Clinical Beacons - towards v2

“Clinical Beacon” - Semantics & Logical Scope

[R<~>M] Wildcard Range Matches (proposed)

Instead of querying for a specific genomic variant (e.g. an A instead of a G at position 7577121 on chromosome 17), Beacons could also employ a “range match” concept, in which all or type specific variants mapping to a genomic interval are being identified.

[H—>O] Beacon Handover for Data Delivery

While the Beacon response should be restricted to aggregate data (yes/no, counts, frequencies …), the usage of the protocol could be greatly expanded by providing an access method to data elements matched by a Beacon query.

Release of Beacon v0.4

Beacon v0.4.0 has been released using the OpenAPI specification.

Release of Beacon v0.3

Beacon v0.3.0 Release

Range Queries and Structural Variants

Genome Coordinate use for Beacon Queries

GA4GH Beacon v1.0

The official Beacon API v1.0.0 has been approved through the GA4GH Product Approval Process.

FAQ - Precise Variants

Precise variants are such with annotated sequences of 0….n length, and bases of [ATCGN] for the referenceBases and alternateBases attributes (N for “not specified”).

Bio-metadata Query Support

Future Beacon API versions will support querying for additional, non-sequence related data types.

Beacon v2.0 - Towards a modular Beacon protocol empowering clinical use

Poster abstract for the GA4GH Plenary, Boston 2019

The Beacon Project is a Global Alliance for Genomics and Health (GA4GH) initiative for the federated discovery of genomic data in biomedical research and clinical applications. Originally implemented as a tool reporting the existence of Single Nucleotide Polymorphisms (SNP) in aggregated genomic data collections, the protocol has evolved towards more complex applications with increased functionality. Implementations of the current Beacon API enable the search for structural variants (e.g. deletions and duplications) and return richer responses (e.g. variant metadata and call counts).

Beacon v2 repositories

Beacon is an ever changing product, and it’s a good thing! Our partners in research and clinical settings are helping us improve version 2, who will soon be submitted for approval to GA4GH. Here is a list of resources, with their corresponding versions, to help you navigate our documentation while we prepare a beautiful repository just for you.

Version 2, draft 3:

Beacon v2 Filters

An v2 extension of the Beacon protocol will allow the query for additional data beyond genome variants, using a proposed filters extension. Such filters are thought to be prefixed attributes, where the (public or private) prefix becomes the basis of scoping the value to the correct database value.

Beacon v2 Code Repositories

These are the official repositories for version 2 of the specification and the Reference Implementation:

Beacon Flavours

Beacons may be able to increase their functionality through the development of distinct flavours, which can extend the core Beacon concept for specific use cases.