Integrated human data repositories for infectious disease-related international cohorts to foster personalized medicine approaches to infectious disease research

Project Information

RECODID

Grant agreement ID: 825746

DOI

10.3030/825746

Project closed

EC signature date 21 November 2018

Start date 1 January 2019

End date 31 December 2023

Funded under

• SOCIETAL CHALLENGES - Health, demographic change and well-being

Total cost

€ 8 770 021,72

EU contribution

€ 7 760 021,72

Coordinated by

UNIVERSITATSKLINIKUM HEIDELBERG
Germany

Periodic Reporting for period 4 - RECODID (Integrated human data repositories for infectious disease-related international cohorts to foster personalized medicine approaches to infectious disease research)

Reporting period: 2023-07-01 to 2023-12-31

Summary of the context and overall objectives of the project

ReCoDID includes a multidisciplinary team of researchers from the global infectious disease arena, leveraging existing infrastructures and partnerships to develop a sustainable model for the storage, curation and analyses of the complex data sets collected from infectious disease-related cohorts. While infectious-disease related cohorts collect both data from (i) participant interviews, clinical assessment, and related geospatial, social, and environmental exposures (hereafter named clinic-epidemiological data, CE data), and (ii) high-dimensional data from advanced laboratory analysis on clinical samples (HDL data or OMICS data), a system is needed to facilitate the synthesis and analysis of these data, which are typically stored in separate repositories, within and across cohorts. Combining data repositories across cohorts for infectious disease research is rare. However, significant investments have been made in sharing CE and HDL data from population-based registries in high- income countries to improve personalised medicine, especially in chronic and rare diseases.

Combining data repositories across cohorts for CE and HDL data, the overarching goal of this project is to develop an integrated, sustainable platform for the sharing, synthesis, and analysis from infectious disease cohorts in keeping with the principles of FAIR (Findable, Accessible, Interoperable, and Reusable) data-driven research. The project will also develop biostatistical methods needed to analyze pooled cohort data. The repository platform will have a tiered permission system for data access. Cohort-specific hubs will facilitate cohorts’ analyses of their own data and cross-cohort analyses within a clearly elaborated legal, ethical, and equitable framework for cross-study data sharing.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the fourth reporting period much of the project's focus shifted towards finalizing activities and gearing up for the concluding Stakeholder meeting in Heidelberg in December 2023. With numerous work packages completing their tasks, emphasis was placed on dissemination activities, particularly as the project's scientific review highlighted the importance of a robust strategy for disseminating and exploiting project outcomes. Simultaneously, significant efforts were dedicated to advancing the ReCoDID data sharing pipeline and its continuation through the CONTAGIO project. Legal negotiations dominated this phase, primarily concerning data-sharing agreements between entities such as the French INSERM/ANRS, Heidelberg University Hospital, and the Colombian University Industrial de Santander. Seven deliverables were completed, ranging from reports on recommended consent practices to methodological guidelines and statistical approaches for data integration.

Additionally, the ReCoDID team formulated a strategy for data sharing, establishing a data access committee to oversee the pipeline, which included representation from data contributors, project leadership, and independent international institutions like WHO. Meanwhile, significant progress was made by the Colombian team in validating methodologies for harmonizing retrospective and prospective cohorts in dengue research, culminating in a successful joint analysis of over five thousand patient records from the AEDES network. This effort showcased the project's ability to harmonize variables and differentiate between dengue, Zika, and chikungunya, presenting its findings at events like the Pandengue conference in Peru and the American Society of Tropical Medicine Meeting in Chicago, both held in November 2023.

We have continued our efforts around sharing biological specimens and developing governance models for a federated biorepository. This research area has become more competitive over time since ReCoDID started, which shows that the ReCoDID researchers had the right intuitions about future areas of high importance. ReCoDID has gained substantial convening power throughout the project, also being involved in many stakeholder interactions over the last years about data sharing and harmonisation, both in the ethical/legal space as well as in the technical area.
Our work successfully integrated COVID-19 cohort metadata into the EMBL COVID-19 Platform, harmonising diverse clinical-epidemiological data from H2020-funded COVID-19 research projects. The team established connected Data Hubs for hosting clinical-epidemiological and SARS-CoV-2 OMICS data in a federated cloud. Additionally, we were able to build a comprehensive framework for harmonising anti-SARS-CoV-2 antibody serosurvey data.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The work in ReCoDID was affected and delayed by the COVID-19 pandemic, but at the same time the project proved to be more relevant than ever, which is reflected in the fact that ReCoDID was selected for additional funding, adding a whole work package on „COVID-19 research response“ (WP8). Subsequently, ReCoDID was featured in high-level consultations and has been included as a project ‚to collaborate with‘ in several new EC calls for proposals.

ReCoDID was also very active within the EU-CAN cross-consortial activities where several cross-consortional working groups were created, among them one on ‚data harmonization‘. The project works toward a broader vision of integrated data sharing platforms and (virtual) federated repositories for biological samples. Both topics have gained substantial traction since the time the project was evaluated and selected for funding. ReCoDID was able to partner with one of the NIH-funded CREID networks (Centers for Research on Emerging Infectious Diseases (CREID). At a conference in November 2022, organized by ‘The Global Health Network’ (TGHN) in Cape Town, ReCoDID and CREID had a common stand. Within the ethical/legal work package (WP2), the group decided to embark on additional work beyond the initial aims of the project and carry out cognitive interviews about the participants‘ perception of broad informed consent in research. This deepened the understanding of the interpretation of the GDPR legislation across institutions and EU member as well as non-member countries.

The project connects across the legacy of several EC projects and open-source infrastructures. More specifically, the ReCoDID project, with its focus on the harmonisation and linking of data across domains, approaches the development of infrastructure, software, tools, and services as a process in which established pre-existing and openly available components, such as databases, data standards and software packages, are brought together to build an ecosystem of connected parts able to support the complex integrative workflows of the project.

The work on the standardization of data, including a model CRF for acute febrile illness data sets has led into the development of a web-based tool, the “eCRF Builder”, for which the pilot stage is being completed. After that, the eCRF Builder has already found its new ‘home’ in the newly funded project “CONTAGIO” and will be further developed by joined team of ReCoDID and the ‘Infectious Disease Data Observatory’. This will increase the visibility as well as the acceptance of the eCRF Builder, increasing the chances of critical input obtained by and be adopted by the scientific community.

Other exploitable results of ReCoDID also include the a) Data Governance Framework and repository of legal templates, b) the methological tools for pooled cohort data, c) the governance of federated biorepositories.