Learn how GA4GH helps expand responsible genomic data use to benefit human health.
Learn how GA4GH helps expand responsible genomic data use to benefit human health.
Our Strategic Road Map defines strategies, standards, and policy frameworks to support responsible global use of genomic and related health data.
Discover how a meeting of 50 leaders in genomics and medicine led to an alliance uniting more than 5,000 individuals and organisations to benefit human health.
GA4GH Inc. is a not-for-profit organisation that supports the global GA4GH community.
To guide our collaborative, globe-spanning alliance, GA4GH relies on a Standards Steering Committee and an Executive Committee.
The Funders Forum brings together organisations that offer both financial support and strategic guidance.
The EDI Advisory Group responds to issues raised in the GA4GH community, finding equitable, inclusive ways to build products that benefit diverse groups.
Distributed across four Host Institutions, our staff team supports the mission and operations of GA4GH.
Curious who we are? Meet the people and organisations across six continents who make up GA4GH.
More than 500 organisations connected to genomics — in healthcare, research, patient advocacy, industry, and beyond — have signed onto the mission and vision of GA4GH as Organisational Members.
These core Organisational Members are genomic data initiatives that have committed resources to guide GA4GH work and pilot our products.
This subset of Organisational Members whose networks or infrastructure align with GA4GH priorities has made a long-term commitment to engaging with our community.
Local and national organisations assign experts to spend at least 30% of their time building GA4GH products.
Anyone working in genomics and related fields is invited to participate in our inclusive community by creating and using new products.
Wondering what GA4GH does? Learn how we find and overcome challenges to expanding responsible genomic data use for the benefit of human health.
Study Groups define needs. Participants survey the landscape of the genomics and health community and determine whether GA4GH can help.
Work Streams create products. Community members join together to develop technical standards, policy frameworks, and policy tools that overcome hurdles to international genomic data use.
GIF solves problems. Organisations in the forum pilot GA4GH products in real-world situations. Along the way, they troubleshoot products, suggest updates, and flag additional needs.
NIF finds challenges and opportunities in genomics at a global scale. National programmes meet to share best practices, avoid incompatabilities, and help translate genomics into benefits for human health.
Communities of Interest find challenges and opportunities in areas such as rare disease, cancer, and infectious disease. Participants pinpoint real-world problems that would benefit from broad data use.
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All GA4GH standards, frameworks, and tools follow the Product Development and Approval Process before being officially adopted.
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4 Oct 2018
Three new deliverables from the GA4GH Connect strategic roadmap, released today at the GA4GH 6th Plenary Meeting, address issues of variant discovery, reference sequence harmonisation, and cloud computing.
BASEL (October 4, 2018) — The Global Alliance for Genomics and Health (GA4GH) today announced the release of three new interoperability standards from the GA4GH Connect strategic roadmap: Beacon API V1.0.0, refget API V1.0.0, and Workflow Execution Service (WES) API V1.0.0.
Part of a larger suite of standards that together aim to create a federated network for responsible, international genomic data sharing, the new standards address issues of data discovery, reference sequence harmonisation, and cloud computing. They are designed to work both independently or in concert, as part of an end-to-end solution for responsible genomic data sharing.
“Together, these schemas and protocols overcome the most pressing technical challenges of sharing genomic and health related data that will help all of us in the genomics community as we work to advance precision medicine,” said Ewan Birney Chair of GA4GH and Director of the European Bioinformatics Institute (EMBL-EBI).
GA4GH CEO Peter Goodhand said, “Active contributors from a diverse cross section of the genomics community have been working hard over the past several months to bring these new deliverables to life. They represent the first major roll out of our multi-year strategic plan, which we believe will advance human health and medicine by enabling real-world genomic data sharing in the foreseeable future.”
About the New Deliverables
Beacon allows institutions to serve their data as a web-accessible service that users may query for information about a specific allele. Currently, researchers or clinicians interested a particular allele must go through lengthy access protocols before even learning whether a dataset contains the allele of interest. Among other benefits, the Beacon API reduces this resource requirement by providing an immediate yes/no answer to simple queries.
Beacon, which grew out of a GA4GH project to demonstrate the willingness of the genomics community to share data, has been implemented across ELIXIR, the European infrastructure for life sciences data, as well as dozens of additional institutions around the globe.
“The new release of the Beacon API builds on existing work by adding support for additional types of genomic variants, making it an even more powerful tool for molecular geneticists around the globe to use in their variant classification efforts,” said said Marc Fiume, Co-Founder and CEO at DNAstack and co-lead of the GA4GH Discovery Work Stream, which, together with ELIXIR, maintains the Beacon API. “By demonstrating the ELIXIR Authorization and Authentication Infrastructure (AAI) with the reference implementation, we have also enabled additional risk mitigation strategies to ensure the data served by Beacons is as secure as possible.”
Refget harmonizes the way reference genome sequences are named, making it easier to ensure that analyses are reproducible regardless of the reference sequence used. While many institutions use different names to refer to the same reference, or the same name to refer to different references, the refget API assigns a unique digital identifier to the sequences themselves, rather than the names used to store them. It also provides a standard API to access sequences, sub-sequences, and their metadata.
Refget underlies the increasingly popular CRAM file format for storing genomic read data, which calls the reference sequence at EMBL-EBI each time it is used (rather than compressing the reference data into the file alongside the reads as do more traditional formats). Refget makes it possible for users to access “mirrors” of the EBI API with deployments within popular compute clouds due to arrive over the coming months.
“Reference sequences are fundamental to how genomic analysis is performed as they provide a baseline of knowledge of the human genome. Without a clear unambiguous link back to that baseline it can be challenging to compare, aggregate and share knowledge between researchers and clinical settings,” said Andrew Yates, Team Leader, Genomics Technology Infrastructure at EMBL-EBI and co-lead of the refget subgroup of the GA4GH Large Scale Genomics Work Stream. “I am confident that in time refget will be so fundamental to how reference sequences are referred to and accessed we will wonder how we managed without it.”
WES allows users to execute the same scientific tools and workflows in a variety of clouds, platforms, and environments without modification. In particular, WES enables users to submit workflow requests to workflow execution systems, and to monitor their execution.
“In order for researchers to analyze the world’s collective genomic information, they need to be able to execute the same scientific workflows in a variety of environments without modifying them each time around,” said Brian O’Connor, Technical Director of the UCSC Computational Genomics Platform and co-lead of the Cloud Work Stream, which maintains the WES API. “WES provides a mechanism to do exactly that, ensuring compatible results when running genomic alignment, variant calling, variant interpretation, and more.”
The Global Alliance for Genomics and Health (GA4GH) is an international, nonprofit alliance formed in 2013 to accelerate the potential of research and medicine to advance human health. Bringing together 500+ leading organizations working in healthcare, research, patient advocacy, life science, and information technology, the GA4GH community is working together to create frameworks and standards to enable the responsible, voluntary, and secure sharing of genomic and health-related data. All of GA4GH builds upon the Framework for Responsible Sharing of Genomic and Health-Related Data.