Beacon and Related Publications

This page lists publications about the Beacon protocol as well as related articles (e.g. GA4GH standards, publications of resources using the Beacon protocol ...).

cancercelllines.org - a Novel Resource for Genomic Variants in Cancer Cell Lines

DATABASE Article

Rahel Paloots and Michael Baudis

Database (Oxford). 2024 Apr 30:2024:baae030. doi: 10.1093/database/baae030
bioarXiv preprint (2023-12-13): https://doi.org/10.1101/2023.12.12.571281

DATABASE logo Abstract: Cancer cell lines are an important component in biological and medical research, enabling studies of cellular mechanisms as well as the development and testing of pharmaceuticals. Genomic alterations in cancer cell lines are widely studied as models for oncogenetic events and are represented in a wide range of primary resources. We have created a comprehensive, curated knowledge resource - cancercelllines.org - with the aim to enable easy access to genomic profiling data in cancer cell lines, curated from a variety of resources and integrating both copy number and single nucleotide variants (SNVs) data. We have gathered over 5,600 copy number profiles as well as SNV annotations for 16,000 cell lines and provide this data with mappings to the GRCh38 reference genome. Both genomic variations and associated curated metadata can be queried through the GA4GH Beacon v2 API and a graphical user interface with extensive data retrieval enabled using GA4GH data schemas under a permissive licensing scheme.

Availability and Implementation: Our resource is publicly available on the web at cancercelllines.org.

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Twelve quick tips for deploying a Beacon

Some hints for Beacon developers & implementers

Lauren A Fromont, Mauricio Moldes, Michael Baudis, Anthony J Brookes, Arcadi Navarro and Jordi Rambla

PLoS Comput Biol. 2024 Mar 1;20(3):e1011817.

Introduction: In the age of data-driven biomedical research and clinical practice, the sharing of genomic and clinical data for health research and personalized medicine has become an important contribu- tor to improved diagnosis and treatment. From the data owner’s perspective, potential benefits include improved treatments, personalization of healthcare practice, and more effective con- trol of disease proliferation. However, the requirement for high levels of data security to pro- tect sensitive information presents a barrier to data discovery and sharing.

Beacon is designed to enable the benefits of data discovery while minimizing the associated risks...

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Phenopacket-tools: Building and validating GA4GH Phenopackets

Bioinformatics tools and examples for working with the Phenopackets standard
Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. (2023) Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 18:e0285433.

Abstract The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Continue reading

Beacon reference implementtaion in Bioinformatics

Beacon V2 Reference Implementation: a Toolkit to enable federated sharing of genomic and phenotypic data

Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla

The Beacon team at the European Genome-phenome Archive (EGA) presents the Beacon v2 Reference Implementation (B2RI), a set of open-source software tools to enable federated sharing of genomic and phenotypic data.

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GA4GH Phenopackets: A Practical Introduction

Phenopackets v2 introduction with practical examples

Ladewig MS, Jacobsen JO, Wagner AH, Danis D, Kassaby BE, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA and Robinson PN

Abstract The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. Continue reading

The GA4GH Phenopacket schema defines a computable representation of clinical data

Phenopackets v2 publication

Cell Genomics logo

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, ... , Haendel MA, Robinson PN, The GAGHPMC.

Abstract Despite great strides made in the development and wide acceptance of standards for exchanging structured information about genomic variants, progress in standards for computational phenotype analysis for translational genomics has lagged behind. Phenotypic features (signs, symptoms, laboratory and imaging findings, results of physiological tests, etc.) are of high clinical importance, yet exchanging them in conjunction with genomic variation information is often overlooked or even neglected. Continue reading

Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond

Beacon v2 publication

Rambla J, Baudis M, Ariosa R, Beck T, Fromont LA, Navarro A, Paloots R, Rueda M, Saunders G, Singh B, Spalding JD.

Human Mutation. 2022 Mar 17. PMID:35297548

Abstract Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human genomic data, through providing simple "yes" or "no" responses to queries about the presence of a given variant in datasets hosted by Beacon providers.

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The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation.

Alex H. Wagner, Lawrence Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel L. Cameron, Melissa Cline , Malachi Griffith, Obi L. Griffith, ..., Melissa Konopko, Heidi L. Rehm, Andrew D. Yates, Robert R. Freimuth, Reece K. Hart

Wagner, Alex H. et al. Cell Genomics, Volume 1, Issue 2, 100027 doi:10.1016/j.xgen.2021.100027
bioRxiv. version 20212021.01.15.426843. (2021-01-15)

Note

Cell Genomics logoThis article was published as part of a special GA4GH edition of Cell Genomics. Continue reading

International federation of genomic medicine databases using GA4GH standards

Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, Ewan Birney

Thorogood, Adrian et al. Cell Genomics, Volume 1, Issue 2, 100032 doi:10.1016/j.xgen.2021.100032

Note

Cell Genomics logoThis article was published as part of a special GA4GH edition of Cell Genomics.

Abstract We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. Continue reading

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K. Bonfield, Tiffany F. Boughtwood, Guillaume Bourque, Sarion R. Bowers, Anthony J. Brookes, Michael Brudno, Matthew H. Brush, David Bujold, Tony Burdett, Orion J. Buske, Moran N. Cabili , Daniel L. Cameron, Robert J. Carroll, Esmeralda Casas-Silva, Debyani Chakravarty, Bimal P. Chaudhari, Shu Hui Chen, J. Michael Cherry, Justina Chung, Melissa Cline, Hayley L. Clissold, Robert M. Cook-Deegan, Mélanie Courtot, ..., Peter Goodhand, Kathryn North, Ewan Birney

Rehm, Heidi L. et al. Cell Genomics, Volume 1, Issue 2, 100029 doi:10.1016/j.xgen.2021.100029

Note

This article was published as part of a special GA4GH edition of Cell Genomics. Continue reading

The Progenetix oncogenomic resource in 2021

Article describing the current content & technical status of progenetix.org

Qingyao Huang, Paula Carrio Cordo, Bo Gao, Rahel Paloots, Michael Baudis

Database (Oxford). 2021 Jul 17;2021:baab043.

DATABASE logo

Abstract In cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cancer CNA profiles and associated metadata from published oncogenomic studies and data repositories with the aim to empower integrative analyses spanning all different cancer biologies. Continue reading

Federated discovery and sharing of genomic data using Beacons

Miroslav Cupak , Stephen Keenan , Jordi Rambla , Sabela de la Torre , Stephanie Dyke , Anthony Brookes , Knox Carey , David Lloyd , Peter Goodhand , Maximilian Haeussler , Michael Baudis , Heinz Stockinger , Lena Dolman , Ilkka Lappalainen , Juha Törnroos , Mikael Linden , John Spalding , Saif Ur-Rehman , Angela Page , Paul Flicek , Susheel Varma , Gary Saunders , Serena Scollen , Stephen Sherry , David Haussler , Beacon Project Team

Nat Biotechnol (2019), accepted 2019-01-23

Abstract The Beacon Project (github.com/ga4gh-beacon/) is a GA4GH initiative that is developing an open specification for genetic variation discovery and sharing. The project is demonstrating the willingness of international organizations to work together to define standards for, and actively engage in, genomic data sharing. In the two years since the project’s inception, over 90 Beacons have been lit by 35 organizations serving over 200 datasets. Continue reading