Risultati finali
CINECA is part of the Open Research Data Pilot (ORDP) and the consortium will therefore submit a first version of a Data Management Plan (DMP) as a deliverable within the first 6 months of the project. The DMP will be updated over the course of the project whenever significant changes arise, such as (but not limited to): - new data - changes in consortium policies (e.g. new innovation potential, decision to file for a patent) - changes in consortium composition and external factors (e.g. new consortium members joining or old members leaving). The DMP will be prepared using the template provided by the Commission (http://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-data-management/data-management_en.htm).
First recommendations needed for implementation implemented in IT Framework We will provide recommendations for the longterm cooperation between European African and Canadian cohorts to intensify collaboration as well as sharing and reuse of data56 ethical and legal recommendations IT solutions such as machine readable solutions to meet ethical and legal requirements and vice versa
Training Programme, detailedTraining Programme a detailed plan of the training programme for the final two years of the project
Training Programme - annual reportTraining Programme Brief annual report on the training delivered shortterm reach and impact
Report of main achievements, impacts, sustainability and exploitationReport of main achievements impacts sustainability and exploitation
Meta-analysis of splicing and expression QTLs across three cohortsA Metaanalysis of splicing and expression QTLs across three cohorts We willdevelop a federated metaanalysis protocol that complies with the data sharing and privacy requirements of the individual cohorts and apply it to the three cohorts participating in the implementation study BIOS EGCUT TwinsUK Finally in collaboration with the eQTL Catalog currently being developed at EMBLEBI and UTartu we will make summary statistics from the federated eQTL metaanalysis available via public APIs
Report of impact and key resultsDevelopment of a sustainability plan of each project result for maximum longterm impact
Training programmeBrief annual reports on the training delivered shortterm reach and impact for the first three years of the project Report at mo 24 to provide a detailed plan of the training programme for the final two years of the project
CINECA Risk Management RegistryThe CINECA Risk Management Registry.The Project Management team will develop a risk management and contingency plan. Risks in CINECA will be assessed in the areas of data security, ethics, dissemination, innovation, and scientific quality. The contingency plan will ensure that items at risk will be closely monitored and if needed followed-up and controlled.
Catalog of Canada, European and African ethical and legal gaps identifiedA catalog of Canada European and African ethical and legal gaps to identify the legal and ethical gaps and roadblocks impairing future collaborations among the cohorts participating in this consortium We will focus on the legal and ethical requirementsrelated to informed consent secondary use of data and cross border exchanges of data between Europe and third countries We will base our analysis on the potential application of the GDPR to transnational datasamples exchanges on the Canadian domestic laws PIPEDA and H3Africa governance and on the respect on the ethical values stated byinternational policies
A report on how the GA4GH researcher ID specifications have been implemented in the ELIXIR AAIA report on how ELIXIR and CanDIG AAI systems will be upgraded to support the GA4GH Library Card concept
Semantic and harmonisation best practiceA report on Semantic and harmonisation best practice to identify the current coding standards for each cohort and the variables recorded for each of the projects cohort
Catalogue on ELSI Issues V1.0A catalogue of the ethical, legal and social issues for international collaboration of cohorts with a special focus on Europe, Canada and Africa noting the cloud context. The mapping exercise will be achieved by literature as well as legal and policy documents.
Report of CINECA kick off meetingA report of CINECA kick off meeting.
Data interoperability documentationAn important use case of the federated discovery services is to discover cohorts of relevant samples or patients across data providers either programmatically or with interactive tools such as the portal of T141 and run uniform pipelines across those items for further analysis with the tools of T42
Integration of new cohort infrastructures to the ELIXIR AAIA report with the status of integration of new service providers to the ELIXIR AAI Due to the federated nature of human data each infrastructure has their own processes and procedures for granting access to datasets hosted We are proposing to harmonise AAI across the CINECA consortium by ensuring that all of the cohort infrastructures are integrated with either ELIXIR or CanDIG AAI or H3Africa
Curation-support for care planningCurationsupport for care planning with the aim to add clinical actionability beyond pathogenicity scales
Report on trust model for partner sites, and between sites and controlled-access researchersA report on trust model for partner sites, and between sites and controlled-access researchers. A machine readable consent ontology mapping of individual cohorts will be used as input to determine the appropriate trust model for partner sites, and between sites and controlled-access researchers.
