GA4GH 2020 Connection Demos highlight the value of interoperability in genomics 

29 Sep 2020

GA4GH has announced the release of its 2020-2021 Strategic Roadmap as well as the 2020 GA4GH Connection Demos.

The Global Alliance for Genomics and Health (GA4GH) has announced the release of its 2020-2021 Strategic Roadmap as well as the 2020 GA4GH Connection Demos. The news was delivered during opening remarks of the virtual GA4GH 8th Plenary Meeting, which drew over 700 attendees from more than 50 countries.

The GA4GH Strategic Roadmap outlines strategies, standards, and policies for enabling the responsible sharing of genomic and related health data. The 2020-2021 version consists of 43 deliverables that aim to address needs in the areas of data use and researcher identities, variation representation and annotation, federated analysis, privacy and security, regulatory and ethics, discovery, clinical and phenotypic data capture, and large scale genomics.

A gap analysis informed the high level strategic vision outlined in the 2020-2021 Roadmap and identified three key community imperatives for GA4GH to successfully advance responsible data sharing: 

  1. improve internal and external interoperability and alignment, 
  2. improve implementation support for technical standards, and 
  3. engage more closely with the healthcare community.

To address the first two imperatives, members of the GA4GH community launched the Federated Analysis Systems Project (FASP), a collaborative effort between several Work Streams and Driver Projects to integrate multiple GA4GH standards and implement them at multiple institutions. The demonstrations presented at the plenary meeting showed how researchers can leverage these implementations to discover controlled access data hosted in one computational environment and analyze them in another, all following best practices in privacy and security. 

Given institutional, regional, national, and international regulations around sharing of genomic and related health data, the ability to perform federated discovery, access, and analysis of controlled access genomic data is of critical importance. The outputs of FASP presented at the 8th plenary meeting, summarized below, mark a major milestone along the GA4GH Roadmap to enable global genomic data sharing:

  1. Horizontal Connection Demo: To emphasize progress of GA4GH in the real world, these demos show reproducibility of analyses run in different environments and portability across analytics workspaces. A GWAS analysis of 1000 Genomes data is replicated across implementations of GA4GH APIs hosted by several organizations—including DNAstack, Terra (Broad Institute/Verily), ELIXIR, and Seven Bridges—implementing GA4GH APIs.
  2. Vertical Connection Demo: Demonstrating the value of GA4GH standards used in combination, DNAstack has integrated multiple standards — Workflow Execution Service (WES), Data Repository Service (DRS), Passports, and Search — to enable discovery, access, and analysis of controlled data. Using real-world implementations of these open standards, this demo highlights how users can search for genomic data of interest and pass the results to inputs of a bioinformatics workflow. The demo includes data hosted on two different cloud computing platforms, Google Cloud Platform and Amazon Web Services.
  3. Cross Platform Connection Demo: Finally, driven by researcher needs in pediatric cancer and other diseases, the FASP team has begun work to explore how a researcher might combine the GA4GH components provided by many different institutions to aggregate data for analysis. This demonstration uses implementations of multiple GA4GH standards and data from multiple GA4GH Driver Projects and organizations—including several of the US National Institutes of Health, the European Genome-phenome Archive, Seven Bridges, and Google. Additionally, this initiative provides a social and technical framework for engaging additional data and tool providers around the globe in 2021.

“The Connection Demos are an enormous success for the members of the GA4GH Work Streams, who have collectively dedicated thousands of hours over the last three years toward standards development,” said Ewan Birney,  Deputy Director General of the European Molecular Biology Laboratory (EMBL), Director of EMBL’s European Bioinformatics Institute (EMBL-EBI), and Chair of GA4GH. “The demos show how this community’s work will enable interoperability across the genomics endeavour.” 

“The gap analysis really drove home the fact that while GA4GH standards development may be on the right track, those standards will be less impactful if they aren’t quickly adopted and pressure tested at institutions with real use cases,” said Heidi Rehm, Medical Director at the Broad Institute, Chief Genomics Officer at Massachusetts General Hospital (MGH), and Vice-Chair of GA4GH, who co-led the gap analysis with Andrew Morris, Director of Health Data Research UK (HDR UK). “The GA4GH Connection Demos go a long way toward instantiating this real-world utility in the research space, but there is still more work to be done in the clinical setting.”

The third community imperative outlined in the 2020/2021 GA4GH Strategic Roadmap focuses on enabling better cross talk between GA4GH and the clinical community. In order to address this need, GA4GH will continue to advance its nascent Genomics in Health Implementation Forum, a collective of large scale initiatives focused on implementing genomics into clinical care which have committed to sharing resources, knowledge, and data using GA4GH standards. In 2021, GA4GH will expand on this work by launching a Clinical Advisory Group, which will bring together key stakeholders from a broader range of healthcare sectors to ensure its work meets the needs of this diverse community. 

“The Genomics in Health Implementation Forum brings together large scale genomics initiatives ready and willing to share resources, knowledge, and (where possible) data, as well as a commitment to adopt GA4GH standards” said Kathryn North, Director of Murdoch Children’s Research Institute, Vice-Chair of GA4GH, and co-lead of the GHIF. “The establishment of the new Clinical Advisory Group will help us expand these efforts by bringing in a broader scope of healthcare stakeholders not yet represented within the GHIF.”

Finally, GA4GH will continue its efforts to align with external standards bodies such as HL7 and CDISC, which are the primary mechanisms by which hospitals, healthcare systems, and clinical research and drug development systems harmonize data. This work also dovetails with the first community imperative, which is focused not just on internal alignment of GA4GH standards, but also alignment with external standards in order to minimize redundancy and incompatibility. 

“The Global Alliance for Genomics and Health has pulled off an enormous feat over the last few years, driving the conversation—and indeed the work—to break down silos within the genomics community and unlock the power of data to fuel precision medicine around the world.” said Morris. “I look forward to seeing this work continue as they advance the deliverables outlined in the 2020-2021 roadmap and beyond.”

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