Implementing a data infrastructure for precision oncology projects leveraging REDCap

Charles Vesteghem, Simon Christian Dahl, Rasmus Froberg Brøndum, Mads Sønderkær, Julie Støve Bødker, Alexander Schmitz, Joachim Weischenfeldt, Inge Søkilde Pedersen, Mia Sommer, Anne Stoffersen Rytter, Marlene Maria Nielsen, Morten Ladekarl, Marianne Tang Severinsen, Karen Dybkær, Kirsten Grønbæk, Tarec El-Galaly, Anne Stidsholt Roug, Martin Bøgsted

Research output: Working paper/PreprintPreprint


Objectives To facilitate clinical implementation and research in precision oncology, notably the pairing of patients, variants and treatments to identify candidates for clinical trials, we have built a data infrastructure to 1) capture and store data, 2) reduce manual tasks for clinical and genomic data collection and management, 3) combine data for quality controls, reporting and findability.Infrastructure The infrastructure uses REDCap repositories to capture and store data. The structure of these repositories is customized for each project. Additionally, a cross-project web platform was developed using software development best practices and state-of-the-art web technologies to circumvent REDCap’s limitations and integrate other third-party resources. Using REDCap’s application programming interfaces, this platform allowed validation of data across multiple repositories, easy import of data from external sources, generation of overviews of included patients and available data, combination of genomic and clinical data to generate tumour board reports and the findability of data. Its design was driven by data stewardship best practices.Usage Across four precision medicine projects, the infrastructure has been used to collect data for 1921 patients, including 453 genomic data files. The custom-built web platform made it possible to import, validate, and present data in a comprehensive manner. This included building tumour board reports for clinicians, combining clinical and genomic data, and search functionalities for researchers.Discussion REDCap allowed us to capitalize on the numerous data capture and management features developed in this solution. Designing a cross-project platform guarantees long-term relevance where developments can be mutualised across projects and allowed us to make the overall solution more compliant with the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. Further developments should be considered, notably automatic retrieval of data from electronic health records to limit the number of manual tasks.Conclusion The proposed infrastructure allowed our precision oncology projects to gain efficiency in data collection and increase data quality by reducing manual work, and it gave a straightforward and customized access to data for researchers and clinicians.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe National Experimental Therapy Partnership (NEXT), the Greater Copenhagen Health Science Partners, as part of the Danish Research Center for Precision Medicine in Blood Cancers, and Aalborg University Hospital funded this project. The Danish Research Center for Precision Medicine in Blood Cancers is funded by the Danish Cancer Society grant no. R223-A1307.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The infrastructure mentioned in the article was used for four onco-haematology prospective clinical protocols, ProSeq, RetroSeq, ProSeq Cancer (the North Denmark Region Committee on Health Research Ethics approval no. N-1706295, N-20160089, and N-20200018, respectively), and the Danish Research Center for Precision Medicine in Blood Cancers (DCCC-Haem) (Danish National Committee on Health Ethic approval no. 1705391).I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesThe data mentioned in this present work were collected in the context of other research projects, their accessibility is therefore defined by these projects.
Original languageEnglish
Number of pages20
Publication statusPublished - 12 May 2022


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