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

Rambla, Jordi / Baudis, Michael / Ariosa, Roberto / Beck, Tim / Fromont, Lauren A / Navarro, Arcadi / Paloots, Rahel / Rueda, Manuel / Saunders, Gary / Singh, Babita / Spalding, John D / Törnroos, Juha / Vasallo, Claudia / Veal, Colin D / Brookes, Anthony J

Human mutation

2022 Volume 43, Issue 6, Page(s) 791–799

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 ... ...

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. 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.
MeSH term(s)	Genomics ; Humans ; Information Dissemination/methods ; Phenotype ; Rare Diseases ; Software
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.24369
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Article ; Online: GA4GH Passport standard for digital identity and access permissions.

Voisin, Craig / Linden, Mikael / Dyke, Stephanie O M / Bowers, Sarion R / Alper, Pinar / Barkley, Maxmillian P / Bernick, David / Chao, Jianpeng / Courtot, Mélanie / Jeanson, Francis / Konopko, Melissa A / Kuba, Martin / Lawson, Jonathan / Leinonen, Jaakko / Li, Stephanie / Ota Wang, Vivian / Philippakis, Anthony A / Reinold, Kathy / Rushton, Gregory A /

Spalding, J Dylan / Törnroos, Juha / Tulchinsky, Ilya / Guidry Auvil, Jaime M / Nyrönen, Tommi H

Cell genomics

2021 Volume 1, Issue 2, Page(s) None

Abstract: The Global Alliance for Genomics and Health (GA4GH) supports international standards that enable a federated data sharing model for the research community while respecting data security, ethical and regulatory frameworks, and data authorization and ... ...

Abstract	The Global Alliance for Genomics and Health (GA4GH) supports international standards that enable a federated data sharing model for the research community while respecting data security, ethical and regulatory frameworks, and data authorization and access processes for sensitive data. The GA4GH Passport standard (Passport) defines a machine-readable digital identity that conveys roles and data access permissions (called "visas") for individual users. Visas are issued by data stewards, including data access committees (DACs) working with public databases, the entities responsible for the quality, integrity, and access arrangements for the datasets in the management of human biomedical data. Passports streamline management of data access rights across data systems by using visas that present a data user's digital identity and permissions across organizations, tools, environments, and services. We describe real-world implementations of the GA4GH Passport standard in use cases from ELIXIR Europe, National Institutes of Health, and the Autism Sharing Initiative. These implementations demonstrate that the Passport standard has provided transparent mechanisms for establishing permissions and authorizing data access across platforms.
Language	English
Publishing date	2021-11-10
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2021.100030
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Article ; Online: Human exposome assessment platform.

Merino Martinez, Roxana / Müller, Heimo / Negru, Stefan / Ormenisan, Alex / Arroyo Mühr, Laila Sara / Zhang, Xinyue / Trier Møller, Frederik / Clements, Mark S / Kozlakidis, Zisis / Pimenoff, Ville N / Wilkowski, Bartlomiej / Boeckhout, Martin / Öhman, Hanna / Chong, Steven / Holzinger, Andreas / Lehtinen, Matti / van Veen, Evert-Ben / Bała, Piotr / Widschwendter, Martin /

Dowling, Jim / Törnroos, Juha / Snyder, Michael P / Dillner, Joakim

Environmental epidemiology (Philadelphia, Pa.)

2021 Volume 5, Issue 6, Page(s) e182

Abstract: The Human Exposome Assessment Platform (HEAP) is a research resource for the integrated and efficient management and analysis of human exposome data. The project will provide the complete workflow for obtaining exposome actionable knowledge from ... ...

Abstract	The Human Exposome Assessment Platform (HEAP) is a research resource for the integrated and efficient management and analysis of human exposome data. The project will provide the complete workflow for obtaining exposome actionable knowledge from population-based cohorts. HEAP is a state-of-the-science service composed of computational resources from partner institutions, accessed through a software framework that provides the world's fastest Hadoop platform for data warehousing and applied artificial intelligence (AI). The software, will provide a decision support system for researchers and policymakers. All the data managed and processed by HEAP, together with the analysis pipelines, will be available for future research. In addition, the platform enables adding new data and analysis pipelines. HEAP's final product can be deployed in multiple instances to create a network of shareable and reusable knowledge on the impact of exposures on public health.
Language	English
Publishing date	2021-12-03
Publishing country	United States
Document type	Journal Article
ISSN	2474-7882
ISSN (online)	2474-7882
DOI	10.1097/EE9.0000000000000182
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Article ; Online: Federated discovery and sharing of genomic data using Beacons.