Outreach and dissemination planA report summarising the outcome of our stakeholder analysis (including training needs analysis), highest priority stakeholder groups and plan for engaging with them throughout the project. This will incorporate a detailed training plan for the first two years of the project and an outline plan for the second two years.
Development and application of optimised polygenic risk scoresA report on the development and application of optimised polygenic risk scores We will focus on the development and implementation of methods to generate polygenic risk scores for traits of mutual interest and to use them both for trait prediction and causal inference in a Mendelian randomisation framework The methods developed will generate novel biological and translational insights including polygenic risk scores for medically relevant traits such as type 2 diabetes and coronary artery disease that are optimised for use across multiple samples andor populations
Final report and impact analysisA final report and impact analysis Summary report of all outreach dissemination and training activities including impact analysis
A text mining processing pipeline to extract meta data content from semi or unstructured text in documents
Access representation ontology developed for project's cohortsAccess representation ontology developed for projects cohorts D35 will refine extend and integrate access representations for cohorts based on feedback from WP17 prior work DUO ADAM and user requirements for the cohort access representation
Cohort minimal meta data modelThe common minimal metadata model is intended to function supporting the analytical translational and federation use cases described in WP124 and 5 There are several nascent models in existence in this space though many of these as yet are untested in a HTP production environment of the type to be delivered by CINECA eg EDMI from EOSC and the GA4GH Clinical and Phenotypic Model Therefore we will locate merge and test the models for the use cases coming from the implementation work packages to ensure they are fit for purpose for CINECA
Populated minimal meta data model for project cohortsA minimal meta data model will provide a common for data discovery WP1 and will be populated by data from each cohort enabling federated analyses WP4 and clinical applications WP5
Framework and APIs for executing federated genomics analysesFramework and APIs for executing federated genomics analyses We will coordinate with an existing ELIXIR Compute platform project to establish interoperable execution platforms at CSC and EMBLEBI using the Toil framework We will collaborate with the ELIXIR Compute platform environments at CSC and EBI to implement new APIs
Universal FAIR Data Compliant Federated Biomarker Discovery Service. In this task (T5.2) myFAIR will be developed to use federated data (T5.1) from the Catalog of FAIR data (T1.2) available via the interactive query portals developed in T1.4. Secure access to these data will be managed with the ELIXIR AAI service delivered in T2.3 and the trust model from T4.1. Federated workflows used to analyse these data from T4.2, T4.3and part of existing Galaxy services for cancer genomics including fusion gene detection (Teles et al., 2015, Hiltemann et al., 2015, Albuquerque et al., 2017).
GDPR and FAIR compliant Diagnostic ServicesGDPR and FAIR compliant Diagnostic Services. We will develop a proof of concept open source diagnostic NGS services.
Query expansion servicesAs part of the Discovery portal T141 we will deliver services for expanding interactive user queries for phenotype and genotype metadata WP3
CanDIG and ELIXIR AAI interoperability demonstrationA public demonstration of showing technical integration and interoperability between Europe and Canada AAI systems
Discovery service catalogA discovery service catalog by which users will be able to search the datasets by genomic information as well as using the variable related metadata standards developed as part of WP4. The unique contribution of CINECA will be the first unified multidimensional cohort discovery platform that can perform real-time search across a disparate set of cohort infrastructures in Canada, Europe, and Africa.
Federated discovery across registry servicesAn important use case of the federated discovery services is to discover cohorts of relevant samples or patients across data providers either programmatically or with interactive tools such as the portal of T141 and run uniform pipelines across those items for further analysis with the tools of T42
Federated Data Analytics for European BiobanksA report outlining the federated data analytics developed by CINECA for European Biobanks.
