Risultati finali Documents, reports (14) Ethico-legal issues for EU partners in EUCANCan Report on ethicolegal issues relevant to the participation of EUCANCan member projects in Spain Germany and other relevant Member States including a description of requirements in German Spanish and EU legislation to share health data for EUCANCans purposes of the project Definition of global and local needs regarding storing solutions for raw data from oncological patients, and the different levels of security required for personalised medicine environments Reporting of the specific needs of each data producing site/partner, the different profiles of user communities and their level of data access. Integrate ethical and legal solutions described in WP6 for the different levels of protection Policy working group briefings, summary reports_1 Briefing documents that were prepared for the health policy group, and documentation of regular meetings and progress File-level federated query system back end Design and implement a pilot version of data query and retrieval systems within EUCanCan federated network. Adaptation to data types and formats defined in WP5. Tools report Best practices including tools, parameters and workflows to analyse the different types of data (just a report, no code at this stage) along with validated and annotated datasets for different use cases (variant calling, RNA-seq analysis, etc.). Policy working group briefings, summary reports_2 Briefing documents that were prepared for the health policy group and documentation of regular meetings and progress Communication plan Guidelines for communication, including key messages, main target audiences, most suitable communication channels, rules to be followed, and a social media strategy EUCANCan Exploitation Plan Overview document listing the Key Exploitable results of the project and responsible partners, including planned exploitation timelines and pathways (to be updated with each periodic report) Description and implementation of exchange of genomics data The investigated and defined exchange formats for genomics data within EUCANCan will be formulary described Based on the chosen standard the API for the exchange will be defined implemented and reported Canadian ethico-legal constraints and considerations report Report on ethico-legal constraints and considerations for Canadian projects in receiving data transfers according to the EU General Data Protection Regulation, and sharing and processing data according to Canadian personal information protection law Protocols for deploying tools and pipelines locally Identify points of integration of eventual storage solutions locally Adaptation of one end to each site according to their needs Guidance to enable the sharing of clinical data within the EUCANCan project This will include a description of the safeguards implemented by EUCANCan to ensure that technical and organisational measures are in place for the processing of data as well as the obligations of parties involved in the data processing Description and implementation of clinical data types and formats for the sharing of datasets within EUCANCan Description of the data attributes in the two tier system of clinical annotation (first mandatory baseline clinicopathological data, second minimal follow-up and outcome information) and their implementation as a consensus across sites for the sharing of datasets within EUCANCan Project Management and Quality Guidelines This deliverable will describe the project’s internal management procedures, detailing the project’s Quality assurance process as well as a detailed Risk evaluation and internal communication tools and mechanisms. Other (4) Updated versions of EGA software and ELIXIR Data Transfer technologies Implement functional versions of software for data transfer in and out of storing systems Software packages with the pipelines able to run within the informatics infrastructure developed in WP3 Stateoftheart pipelines provided in D21 and D22 will be implemented according to harmonised guidelines using best practises of software engineering Portable informatics scripts will be packaged allowing the installation and running of the pipelines within the EUCANCan informatics infrastructure Automated tools to filter and prioritize both genomic and somatic alterations to support decision making during tumour boards A list of analysis tools parameters and databases to compute scores to classify the variants to assess their potential functional impact within the tumor and their druggability will be provided Bioinformatics scripts will be implemented and integrated within the general analysis pipelines to automatically compute these scores Final version of EUCANCan variant extraction and annotation tool Identify the best solutions to replicate and align strategies for the calling and interpretation of somatic and germline variants (SNVs, indels, SVs and CNV) for a concordant and homogeneous sharing of genomic information across EUCANCan nodes. These strategies will be also aligned with current efforts to standardize protocols for genomic analyses in biomedicine (GA4GH and ELIXIR). Websites, patent fillings, videos etc. (2) Dissemination toolkit Corporate identity will be developed, and dissemination materials as well as templates to be used for presentations, reports, meeting- and internal documents Public project website To showcase the project’s activities and results both to the scientific community as well