EUCANCan: a federated network of aligned and interoperable infrastructures for the homogeneous analysis, management and sharing of genomic oncology data for Personalized Medicine.

Deliverables

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

Policy working group briefings, summary reports_3

Briefing documents that were prepared for the health policy group and documentation of regular meetings and progress

Ethico-legal points to consider for future international research collaborations to study other diseases

Generalized guidance to assist future data-driven cancer and medical research initiatives, on topics such as when genomic analysis may be considered a medical device, and thus subject to additional regulatory requirements, and on the difference between anonymization and pseudonymization and its application to concrete circumstances such as the sharing of somatic or germline variants.

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.

Description of the different formulas of connecting these infrastructures into each regional health care system

"EUCANCan trial locator Website with a search tool for genomics-driven clinical trials across EUCANCan sites plus information on Website visits over the period M42-M48"" and ""Framework of the standardised genomics report designed to facilitate therapeutic decision plus feedback from clinical users (molecular tumor board participants) on its usefulness in real-life practice over the period M42-M48"

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 using cloud infrastructures within EUCANCan

Definition of computing environments hardware and software optimal for EUCanCan analysis pipelines and transfer protocols Identification of data and access security protocols according to WP6

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

Metrics for evaluation of the new pipelines and new release of the pipelines with updated tools and parameters

From the reference datasets provided in D21 quality metrics such as sensitivity true positive rate or recall and specificity the true negative rate will be reported for the different pipelines Pipelines with new tools and new parameters will be implemented to improve these quality metrics

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

Description of the integration and report describing the whole process, including data generation and management. Evaluation of the interoperability between EUCANCan nodes

It will be shown in a report how the EUCANCan participation sides providing genomics and clinical data have implemented the exchange requests and API as well as how the data exchange operates functionally

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.

Updated versions of EGA software and ELIXIR Data Transfer technologies

Implement functional versions of software for data transfer in and out of storing systems

Final version 2.0 of variant-level indexing and retrieval system for EUCANCan

Generate and implement systems for data indexing and access at the level of single variant, and other molecular features.

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

Deployable version of EUCANCan data portal, providing search and discovery services for data sets stored at EUCANCan nodes

Generate a version of a web service for data searches and access, within and outside the EUCanCan consortium, according to the guidelines for data embargos and protection defined throughout the project.

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).

Final version of enhanced portal, providing access to variant-level data

Definition and implementation of the final version of the accession portal. Data will be made available and searchable through this portal.

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

Publications

Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines

Author(s): Fabrice Allain; Julien Roméjon; Philippe La Rosa; Frédéric Jarlier; Nicolas Servant; Philippe Hupé
Published in: Open Research Europe, 2021, ISSN 2732-5121
Publisher: F1000
DOI: 10.12688/openreseurope.13861.1

Bridging the European Data Sharing Divide in Genomic Science

Author(s): Fruzsina Molnár-Gábor, Michael J S Beauvais, Alexander Bernier, Maria Pilar Nicolas Jimenez, Mikel Recuero, Bartha Maria Knoppers
Published in: Journal of Medical Internet Research, 2022, ISSN 1438-8871
Publisher: 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

Author(s): 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
Published in: Clinical Cancer Research, 2021, ISSN 1078-0432
Publisher: 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

Author(s): 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 ,
Published in: Journal of Personalized Medicine, 2021, ISSN 2075-4426
Publisher: MDPI
DOI: 10.3390/jpm11020095

GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis

Author(s): Chen Hong, Robin Thiele and Lars Feuerbach
Published in: Bioinformatics, 2022, ISSN 1367-4811
Publisher: Oxford Academic
DOI: 10.1093/bioinformatics/btac037

Toward better governance of human genomic data

Author(s): 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
Published in: Nat Genet, 2021, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-020-00742-6

Ten simple rules for a successful international consortium in big data omics

Author(s): Miranda D. Stobbe; Abel Gonzalez-Perez; Nuria Lopez-Bigas; Ivo Glynne Gut
Published in: PLOS COMPUTATIONAL BIOLOGY, 2022, Page(s) e1010546, ISSN 1553-7358
Publisher: 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

Author(s): Fruzsina Molnar-Gabor, Julian Sellner, Sophia Pagil, Santa Slokenberga, Olga Tzortzatou-Nanopoulou, Katarina Nystrom
Published in: Seminars in Cancer Biology, 2022, ISSN 1044-579X
Publisher: 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

Author(s): Mikel Recuero Linares
Published in: RBD. Revista de Bioética y Derecho, Issue 2, 2020, ISSN 1886-5887
Publisher: Spain
DOI: 10.1344/rbd2020.50.31711

Raising standards for global data-sharing—Response

Author(s): Jasper Bovenberg David PeloquinBarbara BiererMark Barnesand Bartha Maria Knoppers
Published in: Science, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abf5425

A multi-platform reference for somatic structural variation detection

Author(s): 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,
Published in: Cell Genomics, 2022, ISSN 2666-979X
Publisher: Elsevier
DOI: 10.1016/j.xgen.2022.100139

Reconciling the biomedical data commons and the GDPR: three lessons from the EUCAN ELSI collaboratory

Author(s): 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
Published in: European Journal of Human Genetics, 2023, ISSN 1018-4813
Publisher: Natue Publishing Group
DOI: 10.1038/s41431-023-01403-y

Ethical challenges of precision cancer medicine

Author(s): Eva Caroline Winkler, Bartha Maria Knoppers
Published in: Seminars in Cancer Biology, 2020, ISSN 1044-579X
Publisher: Academic Press
DOI: 10.1016/j.semcancer.2020.09.009

Deliverables

Publications

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