Nordic Register and Biobank Data A basis for innovative research on health and welfare Juni Palmgren Karolinska Institutet, Stockholm Nordic conference on Real World Data Helsinki November 2016
Nordic populations 5,5M 0,3M 9,3M 5,3M 4,9M J Palmgren 2
Nordic population based registries LIFE SPAN REGISTRIES EARLY LIFE Cancer Hospital Discharge LATE LIFE Birth Congenital Malformations Clinical Quality Registries Specific Disease Registries Register of prescribed drug sales Cause of Death L I F E GENETICALLY INFORMATIVE Population Multiple Generation Twin Migration 3
The biobank perspective Genomes (Sanger, EBI + NCBI) Nucleotide sequence EMBL-Bank+Genbank+DDBj Gene expression ArrayExpress, GEO Protein families, motifs and domains InterPro (12 collaborators) Protein interactions IntAct with Imex, PRIDE Pathways Kegg; Reactome Protein sequence UniProt(EBI/SIB/PIR) Protein structure wwpdb(rcsb,ebi,pdbj) Chemical entities ChEBI; PubChem From molecules to systems Systems BioModels From Janet Thornton, EBI
A longitudinal perspective on health and disease Personalized diagnostics and treatment Cured Healthy Diagnosis Chronic/current disease Dead time 12 december 2016 5
Type 2 Diabetes > 10 000 individuals National Biobanks Finland portal 130 000 individuals from population cohorts 70 000 individuals from disease collections Cardiovascular events stroke, CHD 25 000 individuals Life course events High Blood pressure Cardiovascular risk factor data 100 000 individuals REGISTROMICS Severe mental health: Social security number Cause of death data - schizophrenia, depression - > 5000 individuals Prescription medication data Migraine 15 000 individuals National Biobank 201 858 individuals 18 000 statin users 20 000 estrogen substitution th Old age dementia, ~ 5000 individuals Cancer > 10 000 cases Life style and socio-economic data - education, economic state, smoking
Data integration and interoperability? Fantastic opportunities! Obstacles: Many data owners Multitude of regulations and practices Weak documentation, metadata, ontologies Secure sharing? Norden? Tedious and complicated within countries more so between countries J Palmgren 7
Nordic research data Nordic Council of Ministers (NCM) Marie Sandberg, CSC, 2012 Challenges from six perspectives: The political perspective The organizational perspective The legal perspective The financial perspective The ethical perspective The technical perspective The lack of a Nordic perspective for research data implies a risk of developing policy directives which are not aligned on the Nordic level.
A vision A Nordic Commons A shared virtual space where scientists can work with the digital objects of biomedical research. This is a system that will allow investigators to find, manage, share, use and reuse data, software, metadata and workflows. From Data Science at NIH
Components of a Commons ecosystem from A computing environment, such as the cloud and/or HPC (High Performance Computing) resources, which support access, utilization and storage of digital objects. Data sets that adhere to a set of Digital Object Compliance Principles which describe the properties of digital objects that enables them to be findable, accessible, interoperable and reproducible (FAIR). Software services and tools that enable; Scalable provisioning of compute resources. Interoperability between digital objects within the Commons. Indexing and thus discoverability of digital objects. Sharing of digital objects between individuals or groups. Access to and deployment of scientific analysis tools and pipeline workflows. Connectivity with other repositories, registries and resources that support scholarly research.
A Nordic context (Common pot initiative) The NordForsk Programme on Health and Welfare Academy of Finland, Danish Research Council for Independent Research/Medical Sciences, Icelandic Centre of Research (Rannis), The Research Council of Norway, The Swedish Research Council for Health, Working Life and Welfare (FORTE) The Swedish Research Council NordForsk. The Programme runs from 2014 to 2018, covers 11 research projects in 2016. The perspective is broad. From 2017 a Research Infrastructure and an education component are planned as part of the Programme
A Nordic Commons would rely on A clear legal and ethical framework for sharing data and tools across borders Transparency and an open access policy Involvement of a broad range of Nordic key stakeholders Political level (legislation and ethics) Research funding level National data-owner institutions escience and einfrastructure expertize Scientists The Nordic countries need to tap into the ongoing discussions on Open Science and data sharing in the contect of the EU Open Science Cloud and other international initiatives.
Open access to scientific information
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Summary Recommendations for Norden Legislation: Coordinate national legislation and legal practices in the wake of new EU GDPR. Harmonize handling of sensitive research data from registers, cohorts, biobanks and molecular data repositories Ethics: Set up a simplified and coherent ethics review process for cross-nordic studies Metadata: Create compatible meta-data models within and across Nordic data sources. Open Access: Coordinate high level demands for open access to data and methods. A Nordic Commons: Work towards an integrated system for finding, managing, sharing, using and reusing data, software, metadata and workflows
Sharing Mine! across organisations disciplines geographical and institutional boarders research groups and scientists Beware of financial, organisational, technical, legal, ethical, cultural obstacles 17