Software application profile: opal and mica: open-source software solutions for epidemiological data management, harmonization and dissemination

Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination.; Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them.; Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models.; Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence

A genealogical study of Alzheimer disease in the Saguenay region of Quebec

We performed an analysis of inbreeding and kinship among the ascending genealogies of 205 autopsy-confirmed Alzheimer disease (AD) subjects recruited in the Saguenay area of Québec. We hypothesized that if some traits pertaining to the disease were determined by inherited factors, and if the corresponding genes were not too frequent in the population, it might be possible to detect some clusters of patients related to common ancestors and presenting a level of kinship and/or inbreeding higher than is observed in the unaffected population of the same age. In view of the heterogeneity of the disease, we also verified if some of the factors investigated could be associated more specifically with subsets of cases based on age of onset and on apolipoprotein E (APOE) genotype. Results were compared with those obtained on 205 controls matched for gender, place and year of birth. We found that late-onset AD cases with an APOE-epsilon 4 were significantly more inbred than controls and that this increase was explained by the high level of inbreeding of a few cases whose parents were related at the first-cousin level. This could possibly indicate the implication of a recessive element in a small subset of AD cases in the Saguenay population. We also found that late-onset epsilon 4+ cases were significantly more closely related among themselves than with controls. This increase in kinship may be attributable to the presence of the epsilon 4 allele or to some other unidentified genetic factor possibly acting in conjunction with APOE-epsilon 4

Biobanks in Europe: Prospects for Harmonisation and Networking

Biobanks (i.e. the organised collections consisting of biological samples and associated data, have gained great significance for research and personalised medicine) are increasingly recognised as a crucial infrastructure for research. However, at the same time the widely varied practices in biobanking regarding for example collection, storage and consent procedures may also pose a barrier to cross-border research and collaboration by limiting access to samples and data. In this context, a recent study indicates that the limited sharing and linkage of samples is a key barrier for research, such as pharmacogenetics. Wide variation is observed in the implementation of relevant existing regulation, which may add further burden to harnessing the public health benefit of these collections. Therefore, it has been suggested that there is a strong need for a harmonised approach on biobanking practices and improved networking of existing and new collections. This Report shows information on the extent of biobanking in Europe, collected through a survey of existing European biobanks regarding both technical aspects (e.g. storage conditions) and aspects of governance and ethics (e.g. sample and data sharing, consent procedures, collaborations etc.). In total, 126 biobanks from 23 countries in Europe were surveyed. Significant lack of harmonisation has been found, especially in the legal aspects (e.g. data protection, consent). This may be partly attributed to the varied interpretation and implementation of EC directives covering aspects of biobanking by national authorities. One of the main complications is that, although the field of data protection is harmonised through the EC directive on data protection, the collection, storage, and sharing of samples is not. Furthermore, in countries that have introduced special biobanks acts it is not always clear where the borderline lies between the scope of these acts and that of the Directive. Indeed, according to the survey, biobanks within the same country reported different practices, suggesting that the problems of harmonization might be higher than expected and claimed. Not only are there different national laws, but apparently within EU member states biobanks do not implement homogenous practices on privacy and data protection issues. Desk research and expert interviews were done to complete the picture presented by the survey. Experts widely recognised the need to improve collaboration and networking among the numerous existing biobanks, as well as new initiatives in Europe (and world-wide). Efficient organisation of these resources through the development, for example, of an infrastructure would potentially facilitate financial sustainability and greatly contribute to the rapid progress of research and development of better diagnostic and therapeutic approaches. The most favoured model involved the development of a virtual biobank that would allow networking of biobanks across different countries and centralisation of data rather than samples. However, several organisational challenges (wide variation in biospecimen collection, storage techniques, data comparability, etc.) may hamper such an effort. The lack of uniform regulatory and ethical requirements and/or practices may pose an additional barrier. The European Commission has already recognised the importance of international biobank projects and many of them have been funded and established in the context of the EU Framework Programmes. To help promote networking of biobanks and thus maximise public health benefits, at least some degree of harmonisation must be achieved. Whether this should be achieved solely at the level of legal/regulatory requirements and practices and/or by technical standardisation requires further investigation. Experts suggested the establishment of an international (rathen than just a European) umbrella (or network) organization, which would establish common operating procedures.JRC.DDG.J.2-The economics of climate change, energy and transpor

Restauro, 1-3/1992.

