In RP3, we made significant progress towards achieving the project objectives as follows:
- Deliver transcontinental security requirements for data access: CINECA WP2 has provided support to ELIXIR and EGA to implement GA4GH Passport for Authorization and Authentication Infrastructure (AAI), and has been involved in its version update (v1.2) used in a pilot implementation for ELIXIR AAI, and later for the European LifeScience AAI.
- Provide solutions to ELSI requirements where data cannot move outside a legal jurisdiction: CINECA contributed to the development and adoption of GA4GH standards, including the Data Use Ontology (WP3), htsget (WP4), and GA4GH Passport and AAI (WP2). The technical demonstrators in RP3 by WP4 and WP5 showcased how the federated analysis model can be practically applied to real-world research and clinical applications.
- Provide federated access to genomic data on demand: In RP3, CINECA showed how components developed by WP1-3 could be integrated into end-to-end federated analysis frameworks created by WP4 and WP5. For example, the eQTL use case showed how datasets with harmonised metadata (WP3) can be discovered via GA4GH Beacon (WP1), how these datasets can be accessed using LifeScience Login AAI (WP2), and how these datasets can be analysed using the portable and modular workflows in Nextflow.
- Deliver access to datasets of the scale and completeness needed to address analytical challenges: WP1 has built a federated platform for cross cohort Discovery and Extended queries, which enables researchers to discover relevant data for their research. We collaborated with the standard-setting organisation GA4GH, as well as with ELIXIR networks in order to build other implementations of Discovery products such as Beacon, ensuring that our work will form part of the global network for the discovery of human cohort data resources.
- Provide harmonised metadata, based on open global standards, driving variant and sample discovery in trans-continental virtual cohort of 1.4 million individuals: In RP3, GECKO (GEnomics Cohorts Knowledge Ontology) was used to create a set of synthetic cohorts which form the basis for the federated research and clinical application demonstrators from WP4 and WP5.
- Wide adoption in international personalised medicine projects: The International Hundred-K Cohorts Consortium (IHCC), which aims to provide access to hundreds of harmonised cohort data dictionaries across continents, has adopted GECKO as a metadata model for cohort data harmonisation. In addition, a collaboration with the Beyond 1 Million Genome (B1MG) and Genome Data Infrastructure (GDI) projects has resulted in the creation of a new Synthetic Dataset for rare diseases, which can be used to develop new tools to access and analyse data interesting for the Rare Disease community.
The CINECA dissemination strategy has continually been updated throughout the project. During RP3, CINECA provided fully remote learning interventions and dissemination together with more traditional in-person training after the COVID-19 pandemic. CINECA also engaged with various stakeholders on topics of common interest, including GA4GH (genomics standards development and implementation), IHCC (using GECKO as cohort model), ELIXIR, and EUCAN working groups.
