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A European standardization framework for data integration and data-driven in silico models for personalized medicine

Periodic Reporting for period 1 - EU-STANDS4PM (A European standardization framework for data integration and data-driven in silico models for personalized medicine)

Reporting period: 2019-01-01 to 2020-06-30

The challenge of making sense of data

Although Big Data already drives fundamental medical/scientific applications and the associated socioeconomic potential forward, a large-scale future exploitation of Big Data in research and health care represents a major challenge (Apweiler et al. 2018). This concerns both technical and safety issues as well as legal, ethical and cultural aspects in dealing with personal health-relevant and large-volume data sets that differ to a great extent in Europe. In addition to country-specific heterogeneities, Europe currently lacks well-functioning, standardized and interoperable information and communication technology (ICT) infrastructure, capable of linking the databases of basic and clinical research with different registries (including those from environmental, food and social sciences and humanities) whilst addressing both legal and ethical frameworks to maintain public trust” (Horizon-2020-Advisory-Group 2018-2020) in a proper legal, ethical and privacy-protective data environment. Publicly accepted strategies and governance frameworks for integrated Big Data to further develop healthcare –quality and –system performance are key factors that have to be implemented before Big Data can unfold its full medical and research potential through in silico analysis and interpretation. Regarding Big Data in health the specific challenge is thus to:

-Develop data-driven computational approaches that are tailored (personalized) to the individual or stratified patient groups addressing clinically relevant questions.
-Harness, utilize and understand (exploit) high volume, high diversity biological, clinical, environmental, and lifestyle information.
-Develop European harmonized standardization guidelines for data integration strategies.
-Ensure that integration of personal and patient-derived data is performed lawful, ethical and fair, while fully respecting patients’ rights.

Standards on a European level for secure interoperable data integration and predictive computational models are essential to utilize the wealth of information that Big Data contain — specifically and efficiently to push a pro-active personalized medicine forward.
A central task of EU-STANDS4PM is thus to assess and evaluate national standardization strategies for health data integration as well as data-driven in silico modelling approaches for personalized medicine with the aim to bundle European standardization efforts. A major goal is to develop harmonized standards as well as recommendations and guidelines for predictive data-driven in silico methodologies applied in personalized medicine. The project will examine to what extent existing standards or standards under development for both, format and semantics, can be used to link clinical healthcare data to computational models that build on these data. As all requirements should be equally understood and fulfilled by users it is important to define them uniformly in an international context.
"WP1-Data sources and standards for predictions in personalized medicine:
-A comprehensive online survey covering a large variety of data sources and model approaches was planned, developed and launched.
-Specific guidance was provided for the development of ISO Technical Reports.
-Official category-C liaison to ISO/TC215/SC1 “Genomics Informatics” and ISO/TC276/WG5 “Data processing and Integration"" were established.

WP2-Integrative data analysis and in silico models in personalized medicine:
-A collection of use cases of modelling approaches with clinical applicability was assembled.
-The stakeholder consultation workshop “Using patient derived data for in silico modelling in personalized medicine” was organized in Feb 2020.
-A collaborative White Paper writing process on state of the art modelling approaches in personalized medicine was initiated
-The writing process of ISO Technical Reports was initiated

WP3-Legal ethics, policy and certification for data-driven in silico models in personalized Medicine:
-A comprehensive analysis of the applicable EU, Council of Europe and international regulation of data protection, biomedical research/clinical trials and patients’ rights relevant for development of in silico modelling was published.
-A collection of opportunities and challenges for in silico modelling and collaborative research within the existing legal and ethical framework was identified and assembled.
-Fruitful working collaboration with the other WP’s regarding mapping of data sources (WP1), development of use cases (WP2), and development of the harmonized Data Access Agreement (see WP4) were established.

WP4-Data access, outreach and governance:
-A workshop was organized in Jan 2020 with key international stakeholders to discuss a framework for the development and implementation of a harmonised Data Access Agreement (hDAA) for controlled access data deposited in the European Genome-phenome Archive (EGA).
-Subsequently a fully GDPR compliant hDAA was developed and released to the public in Aug 2020 on the EGA and EU-STANDS4PM websites.
-Registered Access (RA) under the lead of the European Bioinformatics Institute (EBI) was implemented with input from EU-STANDS4PM partners EBI-ELIXIR (WP1) and UCL (WP4).
-A case study to evaluate Cloud-based Access (CbA) of multi-omics data was completed. Human multi-omics reference data generated by the Personal Genome Project UK (PGP-UK) were selected for this technical evaluation as this is one of the few human multi-omics datasets that are available under open access. The evaluation included making >2TB of human multi-omics data freely available on two commercial clouds (Cancer Genome Cloud and Lifebit Cloud) and one academic cloud (Galaxy.eu).
-A 4 minute animated film was produced explaining the background and work of EU-STANDS4PM.

WP5-Management and Coordination:
-Appropriate management and communication structures were developed.
-Rules of the management structure described in Annex I part B were implemented.
-Specific templates for reports, presentations, etc. were created and made available to the consortium.
-Supervision was performed that objectives and technical goals of the work plan were fulfilled accordingly.
-A transparent communication structure with regular exchange of information between the consortium, the WP-leader and external stakeholders was established."
One of the main impacts of a broad implementation of standardization guidelines to be proposed by EU-STANDS4PM for generating, secure storing, integrating and sharing of data will be the reproducibility of research findings and the ability to compare research results among different scientific, as well as health research communities. This will advance the relevant disciplines and enable rapid exchange of data and knowledge, therefore providing a solid platform for new ideas and research strategies. Within medical research, this will accelerate the detection of novel biomarkers for early detection and monitoring of disease progression and has potential for developing more cost/time efficient, clinical trials guided by the results of rational in silico approaches in personalized medicine.