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 ...
While the Beacon v1 response was restricted to aggregate data (yes/no, counts, frequencies …), the usage of the protocol can be greatly expanded by providing an access method to data elements matched by a Beacon query. Since November 2018, Beacon v1.n has included support for 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 query1.
An early discussion of the topic can e.g. be found in the Beacon developer area on Github. As of 2018-11-13, the handover concept had become part of the code development. ↩
@mbaudis 2022-04-06: more ...
Jordi Rambla, one of the key Beacon v2 leaders, will present the Beacon v2 Specification in Barcelona for the Global Alliance for Genomics And Health (GA4GH) 10th Plenary Meeting.
@AnaT-DCO 2022-08-02: more ...
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 | @laurenfromont 2019-10-21: more ...
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 ...
Future Beacon API versions will support querying for additional, non-sequence related data types.
@mbaudis 2018-10-18: more ...
The Workshop “Tools and techniques to make sensitive data discoverable (Use-cases, hands-on session of Beacon implementation)” will take place on September 15th, in the framework of the 21st European Conference on Computational Biology (ECCB). This workshop aims to provide knowledge and hands-on sessions about the discoverability of sensitive genomics and clinical data without jeopardizing the privacy or ownership of such datasets.
@AnaT-DCO 2022-08-11: more ...
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 ...