GA4GH Genome Beacons

A Driver Project of the Global Alliance for Genomics and Health GA4GH and supported through ELIXIR

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Specification

Clinical Beacons - towards v2

“Clinical Beacon” - Semantics & Logical Scope

In the original Beacon roadmap definitions, “clinical Beacon” (lower case) described a set of use cases instead of a specific Beacon flavour.

2020-03-23: more ...

[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.

@mbaudis 2018-11-16: more ...

[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.

As part of the mid-term product strategy, the ELIXIR Beacon team is evaluating the use of a “handover” protocol, in which rich data content (e.g. variant data, phenotypic information, low-level sequencing results) can be provided from linked services, initiated through a Beacon query (and possibly additional steps like protocol selection, authentication…). A discussion of the topic can e.g. be found in the Beacon developer area on Github (issue #114).

As of 2018-11-13, the handover concept has become part of the ongoing code development.

Possible scenario for a Beacon-initiated "handover" data delivery, involving pre- or post- query authentication steps. Importantly, the identification of matching "rich" data elements (e.g. information about biosamples or individuals) happens internally, and only a data access handle is exposed to the Beacon ecosystem.

@mbaudis 2018-10-18: more ...

Release of Beacon v0.4

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

@mbaudis 2018-01-24: more ...

Release of Beacon v0.3

Beacon v0.3.0 Release

@mbaudis 2016-05-31: more ...

Range Queries and Structural Variants

This page provides some more detailed description of the “4 positions match any continuous region” concept. General examples for variant queries can be found in the “Example Queries” documentation.

@mbaudis 2018-10-17: more ...

Genome Coordinate use for Beacon Queries

The coordinate system that should be used throughout GA4GH standards is 0-based half open.

@mbaudis 2019-03-14: more ...

GA4GH Beacon v1.0

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

@mbaudis 2018-10-02: more ...

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”).

Examples for variant queries can be found in the “Example Queries” documentation.

@mbaudis 2018-10-17: more ...

Bio-metadata Query Support

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

@mbaudis 2018-10-18: more ...

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).

@mbaudis 2019-10-21: more ...

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.

@tb143 | @mbaudis 2020-05-12: more ...

Beacon v2 Code Repositories

Today the Github repositories for the Beacon v2 specification have been created:

  • V2 Specification
  • ELIXIR Reference Implementation

@mbaudis | @sdelatorrep 2020-01-14: more ...

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.

@mbaudis 2018-10-24: more ...