Federated discovery and sharing of genomic data using Beacons

Marc Fiume,J Dylan Spalding,Juha Törnroos,Gary Saunders,Maximilian Haeussler,David Lloyd,Jordi Rambla,David Haussler,Lena Dolman,Michael Baudis,Angela Page,Anthony J Brookes,Knox Carey,Peter Goodhand,Heinz Stockinger,Stephen Keenan,Ilkka Lappalainen,Paul Flicek,Susheel Varma,Stephen T Sherry ,Stephanie O M Dyke ,Miroslav Cupák ,Mikael Lindén ,S De La Torre ,Saif Ur-Rehman,Serena Scollen

doi:10.1038/s41587-019-0046-x

Abstract

To the Editor — The Beacon Project (https://github.com/ga4gh-beacon/) is a Global Alliance for Genomics & Health (GA4GH)1 initiative that enables genomic and clinical data sharing across federated networks. The project is working toward developing regulatory, ethics and security guidance to ensure proportionate safeguards for distribution of data according to the GA4GH-developed “Framework for Responsible Sharing of Genomic and Health-Related Data”2. Here we describe the Beacon protocol and how it can be used as a model for the federated discovery and sharing of genomic data.

Highlights

To the Editor — The Beacon Project is a Global Alliance for Genomics & Health (GA4GH)[1] initiative that enables genomic and clinical data sharing across federated networks
The Beacon protocol considers levels of data aggregation and obfuscation that can be added onto raw data representations to convey useful information without explicitly referring to specific samples or individuals
The conceptual and technical simplicity of the discovery question, “Have you observed this allele?”, enabled rapid and widespread adoption, and this has served to provide practical feedback for the GA4GH to continue to advance its best practices by holistically addressing regulatory, security and technical aspects of global genomics data sharing

Summary

Federated discovery and sharing of genomic data using Beacons

To the Editor — The Beacon Project (https://github.com/ga4gh-beacon/) is a Global Alliance for Genomics & Health (GA4GH)[1] initiative that enables genomic and clinical data sharing across federated networks. Access to Beacons is securable through institutional systems for authentication and authorization (for example, ELIXIR AAI), allowing hosts to enforce proportionate safeguards for datasets that may be sensitive and consented for use only by trusted individuals and/or for specific purposes. The ELIXIR hub (https://elixir-europe.org/) is integrating Beacon to connect geographically distributed data centers and unify their data access methodologies This will enable aggregate sharing of allelic observations between sites, a feature that is not yet available through its services. The Beacon protocol considers levels of data aggregation and obfuscation that can be added onto raw data representations (such as VCF) to convey useful information without explicitly referring to specific samples or individuals. Access can be controlled using established authentication and authorization protocols (for example, OpenID Connect and OAuth2.0) to enforce proportionate safeguards for datasets that may be sensitive and/or consented for use only by trusted individuals for specific purposes

Attribute disclosure attacks and reidentification

Patient record

Conclusions and perspectives