Ambient air pollution increases the risk of respiratory mortality, but evidence for impacts on lung function and chronic obstructive pulmonary disease (COPD) is less well established. The aim was to evaluate whether ambient air pollution is associated with lung function and COPD, and explore potential vulnerability factors.We used UK Biobank data on 303 887 individuals aged 40-69 years, with complete covariate data and valid lung function measures. Cross-sectional analyses examined associations of land use regression-based estimates of particulate matter (particles with a 50% cut-off aerodynamic diameter of 2.5 and 10 µm: PM; 2.5; and PM; 10; , respectively; and coarse particles with diameter between 2.5 μm and 10 μm: PM; coarse; ) and nitrogen dioxide (NO; 2; ) concentrations with forced expiratory volume in 1 s (FEV; 1; ), forced vital capacity (FVC), the FEV; 1; /FVC ratio and COPD (FEV; 1; /FVC <lower limit of normal). Effect modification was investigated for sex, age, obesity, smoking status, household income, asthma status and occupations previously linked to COPD.Higher exposures to each pollutant were significantly associated with lower lung function. A 5 µg·m; -3; increase in PM; 2.5; concentration was associated with lower FEV; 1; (-83.13 mL, 95% CI -92.50- -73.75 mL) and FVC (-62.62 mL, 95% CI -73.91- -51.32 mL). COPD prevalence was associated with higher concentrations of PM; 2.5; (OR 1.52, 95% CI 1.42-1.62, per 5 µg·m; -3; ), PM; 10; (OR 1.08, 95% CI 1.00-1.16, per 5 µg·m; -3; ) and NO; 2; (OR 1.12, 95% CI 1.10-1.14, per 10 µg·m; -3; ), but not with PM; coarse; Stronger lung function associations were seen for males, individuals from lower income households, and "at-risk" occupations, and higher COPD associations were seen for obese, lower income, and non-asthmatic participants.Ambient air pollution was associated with lower lung function and increased COPD prevalence in this large study

Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies

Objectives : Existing individual-level human data cover large populations on many dimensions such as lifestyle, demography, laboratory measures, clinical parameters, etc. Recent years have seen large investments in data catalogues to FAIRify data descriptions to capitalise on this great promise, i.e. make catalogue contents more Findable, Accessible, Interoperable and Reusable. However, their valuable diversity also created heterogeneity, which poses challenges to optimally exploit their richness. Methods : In this opinion review, we analyse catalogues for human subject research ranging from cohort studies to surveillance, administrative and healthcare records. Results : We observe that while these catalogues are heterogeneous, have various scopes, and use different terminologies, still the underlying concepts seem potentially harmonizable. We propose a unified framework to enable catalogue data sharing, with catalogues of multi-center cohorts nested as a special case in catalogues of real-world data sources. Moreover, we list recommendations to create an integrated community of metadata catalogues and an open catalogue ecosystem to sustain these efforts and maximise impact. Conclusions : We propose to embrace the autonomy of motivated catalogue teams and invest in their collaboration via minimal standardisation efforts such as clear data licensing, persistent identifiers for linking same records between catalogues, minimal metadata ‘common data elements’ using shared ontologies, symmetric architectures for data sharing (push/pull) with clear provenance tracks to process updates and acknowledge original contributors. And most importantly, we encourage the creation of environments for collaboration and resource sharing between catalogue developers, building on international networks such as OpenAIRE and research data alliance, as well as domain specific ESFRIs such as BBMRI and ELIXIR

Overview of retrospective data harmonisation in the MINDMAP project : process and results

publishedVersionPaid Open Acces

MINDMAP : establishing an integrated database infrastructure for research in ageing, mental well-being, and the urban environment

