Periodic Reporting for period 3 - EUCANCan (EUCANCan: a federated network of aligned and interoperable infrastructures for the homogeneous analysis, management and sharing of genomic oncology data for Personalized Medicine.)
Reporting period: 2022-01-01 to 2023-06-30
EUCANCan aims to create the first federated and interoperable infrastructure for securely sharing genomic and clinical cancer data across Canada and Europe. This network will link multiple cancer research centers, enabling authorized researchers to search, select, and securely download datasets of interest. The infrastructure is built on distinct pillars covering technical, methodological, and ethico-legal aspects of data sharing. While global initiatives like GA4GH and ELIXIR focus on developing individual components of such infrastructures, EUCANCan concentrates on integrating these components to create an operational system, addressing challenges related to community interactions and interoperability within federated data environments.
Throughout the project, we've developed solutions for discovering and sharing cancer datasets among diverse research and clinical centers. Our efforts target tools and guidance for key layers involved: Technical, Methodological, Cultural, and Ethico-Legal. Technically, EUCANCan has advanced by creating tools and standards for clinical and genomic tumor data, ensuring interoperability across sites. Additionally, the project has introduced practical solutions like ONCOLINER for harmonizing genome analysis, crucial for preventing conflicts arising from differing somatic variants between centers. Finally, we offer guidance on Ethico-Legal considerations regarding data protection, with a continued focus on enabling research endeavors.
Throughout the project, we've developed solutions for discovering and sharing cancer datasets among diverse research and clinical centers. Our efforts target tools and guidance for key layers involved: Technical, Methodological, Cultural, and Ethico-Legal. Technically, EUCANCan has advanced by creating tools and standards for clinical and genomic tumor data, ensuring interoperability across sites. Additionally, the project has introduced practical solutions like ONCOLINER for harmonizing genome analysis, crucial for preventing conflicts arising from differing somatic variants between centers. Finally, we offer guidance on Ethico-Legal considerations regarding data protection, with a continued focus on enabling research endeavors.
This project has significantly advanced towards personalized medicine, focusing on cancer clinical and genomic data. The urgent need to store, manage, and make this data discoverable spurred our efforts to promote clinical and molecular discoveries through sharing and reuse. Notable achievements of EUCANCan include:
(1) Establishment of a computing infrastructure to index, transfer, and store clinical and genomic data, enabling cancer datasets' discoverability within a federated network. Legitimate researchers can explore datasets using complex queries, facilitating formal access requests. These advances have enriched Local EGA models for GA4GH and Cloud computing systems. (2) Adoption of standards for clinical and genomic data representation, essential for network-level interoperability and interaction with other research systems. These standards primarily focus on somatic variant representation and clinical fields. (3) Finalization of a cloud system compatible with EUCANCan, with evaluations of potential nodes' environments and recommendations on cloud environment construction (D2.3 and D3.4). (4) Development of innovative solutions to improve and harmonize genome analysis protocols across diverse research and clinical centers. The aim is to align variant analysis pipelines, enhancing the integration of results across datasets and centers. The ONCOLINER method offers a user-friendly approach to harmonizing somatic variant pipelines, minimizing user effort. Additionally, a collection of benchmarking genomes (mosaic and tumorirzed genomes) aids in testing data management and analysis infrastructures. And (5) substantial work on ethico-legal frameworks protecting biomedical research data in European and Canadian legal domains. WP6 produced guidelines and proposals to align research with data protection laws (D6.1-4).
(1) Establishment of a computing infrastructure to index, transfer, and store clinical and genomic data, enabling cancer datasets' discoverability within a federated network. Legitimate researchers can explore datasets using complex queries, facilitating formal access requests. These advances have enriched Local EGA models for GA4GH and Cloud computing systems. (2) Adoption of standards for clinical and genomic data representation, essential for network-level interoperability and interaction with other research systems. These standards primarily focus on somatic variant representation and clinical fields. (3) Finalization of a cloud system compatible with EUCANCan, with evaluations of potential nodes' environments and recommendations on cloud environment construction (D2.3 and D3.4). (4) Development of innovative solutions to improve and harmonize genome analysis protocols across diverse research and clinical centers. The aim is to align variant analysis pipelines, enhancing the integration of results across datasets and centers. The ONCOLINER method offers a user-friendly approach to harmonizing somatic variant pipelines, minimizing user effort. Additionally, a collection of benchmarking genomes (mosaic and tumorirzed genomes) aids in testing data management and analysis infrastructures. And (5) substantial work on ethico-legal frameworks protecting biomedical research data in European and Canadian legal domains. WP6 produced guidelines and proposals to align research with data protection laws (D6.1-4).
The project's developments have pushed boundaries, enhancing technical, methodological, and Ethico-Legal frameworks for cancer genomics data sharing and reusability. Immediate impacts include harmonizing analysis pipelines in WP2 and extending to projects like B1MG, OpenEBench, and GA4GH. ARGO leverages advancements in WP4, using EUCANCan's model for a federated data access system, including variant and file indexing, and Beacon-based query systems.
Beyond progress in data standards and analysis, EUCANCan significantly impacts the biomedical research community. Interactions with initiatives like GA4GH and B1MG highlight its broader influence. Notable contributions include technical solutions for synthetic tumor genomes, aiding variant calling pipeline benchmarking.
EUCANCan acknowledges that achieving Personalized Medicine demands unprecedented collaboration among diverse research communities. It has cultivated multidisciplinary scenarios through forums and scientific objectives, exemplified in collaborative efforts like WP2. Partners from clinical, bioinformatics, computing, and legal fields converge to harmonize variant calling across independent research silos.
Beyond progress in data standards and analysis, EUCANCan significantly impacts the biomedical research community. Interactions with initiatives like GA4GH and B1MG highlight its broader influence. Notable contributions include technical solutions for synthetic tumor genomes, aiding variant calling pipeline benchmarking.
EUCANCan acknowledges that achieving Personalized Medicine demands unprecedented collaboration among diverse research communities. It has cultivated multidisciplinary scenarios through forums and scientific objectives, exemplified in collaborative efforts like WP2. Partners from clinical, bioinformatics, computing, and legal fields converge to harmonize variant calling across independent research silos.