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Beacon v2 - Towards Flexible Use and Clinical Applications for a Reference Genomic Data Sharing Protocol

Personalized Health Technologies 2020

Michael Baudis

Beacons provide discovery services for genomic data using the Beacon API developed under the leadership of ELIXIR, as a key driver project of the Global Alliance for Genomics and Health (GA4GH). The Beacon protocol itself defines an open standard for genomics data discovery. It provides a framework for public web services responding to queries against genomic data collections, for instance from population based or disease specific genome repositories. Sites offering beacons can scale through aggregation in "Beacon Networks", which distribute single genome queries among a potentially large number of international beacons and assemble their responses.

As part of ELIXIR’s Beacon 2019-21 project work has started on a radically re-designed Beacon protocol, with the aim to provide a maximum of flexibility while closely adhering to data and security standards promoted by the international research community, and especially as part of projects in the GA4GH ecosystem. Upcoming features have been designed with view to biomedical applications, e.g. for variant evidence and annotation data or the retrieval of phenotype and other clinical data when used in secure (network) environments.

Recently, the efficient use of the Beacon protocol for non-human genome data has been demonstrated for COVID-19 repositories, showcasing the flexibility of the protocol.

Here I will provide an overview about the history, current status future directions of the Beacon protocol, including details about the Beacon+ service on top of the cancer genomics resource.