The project implemented a work plan consisting of five technical work packages, one work package devoted to coordinate them and one work package facing how to influence the policy makers in order to achieve high impact results.
Management and Coordination
WP1 was dedicated to coordinate the overall technical and scientific work of the whole project. Moreover, it established quality control actions and detected training needs of the consortium.
Genome analysis pipelines to support the therapeutic decision
WP2 took care of the data flow between healthcare institutions and sequencing facilities to EUCANCan nodes and the EGA.
Repository and cloud infrastructures
WP3 aimed at harmonizing and unifying in silico analysis protocols (including variant identification and functional interpretation) across EUCANCan nodes, to allow the posterior exchange and integration of the results of the different studies generated, setting up a common technical environment for genome analysis that allows and promotes the sharing of data. Deliverables from this WP include compute facilities, open to EUCANCan and ARGO participants, which implement standard alignment, variant-calling, and genome annotation pipelines.
A federation of data portals for interoperability across EUCANCan nodes and responsible sharing of patient genomic data
WP4 worked to (1) install a toolset in each EUCANCan node to index genomic data files and publish the metadata that describes these files to the Internet; (2) develop a metadata browser allowing researchers to discover EUCANCan-produced clinical/genomic data sets; (3) develop a service installed on each EUCANCan node to initiate a file transfer of a selected set of genomic files and their associated metadata; (4) informed by WP2, implement a uniform software pipeline for annotating the nature and functional impact of somatic and germline variants identified by genomic and transcriptomic sequencing; and (5) provide metadata search.
Standardized clinical reporting across sites
This demonstrator of the EUCANCan project implemented the technologies and standards developed and implemented by WP2, WP3 and WP4 in real clinical cases by defining common data formats, standards and terminologies for the sharing of genomic oncology data.
Ethico-legal framework for clinical oncology data
The overall strategy of the project was only possible with the appropriate ethical and legal advising from experts in the topic. MCG, UPV/EHU and HdAW were involved in several genomic and clinical initiatives, such as ICGC, assuring the accomplishment of WP6 objectives, which aimed at assessing the sharing of genomic and clinical data across borders. WP6 was connected with WPs 1 through 5, as it was required to map and identify the data life cycle of the health data involved in the system and to identify ethico-legal considerations that arose in the data-sharing workflows. WP5 served as a direct use case for the development of prototype tools for legal compliance in research collaborations beyond human genome oncology.
Dissemination and Exploitation
WP7 helped optimize the impact of the overall project by disseminating results to various target audiences and by supporting and guiding their uptake and use. Dedicated activities streamlined communication, facilitate networking, and paved the way to translating results into policy.