EUCANCan recently entered the final project phase. The Horizon 2020-funded project is designed as a testbed for testing out different technical and sociological solutions to challenges related with the sharing of genomic and clinical data across different institutions in the context of modern oncology. As part of this effort, the consortium aims at building a pilot-platform that enables transfers of cancer genomic data between the project nodes in Europe and Canada.
After completing the second reporting period, the project communications team wants to take this opportunity to take stock of the project’s progress to date and look at the activities planned for the final months.
The EUCANCan portal is taking shape
One important pilar of creating the EUCANCan infrastructure is aligning and interconnecting existing European and Canadian infrastructures for the analysis and management of genomic oncology data. As one major milestone in this context, EUCANCan accomplished the operative connection of three partner nodes (OICR, BSC and Charité) by creating a data model and schema that is used by the participating partner nodes. It is the aim to include more EUCANCan partner nodes in this network in the next months.
Connecting the EUCANCan partner nodes goes hand in hand with the implementation of Maestro, a component for user query and interaction that will serve as the backbone of the EUCANCan data portal. Currently, indexing and transfer of data between these three nodes as well as the access and query through this centralized EUCANCan portal is in production. This demonstrates the feasibility of cancer data sharing between Europe and Canada which is one of the central objectives of EUCANCan.
Having the technical part nearly complete, the EUCANCan team is currently putting effort into finding legal paths that allow for populating the network with real research data.
Tools for harmonizing genome analysis approaches
Ensuring the interoperability of the different EUCANCan nodes requires providing a uniform computing environment for processing and harmonizing data. In the context of building the EUCANCan genome analysis homogenization system, a Variant Call Format (VCF) benchmarking tool is now available for the EUCANCan partners and will be published soon. It builds on the efforts to benchmark genome analysis pipelines of different EUCANCan partners and enables the extension and automatization of the EUCANCan benchmarking efforts to other centres. These efforts constitute the foundation for building a benchmarking platform that allows the evaluation, improvement, and homogenisation of genome analysis pipelines. To ensure that this tool is not only useful within the EUCANCan context, EUCANCan closely collaborates with other initiatives such as the Beyond 1 Million Genomes project and the OpenEBench project.
EUCANCan also published the harmonization tool geniac, a platform for implementing Nextflow pipelines, which provides a toolbox for genome analysis and benchmarking efforts that align with the EUCANCan portal development.
User-centric tool development
To increase the value of the EUCANCan tools for users, the team has evaluated the processes for data generation and flow of typical clinical research centres. In this way, EUCANCan identified specific critical data storage and management points that should be taken into consideration when designing European Genome-phenome Archive (EGA) based local solutions for data storage and management.
The Onco Trials Track application serves as a clinical trial locator and aims to improve patient recruitment in clinical trials by providing the medical oncology and patient communities with a web application that allows searching for the most appropriate clinical trial in oncology care. To create a tool that is as user-friendly as possible, the team assessed the user-needs in interviews with physicians and worked with a user experience specialist to design the application’s interface.
Considering ethical and legal aspects of international cancer genome data sharing
Besides the technical component of finding solutions for international cancer genome data sharing, EUCANCan researchers further investigated the ethical and legal implications of sharing cancer genome data internationally over the past 18 months. The EUCANCan ELSI team worked on an extensive guide to enable the sharing of clinical data within the EUCANCan project, relevant not only for EUCANCan itself, but also for any other similar clinical data sharing initiatives from the European Union and/or Canada. This activity has been accomplished in cooperation with the EUCAN ELSI Collaboratory, a forum for knowledge exchange between ethical and legal experts from different Horizon 2020-funded projects.
The way forward: Plans for the final project phase
In the final phase of the project, the EUCANCan consortium will focus on integrating these different elements to build and publish the EUCANCan data portal. Part of this is providing detailed guidance for further developments and implementations, demonstrating the feasibility of this federated infrastructure, its functionality, and its benefits within real and common genomic oncology research scenarios.
Prof David Torrents, EUCANCan coordinator, sums up the current achievements and ambitions for the final project phase:
“We are very happy with how EUCANCan is progressing, despite the difficulties associated with the pandemic scenario. During the first part, our energy was devoted to generate and prepare all the different components of the EUCANCan network. In this second part and, particularly in this final stretch of the project, we are already connecting these pieces and having the first partner centres connected and able to exchange data in a federated way. Next and final steps will be devoted to set up the ethico-legal frame that will allow us to populate the network with real research data.”