Suchergebnisse

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. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects. ; This study was funded by ELIXIR, the research infrastructure for life-science data and also by LaCaixa Foundation (grant number 004745/008034). Tim Beck was supported by a UKRI Innovation Fellowship at Health Data Research UK (MR/S003703/1). Anthony J. Brookes and Jordi Rambla were supported, in part, by the European Union's Horizon 2020 research and innovation program under the EJP RD COFUND-EJP #825575. Michael Baudis acknowledges funding under the BioMedIT Network project of Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN). ; Peer reviewed

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. The popularity of this concept has fostered the design of a version 2, that better serves real-world requirements and addresses the needs of clinical genomics research and healthcare, as assessed by several contributing projects and organizations. Particularly, rare disease genetics and cancer research will benefit from new case level and genomic variant level requests and the enabling of richer phenotype and clinical queries as well as support for fuzzy searches. Beacon is designed as a "lingua franca" to bridge data collections hosted in software solutions with different and rich interfaces. Beacon version 2 works alongside popular standards like Phenopackets, OMOP, or FHIR, allowing implementing consortia to return matches in beacon responses and provide a handover to their preferred data exchange format. The protocol is being explored by other research domains and is being tested in several international projects. ; This study was funded by ELIXIR, the research infrastructure for lifescience data and also by La Caixa Foundation (grant number 004745/ 008034). Tim Beck was supported by a UKRI Innovation Fellowship at Health Data Research UK (MR/S003703/1). Anthony J. Brookes and Jordi Rambla were supported, in part, by the European Union's Horizon 2020 research and innovation program under the EJP RD COFUND‐EJP #825575. Michael Baudis acknowledges funding under the BioMedIT Network project of Swiss Institute of Bioinformatics (SIB) and Swiss Personalized Health Network (SPHN)

The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical research projects. Its mission is to foster hosted data reuse, enable reproducibility, and accelerate biomedical and translational research in line with the FAIR principles. Launched in 2008, the EGA has grown quickly, currently archiving over 4,500 studies from nearly one thousand institutions. The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which conditions. Given the size and value of data hosted, the EGA is constantly improving its value chain, that is, how the EGA can contribute to enhancing the value of human health data by facilitating its submission, discovery, access, and distribution, as well as leading the design and implementation of standards and methods necessary to deliver the value chain. The EGA has become a key GA4GH Driver Project, leading multiple development efforts and implementing new standards and tools, and has been appointed as an ELIXIR Core Data Resource. ; Horizon 2020 Programme of the European Union [CORBEL [654248], ELIXIR-EXCELERATE [676559], Solve-RD [779257], EASI-Genomics [824110], EJP-RD [825575], CINECA [825775], EuCanCan [825835], EUCanshare [825903], ELIXIR-CONVERGE [871075]]; Wellcome Trust Global Alliance for Genomics and Health [201535/Z/16/Z]; UK Biobank; Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation [2017-171304 (5022)]; European Molecular Biology Laboratory (EMBL); LaCaixa Foundation [004745/008034]; [LCF/PR/CE20/50740008]. Funding for open access charge: LaCaixa Foundation [LCF/PR/CE20/50740008].