Beacon Project News and Updates


Federated genomic discoveries: Deploying the GA4GH Beacon protocol

Virtual Seminar
GHGA Lecture Series

GHGA logo With the ever increasing amount of genomic data produced in the context of research studies, population analyses and medical diagnostics the need for access to genomic information beyond administrative or geographic boundaries has become a matter of eminent importance. Continue reading

GA4GH Connect April 2024 in Ascona

Spring 2024 GA4GH Connect working meeting co-organized by our group

elixir logo We're proud to host the next Spring GA4GH Connect meeting in April 2024 at the Congressi Stefano Franscini on the Monte Verità in Ascona. This will provide an excellent opportunity for Swiss genomics and bioinformatics to, well, connect with the international "genomics and health" community and projects.

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Discovery Co-Lead Appointed

GA4GH Discovery Work Stream welcomes new Co-Lead Nara Sobreira of Johns Hopkins Medicine

Nara Lygia De Macena Sobreira, associate professor of genetic medicine at Johns Hopkins University School of Medicine, joins the GA4GH Standards Steering Committee as Discovery Work Stream Co-Lead.

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Beacon v2 standard highlighted during the GA4GH April Connect 2023

Last month Beacon was present at the GA4GH Connect 2023, the working meeting to advance the GA4GH Roadmap and gather feedback on product development and needs.

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Beacon v2 at the International Congress of Human Genetics with hands-on sessions on Discovery

These Hands-on workshops will take place on February the 26th and 27th, in the framework of the International Congress of Human Genetics (ICHG), that is being held in Cape Town from February 22 – 26.

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Beacon v2 - Onboarding Strategies & Feature Examples

Beacon Sessions at GA4GH Connect

Michael Baudis

The Beacon Sessions at GA4GH Connect November 2022 targeted the migration of existing and implementation of new v2 Beacons, with emphasis on the "how to get there easily" rather than on all Beacon v2 features. Continue reading

Beacon training course: How to make COVID-19 sensitive data discoverable using Beacons

The online workshop BEACON - How to make sensitive data discoverable will take place on November 2 and 3. The European Genome-phenome Archive (EGA) Beacon Team will provide a special hands-on training session for the BY-COVID partners for "Beaconising" the datasets.

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Genomics Data Federation through Global Alliance for Genomics and Health Standards: Development and Implementation of the GA4GH Beacon Protocol

Seminar Yonsei University Medical School Seoul

Michael Baudis

In this Seoul meeting presentation Michael introduces the Global Alliance for Genomics and Healt and its involvement in Genomics standards development, followed by a discussion of the Beacon protocol and the role of the Progenetix resouce in its development. Continue reading

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. Continue reading

Beacon v2 will be at the European Conference on Computational Biology with a Workshop on tools and techniques to make sensitive data discoverable

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.

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GA4GH 2022 — Beacon v2 standard highlighted at the GA4GH plenary

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.

CosmoCaixa building in Barcelona.
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Progenetix & BeaconPlus - An open cancer genomics resource on a stack of Beacon code...

ELIXIR All Hands Amsterdam 2022

Michael Baudis

Here Michael provides some overview of the multi-year trajectory of the Beacon API development, and how BeaconPlus & Progenetix have been utilized for "implementation driven design".

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Beacon implementations: Beaconize your genomics data

Beacon v2 Workshop at ELIXIR All Hands

Hosts: Lauren Fromont, Michael Baudis & Jordi Rambla

One of the main bottlenecks in human genomics research is the lack of tools for federated discovery of identifiable genomics data that requires tight privacy controls. This problem needs even more attention since genomics data sees an ever greater application in clinical settings, such as for medical diagnostic or prognostic purposes, in rare diseases or cancer. Currently, most of the molecular analyses generated in hospitals are not utilised for further research due to lack of proper tools for an interoperable and ethical sharing of the data. The Beacon project (ELIXIR, see also the Global Alliance in Health and Genomics for the standard) aims to alleviate the problem of genomics data sharing through enabling the search of genomic variants and associated information without jeopardising the privacy of the dataset. This way, any hospital or research entity can choose to 'beaconize' their dataset without compromising its privacy or ownership.

With growing interest from the community in the implementation of the Beacon protocol into resources and workflows, the release 2.0 introduces new features considered important by the community: e.g. queries by entity type, filters, schema versions, and access levels. While both the research and the clinical community recognizes the value of these additions, practical implementation of the Beacon could still be a challenging task, especially for institutions with limited IT resources. The ELIXIR implementation studies (2019-2021; 2022-2024) aim to develop a reference implementation so researchers and clinicians can use it as an example to deploy their own Beacon without needing extensive knowledge on how to build an API.

This workshop has two objectives, to provide participants with:

1- Demos and insights on Beacon implementations. For this objective we will invite early Beacon v2 implementers who provided valuable feedback to the specification and will share their use-cases and experiences: Michael Baudis (Progenetix), Tim Beck (Café Variome), and Carles Hernandez (CNAG-CRG).

2- A training session on how to d eploy a Beacon using the reference implementation. For this objective we will invite members of the European Genome-phenome Archive (Manuel Rueda) who support Beacon deployment in hospitals and clinical institutions and will provide a hands-on session.

Beacon version 2 is a highly expected product in the genomics research and clinical communities. Now that the Beacon community has released a stable version, it is time to provide beacon implementers guidelines and resources to implement or deploy their own Beacons to foster data discovery and data re-use.

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The Beacon: a data discovery solution in genomics and health

Beacon v2 Webinar at CINECA

Presenter: Lauren Fromont

Personalised medicine is making great progress: facilitating secure access to human data for researchers and clinicians has become key to achieving this. The Beacon aims to promote this by delivering a federated infrastructure for data discovery of human genetic and phenotypic data.