Pubblicazioni
Autori:
Alasoo, Kaur; Warmerdam, Robert; Westra, Harm-Jan
Pubblicato in:
2022
Editore:
Zenodo
DOI:
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Nicola Mulder, Mamana Mbiyavanga, Saskia Hiltemann, Vera Matser
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2020
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Zenodo
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10.5281/zenodo.6223125
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Garcia, Carles
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2023
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Zenodo
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10.5281/zenodo.8099739
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2019
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Zenodo
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2020
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Zenodo
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Nurlan Kerimov, Ralf Tambets, James D. Hayhurst, Ida Rahu, Peep Kolberg, Uku Raudvere, Ivan Kuzmin, Anshika Chowdhary, Andreas Vija, Hans J. Teras, Masahiro Kanai, Jacob Ulirsch, Mina Ryten, John Hardy, Sebastian Guelfi, Daniah Trabzuni, Sarah Kim-Hellmuth, Will Rayner, Hilary Finucane, Hedi Peterson, Abayomi Mosaku, Helen Parkinson, Kaur Alasoo
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Cold Spring Harbor Laboratory
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Spalding, Dylan
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2023
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Zenodo
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Keane, Thomas; Glass, Leslie
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2019
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Tanzer, Romain; Naderi, Nona; Teodoro, Douglas; Mottaz, Anais; Ruch, Patrick; Dursi, Jonathan; Rambla de Argila, Jordi
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Numero 4, 2020
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Zenodo
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Jin, Vivian; Brinkman, Fiona
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Brinkman, Fiona
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2023
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Courtot, Melanie; Liyanage, Isuru
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Fromont; Milla
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2023
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Linden, Mikael; Kuba, Martin; Izquierdo, Jorge; Mbiyavanga, Mamana
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Autori:
Goisauf, Melanie; Fériol, Lisa; Rial-Sebbag, Emmanuelle
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2022
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Copara, Jenny; Naderi, Nona; Kellmann, Alexander; Gosal, Gurinder; Hsiao, William; Teodoro, Douglas
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Editore:
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Courtot, Melanie; Dursi, Jonathan; Mulder, Nicola; Swertz, Morris
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2020
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Gennet, ��lo��se; Goisauf, Melanie; Pichereau, Delphine; Rial-Sebbag, Emmanuelle
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Cell Genomics, 2021, ISSN 2666-979X
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New York: Elsevier Inc.
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Nurlan Kerimov, James D. Hayhurst, Kateryna Peikova, Jonathan R. Manning,Peter Walter, Liis Kolberg, Marija Samoviča, Manoj Pandian Sakthivel, Ivan Kuzmin, Stephen J. Trevanion, Tony Burdett, Simon Jupp, Helen Parkinson, Irene Papatheodorou,Andrew D. Yates, Daniel R. Zerbino and Kaur Alasoo
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10.1038/s41588-021-00924-w
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Helena Rasche, Saskia Hiltemann
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GigaScience, Numero 9/6, 2020, ISSN 2047-217X
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Oxford Academic
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10.1093/gigascience/giaa065
Autori:
Julien Knafou, Quentin Haas, Nikolay Borissov, Michel Counotte , Nicola Low, Hira Imeri, Aziz Mert Ipekci, Diana Buitrago-Garcia, Leonie Heron, Poorya Amini, Douglas Teodoro
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BioMed Central
DOI:
10.1186/s13643-023-02247-9
Autori:
Jordi Rambla, Michael Baudis, Roberto Ariosa, Tim Beck, Lauren A Fromont, Arcadi Navarro, Rahel Paloots, Manuel Rueda, Gary Saunders, Babita Singh, John D Spalding, Juha Törnroos, Claudia Vasallo, Colin D Veal, Anthony J Brookes
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Human Mutation, Numero 2022 Jun;43(6), 2022, Pagina/e 791-799, ISSN 1098-1004
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Wiley Online Library
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10.1002/humu.24369
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Nona Naderi, Julien Knafou, Jenny Copara, Patrick Ruch, Douglas Teodoro
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Frontiers in Research Metrics and Analytics, 2021, ISSN 2504-0537
Editore:
Lausanne: Frontiers Media S.A.
DOI:
10.3389/frma.2021.689803
Autori:
Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch
Pubblicato in:
Studies in Health Technology and Informatics, Numero Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Pagina/e 839 - 843
Editore:
IOS Press
DOI:
10.3233/shti220603
Autori:
Nona Naderi, Anaïs Mottaz, Douglas Teodoro, Patrick Ruch
Pubblicato in:
Studies in Health Technology and Informatics, Numero Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Pagina/e 876 - 877
Editore:
IOS Press
DOI:
10.3233/shti220614
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