as to the public at large Pubblicazioni Peer reviewed articles (13) Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines Autori: Fabrice Allain; Julien Roméjon; Philippe La Rosa; Frédéric Jarlier; Nicolas Servant; Philippe Hupé Pubblicato in: Open Research Europe, 2021, ISSN 2732-5121 Editore: F1000 DOI: 10.12688/openreseurope.13861.1 Bridging the European Data Sharing Divide in Genomic Science Autori: Fruzsina Molnár-Gábor, Michael J S Beauvais, Alexander Bernier, Maria Pilar Nicolas Jimenez, Mikel Recuero, Bartha Maria Knoppers Pubblicato in: Journal of Medical Internet Research, 2022, ISSN 1438-8871 Editore: Journal of medical Internet Research DOI: 10.2196/37236 Mutational Landscape and Tumor Burden Assessed by Cell-free DNA in Diffuse Large B-Cell Lymphoma in a Population-Based Study Autori: Alfredo Rivas-Delgado, Ferran Nadeu, Anna Enjuanes; Sebastián Casanueva-Eliceiry, Pablo Mozas, Laura Magnano; Natalia Castrejón de Anta; Jordina Rovira; Ivan Dlouhy; Silvia Martín; Miguel Osuna; Sonia Rodríguez; Marc Simó; Magda Pinyol; Tycho Baumann; Silvia Beà Olga Balagué; Julio Delgado; Neus Villamor; Xavier Setoain; Elías Campo Eva Giné; Armando López-Guillermo Pubblicato in: Clinical Cancer Research, 2021, ISSN 1078-0432 Editore: American Association for Cancer Research DOI: 10.1158/1078-0432.ccr-20-2558 Women’s Views on Multifactorial Breast Cancer Risk Assessment and Risk-Stratified Screening: A Population-Based Survey from Four Provinces in Canada Autori: Cynthia Mbuya-Bienge , Nora Pashayan, Jennifer D. Brooks, Michel Dorval, Jocelyne Chiquette, Laurence Eloy, Annie Turgeon, Laurence Lambert-Côté , Jean-Sébastien Paquette , Emmanuelle Lévesque , Julie Hagan , Meghan J. Walker , Julie Lapointe , Gratien Dalpé, Palmira Granados Moreno , Kristina Blackmore, Michael Wolfson, Yann Joly, Mireille Broeders , Bartha M. Knoppers , Anna M. Chiarelli , Pubblicato in: Journal of Personalized Medicine, 2021, ISSN 2075-4426 Editore: MDPI DOI: 10.3390/jpm11020095 GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis Autori: Chen Hong, Robin Thiele and Lars Feuerbach Pubblicato in: Bioinformatics, 2022, ISSN 1367-4811 Editore: Oxford Academic DOI: 10.1093/bioinformatics/btac037 Toward better governance of human genomic data Autori: Kieran C. O’Doherty, Mahsa Shabani, Edward S. Dove, Heidi Beate Bentzen, Pascal Borry, Michael M. Burgess, Don Chalmers, Jantina De Vries, Lisa Eckstein, Stephanie M. Fullerton, Eric Juengst, Kazuto Kato, Jane Kaye, Bartha Maria Knoppers, Barbara A. Koenig, Spero M. Manson, Kimberlyn M. McGrail, Amy L. McGuire, Eric M. Meslin, Dianne Nicol, Barbara Prainsack, Sharon F. Terry, Adrian Thorogood an Pubblicato in: Nat Genet, 2021, ISSN 1061-4036 Editore: Nature Publishing Group DOI: 10.1038/s41588-020-00742-6 Ten simple rules for a successful international consortium in big data omics Autori: Miranda D. Stobbe; Abel Gonzalez-Perez; Nuria Lopez-Bigas; Ivo Glynne Gut Pubblicato in: PLOS COMPUTATIONAL BIOLOGY, 2022, Page(s) e1010546, ISSN 1553-7358 Editore: Public Library of Science DOI: 10.1371/journal.pcbi.1010546 Harmonization after the GDPR? Divergences in the rules for genetic and health data sharing in four member states and ways to overcome them by EU measures: Insights from Germany, Greece, Latvia and Sweden Autori: Fruzsina Molnar-Gabor, Julian Sellner, Sophia Pagil, Santa Slokenberga, Olga Tzortzatou-Nanopoulou, Katarina Nystrom Pubblicato in: Seminars in Cancer Biology, 2022, ISSN 1044-579X Editore: Academic Press DOI: 10.1016/j.semcancer.2021.12.001 La compartición internacional de datos personales relativos a la salud en tiempos de la COVID-19: aspectos éticos y legales para el impulso de la necesaria cooperación Autori: Mikel Recuero Linares Pubblicato in: RBD. Revista de Bioética y Derecho, Issue 2, 2020, ISSN 1886-5887 Editore: Spain DOI: 10.1344/rbd2020.50.31711 Raising standards for global data-sharing—Response Autori: Jasper Bovenberg David PeloquinBarbara BiererMark Barnesand Bartha Maria Knoppers Pubblicato in: Science, 2021, ISSN 0036-8075 Editore: American Association for the Advancement of Science DOI: 10.1126/science.abf5425 A multi-platform reference for somatic structural variation detection Autori: Jose Espejo Valle-Inclan, Nicolle J.M. Besselink, Ewart de Bruijn, Daniel L. Cameron, Jana Ebler, Joachim Kutzera, Stef van Lieshout, Tobias Marschall, Marcel Nelen, Peter Priestley, Ivo Renkens, Margaretha G.M. Roemer, Markus J. van Roosmalen, Aaron M. Wenger, Bauke Ylstra, Remond J.A. Fijneman, Wigard P. Kloosterman, Edwin Cuppen, Pubblicato in: Cell Genomics, 2022, ISSN 2666-979X Editore: Elsevier DOI: 10.1016/j.xgen.2022.100139 Reconciling the biomedical data commons and the GDPR: three lessons from the EUCAN ELSI collaboratory Autori: Alexander Bernier, Fruzsina Molnár-Gábor, Bartha M. Knoppers, Pascal Borry, Priscilla M. D. G. Cesar, Thijs Devriendt, Melanie Goisauf, Madeleine Murtagh, Pilar Nicolás Jiménez, Mikel Recuero, Emmanuelle Rial-Sebbag, Mahsa Shabani, Rebecca C. Wilson, Davide Zaccagnini and Lauren Maxwell Pubblicato in: European Journal of Human Genetics, 2023, ISSN 1018-4813 Editore: Natue Publishing Group DOI: 10.1038/s41431-023-01403-y Ethical challenges of precision cancer medicine Autori: Eva Caroline Winkler, Bartha Maria Knoppers Pubblicato in: Seminars in Cancer Biology, 2020, ISSN 1044-579X Editore: Academic Press DOI: 10.1016/j.semcancer.2020.09.009 È in corso la ricerca di dati su OpenAIRE... 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