EATRIS-Plus – Flagship in Personalised Medicine

For biological data as produced in the EATRIS-Plus project, an essential criterion for re-usability is data quality. Participants in this project aim at highest quality, to ensure value of the data for personalized medical applications. This deliverable (D.1.1.) collects the current protocols of the participating research centres, which are used to generate the data.

EATRIS-Plus sites have provided their protocols, which have been developed, validated, and established over years and proven of high quality in both academic and industry partnership projects with returning users or customers. Several sites have also participated in one or more international quality assessment consortia projects, such as the FDA-guided SEQC. The current protocols will also be used in WP3 of EATRIS-Plus.

Within work packages 1, 2, and 3, we implement practices based on the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles to ensure reproducibility of our work and to make the multi-omics cohort data reusable for future translational research. The aim of this deliverable (D2.1) is to describe the EATRIS-Plus FAIRification process, and list standards, formats, and tools used in this process.

As part of this deliverable (D2.1), we describe the EATRIS-Plus FAIRification strategy (Appendix 1: EATRIS-Plus FAIRification strategy) to make the generated multi-omics cohort data reusable for future translational research. We identified relevant data and metadata standards to report and describe data generated by different omics technologies. The existing ISA (Investigation, Study, Assay) metadata framework (https://isa-tools.org/)1 is used to capture experimental metadata. ISA-Tab metadata is used and supported by a wide range of single-omics data repositories (https://www.isacommons.org/). We develop a Jupyter notebook to generate ISA-Tab files for the multi-omics data set that complies with reporting guidelines for individual omics types. Importantly, the ISA framework enables the use of controlled vocabularies and ontologies supporting both human-readability and machine-readability. The ISA-Tab template files being developed in EATRIS-Plus will serve as templates for collecting the required metadata for integration of multi-omics in the context of research projects around personalized health and personalized medicine. They will be published and shared and as part of the EATRIS-Plus multi-omics toolbox.

In this deliverable we report on efforts of EATRIS-Plus sites in the certification of pre-analytical sample processing and in the development of reference values and material for omics technologies used to generate the multiomics data in WP1.
The technical validity of an experimental process, the quality of the resulting data and reproducibility of the results can be assessed by comparing the data to a known range of values that were developed from well-characterized samples and controlled experimental conditions. Since the experimental processes can differ widely, it is useful to develop target ranges of detection, that are applicable to most commonly used technologies. The development of reference material and the use of target value ranges is discussed in principle and in examples.

One of the main objectives of the project is to accelerate outreach to SMEs and build long-term engagement with bioclusters. In order to be able to reach more potential industry users and further diversify EATRIS’ revenue streams, this task will pilot a collaboration programme with Biocat (comprising 1,060 companies, 580 of which biotech, medtech and pharma). Activities designed to raise the profile of the research infrastructure (RI) towards industry associations and their member companies will be evaluated, with impactful activities to be further expanded to other cluster regions. As one of the first activities, Task 6.2 – Accelerate outreach to SMEs: build long-term engagement with bioclusters aimed to further these efforts, Biocat has now performed a survey of SMEs’ needs in relation to infrastructure support and access to academic expertise and high-end facilities. The results and discussion are summarised in this Deliverable 6.1. The results of the survey will help EATRIS-Plus consortium partners refine their engagement strategy towards SMEs.