Beacon v2 - Feature-rich Implementation of the Genomic Data Discovery Protocol

GA4GH 2022 Plenary Barcelona

Michael Baudis

The “Beacon” protocol - developed with support from ELIXIR, the European bioinformatics infrastructure organization, as a standard of the Global Alliance for Genomics and Health (GA4GH) - represents an emerging standard for an “Internet for Genomics”. While the initial version of the protocol served as a widely adopted test bed for the sharing of genomic variants over federated query systems connecting hundreds of internationally distributed resources, the version 2 of the protocol provides a framework for extended, metadata-rich query and response options in both public and restricted federated access scenarios.

With the adoption of Beacon v2 as a GA4GH standard in 2022, a current focus of the Beacon development lies is in the implementation of Beacon networks employing the new query and data delivery options, as well as in supporting the transition of existing Beacon instances to v2. In the context of ELIXIR, these developments are supported through a dedicated Beacon Infrastructure Service project as well as by supporting the utilization of Beacon throughout ELIXIR resources and platforms. As example of the latter, members of the ELIXIR hCNV community work to “beaconize” and network existing resources focussed on genomic copy number variations in the areas of rare diseases and cancer.

Here we highlight some of the new features of the Beacon v2 protocol and how the Progenetix oncogenomic resource serves as a driver for the Beacon protocol development, as well as to demonstrate extensive use of the Beacon protocol as foundation of a networked genomics resource including tight integration with ELIXIR community projects.