Background: Urbanization and ageing have important implications for public mental health and well-being. Cities pose major challenges for older citizens, but also offer opportunities to develop, test, and implement policies, services, infrastructure, and interventions that promote mental well-being. The MINDMAP project aims to identify the opportunities and challenges posed by urban environmental characteristics for the promotion and management of mental well-being and cognitive function of older individuals. Methods: MINDMAP aims to achieve its research objectives by bringing together longitudinal studies from 11 countries covering over 35 cities linked to databases of area-level environmental exposures and social and urban policy indicators. The infrastructure supporting integration of this data will allow multiple MINDMAP investigators to safely and remotely co-analyse individual-level and area-level data. Individual-level data is derived from baseline and follow-up measurements of ten participating cohort studies and provides information on mental well-being outcomes, sociodemographic variables, health behaviour characteristics, social factors, measures of frailty, physical function indicators, and chronic conditions, as well as blood derived clinical biochemistry-based biomarkers and genetic biomarkers. Area-level information on physical environment characteristics (e.g. green spaces, transportation), socioeconomic and sociodemographic characteristics (e.g. neighbourhood income, residential segregation, residential density), and social environment characteristics (e.g. social cohesion, criminality) and national and urban social policies is derived from publically available sources such as geoportals and administrative databases. The linkage, harmonization, and analysis of data from different sources are being carried out using piloted tools to optimize the validity of the research results and transparency of the methodology. Discussion: MINDMAP is a novel research collaboration that is combining population-based cohort data with publicly available datasets not typically used for ageing and mental well-being research. Integration of various data sources and observational units into a single platform will help to explain the differences in ageing-related mental and cognitive disorders both within as well as between cities in Europe, the US, Canada, and Russia and to assess the causal pathways and interactions between the urban environment and the individual determinants of mental well-being and cognitive ageing in older adults.Peer reviewe

Rationale for a Swedish cohort consortium

We herein outline the rationale for a Swedish cohort consortium, aiming to facilitate greater use of Swedish cohorts for world-class research. Coordination of all Swedish prospective population-based cohorts in a common infrastructure would enable more precise research findings and facilitate research on rare exposures and outcomes, leading to better utilization of study participants' data, better return of funders' investments, and higher benefit to patients and populations. We motivate the proposed infrastructure partly by lessons learned from a pilot study encompassing data from 21 cohorts. We envisage a standing Swedish cohort consortium that would drive development of epidemiological research methods and strengthen the Swedish as well as international epidemiological competence, community, and competitiveness.Peer reviewe

Maelstrom Research guidelines for rigorous retrospective data harmonization

Background: It is widely accepted and acknowledged that data harmonization is crucial: in its absence, the co-analysis of major tranches of high quality extant data is liable to inefficiency or error. However, despite its widespread practice, no formalized/systematic guidelines exist to ensure high quality retrospective data harmonization. Methods: To better understand real-world harmonization practices and facilitate development of formal guidelines, three interrelated initiatives were undertaken between 2006 and 2015. They included a phone survey with 34 major international research initiatives, a series of workshops with experts, and case studies applying the proposed guidelines. Results: A wide range of projects use retrospective harmonization to support their research activities but even when appropriate approaches are used, the terminologies, procedures, technologies and methods adopted vary markedly. The generic guidelines outlined in this article delineate the essentials required and describe an interdependent step-by-step approach to harmonization: 0) define the research question, objectives and protocol; 1) assemble pre-existing knowledge and select studies; 2) define targeted variables and evaluate harmonization potential; 3) process data; 4) estimate quality of the harmonized dataset(s) generated; and 5) disseminate and preserve final harmonization products. Conclusions: This manuscript provides guidelines aiming to encourage rigorous and effective approaches to harmonization which are comprehensively and transparently documented and straightforward to interpret and implement. This can be seen as a key step towards implementing guiding principles analogous to those that are well recognised as being essential in securing the foundational underpinning of systematic reviews and the meta-analysis of clinical trials