The Beacon is a protocol for sharing information about the presence or absence of a specific mutation in a given dataset. The latest version (v2) of the Beacon also allows to: filter by variables or interest (e.g. gender or age), trigger the data access process, and consult clinical annotation about the variants found, among others. Further, it inserts a brand new feature that was developed for CINECA’s needs: a cohort model, allowing researchers to find appropriate populations (e.g., a group of patients with a specific disease) to help answer their research questions.

Watch the public recording of the presentation here

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Beacon v2 submitted to GA4GH

Beacon v2 was submitted to the Global Alliance for Genomics and Health and is now available for public review! Our specification is available on Github and several implementations are already available!

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A Standardized Format for Federated Genomic Data Exchange

The GA4GH Beacon Protocol Presented at BC2 Basel 2021
Session "Federating computational analyses with GA4GH standards"

Michael Baudis

BC2 logoDuring the "Federating computational analyses with GA4GH standards" workshop at BC2 2021 Michael presented history and the current status of the Beacon project, as well as its integration with specific data resources and analysis initiatives.

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Beacon Workshop at ELIXIR AllHands

Chairs: Gary Saunders, Juha Tornroos, Michael Baudis, Dylan Spalding, Lauren Fromont, Jordi Rambla

Beacon now stands as the ‘default’ data discovery solution in GA4GH and ELIXIR portfolios, and is increasingly adopted by third-party projects. Beacons become particularly successful through their aggregation in Beacon networks, which provide a way to query many genomic variant resources through a central federation node while receiving aggregated responses all at once. Both Beacon and Beacon Network are part of the 1+MG and B1MG service catalogs and represent core discovery solutions in ELIXIR across the Federated Human Data, Rare Diseases, and human Copy Number Variation Communities.

During this workshop we will discuss:

1) progress of the fruitful collaboration with the GA4GH Beacon community 2) latest developments of the ELIXIR Beacon project including deployment tested instances in clinical and non-clinical settings (via various H2020 projects, GA4GH Driver projects and ELIXIR partners) 3) extensions to the ELIXIR Services specification in order to manage Beacon v2 instances 4) security features of Beacon v2 according to real world needs 5) an extended and improved ELIXIR Beacon Network service.

As a result this workshop will describe how Beacons that are integrated in the ELIXIR Beacon Network Infrastructure can further the contribution and implementation of GA4GH standards, and empower nodes to be part of the federated sensitive human data infrastructure.

Agenda here

All hands 2021
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Progenetix, Beacon and GA4GH at RDA

Research Data Alliance - RDA Virtual Plenary 17

Concepts | Status | History | Outlook

Michael Baudis

Research Data Alliance - RDA Virtual Plenary 17

This seminar gives an overview of current state of the Progenetix Beacon project and the overall connection to the Global Alliance for Genomics and Health (GA4GH).

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GA4GH Connect - Beacon v2 Structural Variants

GA4GH Connect 2021

Michael Baudis

Beacon v2 Structural Variants [slides]

Lauren Fromont & Jordi Rambla

Beacon v2 Cohort model [slides]
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Happy 2021 from the Beacon Team

The Beacon Team wishes everybody a happy and healthy 2021! We're excited about our upcoming Beacon v2, expected to be finalized later this year.

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GA4GH Beacon v2 at GA4GH Plenary

Evolving Reference Standard for Genomic Data Exchange

GA4GH 8th Plenary

Gary Saunders, Jordi Rambla de Argila, Anthony Brookes, Juha Törnroos and Michael Baudis

For the ELIXIR Beacon project, GA4GH Discovery work stream and the international network of Beacon API developers

The Beacon driver project was one of the earliest initiatives of the Global Alliance for Genomics and Health with the Beacon v1.0 API as first approved GA4GH standard. Version 2 of the protocol is slated to provide fundamental changes, towards a Internet of Genomics foundational standard: * requests beyond genomic variants ("filters") * payload responses, secured through open AAI * aligning w/ GA4GH standards (Phenopackets, VRS, DUO...) through SchemaBlocks {S}[B] * Working with international partners on deployment of advanced implementations

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Progenetix - A cancer genomics reference resource around GA4GH standards

GA4GH 8th Plenary

Michael Baudis

The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts.

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CNV Beacon at Biohackathon Europe

For the Biohackathon Europe (Nov 18-22), the hCNV project submitted a proposal which was accepted for the event near Paris.

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GA4GH 2019 — Beacon v2: 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).

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Barcelona Goes Zurich - Beacon Code Alignment Workshop

The Zurich meeting is intended to align the current development version of the Beacon API and the Beacon+ driver, and to improve the documentation structure of the Beacon project.

In another part of the 2-days meeting we will explore further the concept and possible implementation of "Evidence Beacons", together with developers from the SVIP project.

The tentative agenda for the meeting is linked below.

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ELIXIR Beacons at ELIXIR All Hands 2019 Workshop

Purpose of this workshop:

  • Update on GA4GH Beacon API and Beacon Network developments
  • Demonstrate ELIXIR Beacon implementation of new API and Network features
  • Present the future vision for Beacons - Beacon 2.0


Please see the link below for more information.

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Beacons Hackathon Stockholm

On March 7, Beacon team members from ELIXIR and DNAstack will meet at the SciLife Center Stockholm for Face-to-face meeting and Hackathon.

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Plant Beacons Hackathon Bordeaux

The hackaton took place the 2019-02-28 in the center of Bordeaux in the room "RE" of the former Law Faculty of the University of Bordeaux.

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