne Hospital
  • Monash Health
  • Australian Genome Research Facility
  • The Alfred Hospital

Melbourne Genomics developed the platform using Amazon Web Services (AWS) secure cloud services hosted within Australia [62], and partnered with Agilent, the commercial developers of curation application Alissa Interpret [151], [152], to deliver a standards-based orchestration service using FHIR APIs to manage genomic and clinical data,

While the initial focus has been on delivery of clinical testing, the program has also integrated key applications to support better clinical outcomes. Real-time sharing of detailed scientific evidence about clinically interpreted variants is available using Shariant, a service delivered by Australian Genomics [153]. A knowledgebase of genes related to human disorders developed by Genomics England called PanelApp has been integrated and allows users to synchronise gene lists using a custom portal [154].

Melbourne Genomics have developed and deployed data access and sharing policies, procedures and agreements to support their research programs and are applying these learnings to clinical data sharing efforts [45].

This project demonstrated that a combination of commercial applications and a standards-based approach to solutions could deliver a functional clinical genomics platform. Further, due to the selection of commonly available standards, the platform can work with other commercial products that support these standards. However, without establishing data sharing agreements and underlying data governance, the technical solution may not have been as successful. Commercial partnering and common data governance arrangements are critical for InGeNA and industry participants.