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  1. Article ; Online: Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem.

    Dyke, Stephanie O M / Connor, Kathleen / Nembaware, Victoria / Munung, Nchangwi S / Reinold, Kathy / Kerry, Giselle / Mbiyavanga, Mamana / Zass, Lyndon / Moldes, Mauricio / Das, Samir / Davis, John M / De Argila, Jordi Rambla / Spalding, J Dylan / Evans, Alan C / Mulder, Nicola / Karamchandani, Jason

    Neuroinformatics

    2022  Volume 21, Issue 1, Page(s) 89–100

    Abstract: We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing uncertainty about permissible re- ... ...

    Abstract We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing uncertainty about permissible re-use of shared data. Here we discuss clarifications and subsequent updates to the Consent Codes (v4) based on new areas of application (e.g., the neurosciences, biobanking, H3Africa), policy developments (e.g., return of research results), and further practical considerations, including developments in automated approaches to consent management.
    MeSH term(s) Informed Consent ; Biological Specimen Banks ; Ecosystem ; Genomics
    Language English
    Publishing date 2022-12-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2111941-7
    ISSN 1559-0089 ; 1539-2791
    ISSN (online) 1559-0089
    ISSN 1539-2791
    DOI 10.1007/s12021-022-09577-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5816: Show issues Location:
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  2. Article ; Online: Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.

    Maier, Wolfgang / Bray, Simon / van den Beek, Marius / Bouvier, Dave / Coraor, Nathan / Miladi, Milad / Singh, Babita / De Argila, Jordi Rambla / Baker, Dannon / Roach, Nathan / Gladman, Simon / Coppens, Frederik / Martin, Darren P / Lonie, Andrew / Grüning, Björn / Kosakovsky Pond, Sergei L / Nekrutenko, Anton

    Nature biotechnology

    2021  Volume 39, Issue 10, Page(s) 1178–1179

    MeSH term(s) COVID-19/epidemiology ; COVID-19/virology ; Databases, Factual ; Genome, Viral/genetics ; Humans ; Pandemics ; SARS-CoV-2/pathogenicity
    Language English
    Publishing date 2021-09-01
    Publishing country United States
    Document type Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-021-01069-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2167: Show issues Location:
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  3. Article: Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring.

    Maier, Wolfgang / Bray, Simon / van den Beek, Marius / Bouvier, Dave / Coraor, Nathaniel / Miladi, Milad / Singh, Babita / De Argila, Jordi Rambla / Baker, Dannon / Roach, Nathan / Gladman, Simon / Coppens, Frederik / Martin, Darren P / Lonie, Andrew / Grüning, Björn / Kosakovsky Pond, Sergei L / Nekrutenko, Anton

    bioRxiv : the preprint server for biology

    2021  

    Abstract: The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is ... ...

    Abstract The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org .
    Language English
    Publishing date 2021-03-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.03.25.437046
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. 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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    Zs.A 3589: Show issues Location:
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  5. Article ; Online: The European Genome-phenome Archive of human data consented for biomedical research.

    Lappalainen, Ilkka / Almeida-King, Jeff / Kumanduri, Vasudev / Senf, Alexander / Spalding, John Dylan / Ur-Rehman, Saif / Saunders, Gary / Kandasamy, Jag / Caccamo, Mario / Leinonen, Rasko / Vaughan, Brendan / Laurent, Thomas / Rowland, Francis / Marin-Garcia, Pablo / Barker, Jonathan / Jokinen, Petteri / Torres, Angel Carreño / de Argila, Jordi Rambla / Llobet, Oscar Martinez /
    Medina, Ignacio / Puy, Marc Sitges / Alberich, Mario / de la Torre, Sabela / Navarro, Arcadi / Paschall, Justin / Flicek, Paul

    Nature genetics

    2015  Volume 47, Issue 7, Page(s) 692–695

    MeSH term(s) Access to Information ; Biomedical Research ; Databases, Genetic ; Europe ; Genome, Human ; Humans
    Language English
    Publishing date 2015-07-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/ng.3312
    Database MEDical Literature Analysis and Retrieval System OnLINE

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