Fiume, Marc / Cupak, Miroslav / Keenan, Stephen / Rambla, Jordi / de la Torre, Sabela / Dyke, Stephanie O M / Brookes, Anthony J / Carey, Knox / Lloyd, David / Goodhand, Peter / Haeussler, Maximilian / Baudis, Michael / Stockinger, Heinz / Dolman, Lena / Lappalainen, Ilkka / Törnroos, Juha / Linden, Mikael / Spalding, J Dylan / Ur-Rehman, Saif /

Page, Angela / Flicek, Paul / Sherry, Stephen / Haussler, David / Varma, Susheel / Saunders, Gary / Scollen, Serena

Nature biotechnology

2019 Volume 37, Issue 3, Page(s) 220–224

MeSH term(s)	Genomics/trends ; Humans ; Information Dissemination ; Information Storage and Retrieval/trends
Language	English
Publishing date	2019-02-28
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-019-0046-x
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Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

Page, Angela / Flicek, Paul / Sherry, Stephen / Haussler, David / Varma, Susheel / Saunders, Gary / Scollen, Serena

Nature biotechnology

2019 Volume 37, Issue 4, Page(s) 480

Abstract: In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, ... ...

Abstract	In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article.
Keywords	covid19
Language	English
Publishing date	2019-02-20
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-019-0094-2
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Article ; Online: Registered access: authorizing data access.

Dyke, Stephanie O M / Linden, Mikael / Lappalainen, Ilkka / De Argila, Jordi Rambla / Carey, Knox / Lloyd, David / Spalding, J Dylan / Cabili, Moran N / Kerry, Giselle / Foreman, Julia / Cutts, Tim / Shabani, Mahsa / Rodriguez, Laura L / Haeussler, Maximilian / Walsh, Brian / Jiang, Xiaoqian / Wang, Shuang / Perrett, Daniel / Boughtwood, Tiffany /

Matern, Andreas / Brookes, Anthony J / Cupak, Miro / Fiume, Marc / Pandya, Ravi / Tulchinsky, Ilia / Scollen, Serena / Törnroos, Juha / Das, Samir / Evans, Alan C / Malin, Bradley A / Beck, Stephan / Brenner, Steven E / Nyrönen, Tommi / Blomberg, Niklas / Firth, Helen V / Hurles, Matthew / Philippakis, Anthony A / Rätsch, Gunnar / Brudno, Michael / Boycott, Kym M / Rehm, Heidi L / Baudis, Michael / Sherry, Stephen T / Kato, Kazuto / Knoppers, Bartha M / Baker, Dixie / Flicek, Paul

European journal of human genetics : EJHG

2018 Volume 26, Issue 12, Page(s) 1721–1731

Abstract: The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in ... ...

Abstract	The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.
MeSH term(s)	Access to Information ; Genetics, Medical/ethics ; Genetics, Medical/legislation & jurisprudence ; Genetics, Medical/standards ; Genomics/ethics ; Genomics/legislation & jurisprudence ; Genomics/standards ; Humans ; Information Dissemination ; Licensure ; Practice Guidelines as Topic
Language	English
Publishing date	2018-08-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1141470-4
ISSN	1476-5438 ; 1018-4813
ISSN (online)	1476-5438
ISSN	1018-4813
DOI	10.1038/s41431-018-0219-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: GA4GH: International policies and standards for data sharing across genomic research and healthcare.

Rehm, Heidi L / Page, Angela J H / Smith, Lindsay / Adams, Jeremy B / Alterovitz, Gil / Babb, Lawrence J / Barkley, Maxmillian P / Baudis, Michael / Beauvais, Michael J S / Beck, Tim / Beckmann, Jacques S / Beltran, Sergi / Bernick, David / Bernier, Alexander / Bonfield, James K / Boughtwood, Tiffany F / Bourque, Guillaume / Bowers, Sarion R / Brookes, Anthony J /

Brudno, Michael / Brush, Matthew H / Bujold, David / Burdett, Tony / Buske, Orion J / Cabili, Moran N / Cameron, Daniel L / Carroll, Robert J / Casas-Silva, Esmeralda / Chakravarty, Debyani / Chaudhari, Bimal P / Chen, Shu Hui / Cherry, J Michael / Chung, Justina / Cline, Melissa / Clissold, Hayley L / Cook-Deegan, Robert M / Courtot, Mélanie / Cunningham, Fiona / Cupak, Miro / Davies, Robert M / Denisko, Danielle / Doerr, Megan J / Dolman, Lena I / Dove, Edward S / Dursi, L Jonathan / Dyke, Stephanie O M / Eddy, James A / Eilbeck, Karen / Ellrott, Kyle P / Fairley, Susan / Fakhro, Khalid A / Firth, Helen V / Fitzsimons, Michael S / Fiume, Marc / Flicek, Paul / Fore, Ian M / Freeberg, Mallory A / Freimuth, Robert R / Fromont, Lauren A / Fuerth, Jonathan / Gaff, Clara L / Gan, Weiniu / Ghanaim, Elena M / Glazer, David / Green, Robert C / Griffith, Malachi / Griffith, Obi L / Grossman, Robert L / Groza, Tudor / Auvil, Jaime M Guidry / Guigó, Roderic / Gupta, Dipayan / Haendel, Melissa A / Hamosh, Ada / Hansen, David P / Hart, Reece K / Hartley, Dean Mitchell / Haussler, David / Hendricks-Sturrup, Rachele M / Ho, Calvin W L / Hobb, Ashley E / Hoffman, Michael M / Hofmann, Oliver M / Holub, Petr / Hsu, Jacob Shujui / Hubaux, Jean-Pierre / Hunt, Sarah E / Husami, Ammar / Jacobsen, Julius O / Jamuar, Saumya S / Janes, Elizabeth L / Jeanson, Francis / Jené, Aina / Johns, Amber L / Joly, Yann / Jones, Steven J M / Kanitz, Alexander / Kato, Kazuto / Keane, Thomas M / Kekesi-Lafrance, Kristina / Kelleher, Jerome / Kerry, Giselle / Khor, Seik-Soon / Knoppers, Bartha M / Konopko, Melissa A / Kosaki, Kenjiro / Kuba, Martin / Lawson, Jonathan / Leinonen, Rasko / Li, Stephanie / Lin, Michael F / Linden, Mikael / Liu, Xianglin / Udara Liyanage, Isuru / Lopez, Javier / Lucassen, Anneke M / Lukowski, Michael / Mann, Alice L / Marshall, John / Mattioni, Michele / Metke-Jimenez, Alejandro / Middleton, Anna / Milne, Richard J / Molnár-Gábor, Fruzsina / Mulder, Nicola / Munoz-Torres, Monica C / Nag, Rishi / Nakagawa, Hidewaki / Nasir, Jamal / Navarro, Arcadi / Nelson, Tristan H / Niewielska, Ania / Nisselle, Amy / Niu, Jeffrey / Nyrönen, Tommi H / O'Connor, Brian D / Oesterle, Sabine / Ogishima, Soichi / Wang, Vivian Ota / Paglione, Laura A D / Palumbo, Emilio / Parkinson, Helen E / Philippakis, Anthony A / Pizarro, Angel D / Prlic, Andreas / Rambla, Jordi / Rendon, Augusto / Rider, Renee A / Robinson, Peter N / Rodarmer, Kurt W / Rodriguez, Laura Lyman / Rubin, Alan F / Rueda, Manuel / Rushton, Gregory A / Ryan, Rosalyn S / Saunders, Gary I / Schuilenburg, Helen / Schwede, Torsten / Scollen, Serena / Senf, Alexander / Sheffield, Nathan C / Skantharajah, Neerjah / Smith, Albert V / Sofia, Heidi J / Spalding, Dylan / Spurdle, Amanda B / Stark, Zornitza / Stein, Lincoln D / Suematsu, Makoto / Tan, Patrick / Tedds, Jonathan A / Thomson, Alastair A / Thorogood, Adrian / Tickle, Timothy L / Tokunaga, Katsushi / Törnroos, Juha / Torrents, David / Upchurch, Sean / Valencia, Alfonso / Guimera, Roman Valls / Vamathevan, Jessica / Varma, Susheel / Vears, Danya F / Viner, Coby / Voisin, Craig / Wagner, Alex H / Wallace, Susan E / Walsh, Brian P / Williams, Marc S / Winkler, Eva C / Wold, Barbara J / Wood, Grant M / Woolley, J Patrick / Yamasaki, Chisato / Yates, Andrew D / Yung, Christina K / Zass, Lyndon J / Zaytseva, Ksenia / Zhang, Junjun / Goodhand, Peter / North, Kathryn / Birney, Ewan

Cell genomics

2022 Volume 1, Issue 2

Abstract: The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic ... ...

Abstract	The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
Language	English
Publishing date	2022-02-24
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2021.100029
Database	MEDical Literature Analysis and Retrieval System OnLINE

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

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Article ; Online: GA4GH Passport standard for digital identity and access permissions.

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Article ; Online: Human exposome assessment platform.

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Article ; Online: Federated discovery and sharing of genomic data using Beacons.

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Article ; Online: Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

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Article ; Online: Registered access: authorizing data access.

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Article ; Online: GA4GH: International policies and standards for data sharing across genomic research and healthcare.

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