Data harmonization and federated analysis of population-based studies: the BioSHaRE project

Evaluating the harmonization potential of oral health-related questionnaires in national longitudinal birth and child cohort surveys

BACKGROUND/OBJECTIVES

Effective use of longitudinal study data is challenging because of divergences in the construct definitions and measurement approaches over time, between studies and across disciplines. One approach to overcome these challenges is data harmonization. Data harmonization is a practice used to improve variable comparability and reduce heterogeneity across studies. This study describes the process used to evaluate the harmonization potential of oral health-related variables across each survey wave.

METHODS

National child cohort surveys with similar themes/objectives conducted in the last two decades were selected. The Maelstrom Research Guidelines were followed for harmonization potential evaluation.

RESULTS

Seven nationally representative child cohort surveys were included and questionnaires examined from 50 survey waves. Questionnaires were classified into three domains and fifteen constructs and summarized by age groups. A DataSchema (a list of core variables representing the suitable version of the oral health outcomes and risk factors) was compiled comprising 42 variables. For each study wave, the potential (or not) to generate each DataSchema variable was evaluated. Of the 2100 harmonization status assessments, 543 (26%) were complete. Approximately 50% of the DataSchema variables can be generated across at least four cohort surveys while only 10% (n = 4) variables can be generated across all surveys. For each survey, the DataSchema variables that can be generated ranged between 26% and 76%.

CONCLUSION

Data harmonization can improve the comparability of variables both within and across surveys. For future cohort surveys, the authors advocate more consistency and standardization in survey questionnaires within and between surveys.

Cohort profile: Worldwide Collaboration on OsteoArthritis prediCtion for the Hip (World COACH) - an international consortium of prospective cohort studies with individual participant data on hip osteoarthritis

PURPOSE

Hip osteoarthritis (OA) is a major cause of pain and disability worldwide. Lack of effective therapies may reflect poor knowledge on its aetiology and risk factors, and result in the management of end-stage hip OA with costly joint replacement. The Worldwide Collaboration on OsteoArthritis prediCtion for the Hip (World COACH) consortium was established to pool and harmonise individual participant data from prospective cohort studies. The consortium aims to better understand determinants and risk factors for the development and progression of hip OA, to optimise and automate methods for (imaging) analysis, and to develop a personalised prediction model for hip OA.

PARTICIPANTS

World COACH aimed to include participants of prospective cohort studies with ≥200 participants, that have hip imaging data available from at least 2 time points at least 4 years apart. All individual participant data, including clinical data, imaging (data), biochemical markers, questionnaires and genetic data, were collected and pooled into a single, individual-level database.

FINDINGS TO DATE

World COACH currently consists of 9 cohorts, with 38 021 participants aged 18-80 years at baseline. Overall, 71% of the participants were women and mean baseline age was 65.3±8.6 years. Over 34 000 participants had baseline pelvic radiographs available, and over 22 000 had an additional pelvic radiograph after 8-12 years of follow-up. Even longer radiographic follow-up (15-25 years) is available for over 6000 of these participants.

FUTURE PLANS

The World COACH consortium offers unique opportunities for studies on the relationship between determinants/risk factors and the development or progression of hip OA, by using harmonised data on clinical findings, imaging, biomarkers, genetics and lifestyle. This provides a unique opportunity to develop a personalised hip OA risk prediction model and to optimise methods for imaging analysis of the hip.

Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study

Introduction

Type 2 diabetes (T2D) onset, progression and outcomes differ substantially between individuals. Multi-omics analyses may allow a deeper understanding of these differences and ultimately facilitate personalised treatments. Here, in an unsupervised "bottom-up" approach, we attempt to group T2D patients based solely on -omics data generated from plasma.

Methods

Circulating plasma lipidomic and proteomic data from two independent clinical cohorts, Hoorn Diabetes Care System (DCS) and Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS), were analysed using Similarity Network Fusion. The resulting patient network was analysed with Logistic and Cox regression modelling to explore relationships between plasma -omic profiles and clinical characteristics.

Results

From a total of 1,134 subjects in the two cohorts, levels of 180 circulating plasma lipids and 1195 proteins were used to separate patients into two subgroups. These differed in terms of glycaemic deterioration (Hazard Ratio=0.56;0.73), insulin sensitivity and secretion (C-peptide, p=3.7e-11;2.5e-06, DCS and GoDARTS, respectively; Homeostatic model assessment 2 (HOMA2)-B; -IR; -S, p=0.0008;4.2e-11;1.1e-09, only in DCS). The main molecular signatures separating the two groups included triacylglycerols, sphingomyelin, testican-1 and interleukin 18 receptor.

Conclusions

Using an unsupervised network-based fusion method on plasma lipidomics and proteomics data from two independent cohorts, we were able to identify two subgroups of T2D patients differing in terms of disease severity. The molecular signatures identified within these subgroups provide insights into disease mechanisms and possibly new prognostic markers for T2D.

INSPIRE datahub: a pan-African integrated suite of services for harmonising longitudinal population health data using OHDSI tools

Introduction

Population health data integration remains a critical challenge in low- and middle-income countries (LMIC), hindering the generation of actionable insights to inform policy and decision-making. This paper proposes a pan-African, Findable, Accessible, Interoperable, and Reusable (FAIR) research architecture and infrastructure named the INSPIRE datahub. This cloud-based Platform-as-a-Service (PaaS) and on-premises setup aims to enhance the discovery, integration, and analysis of clinical, population-based surveys, and other health data sources.

Methods

The INSPIRE datahub, part of the Implementation Network for Sharing Population Information from Research Entities (INSPIRE), employs the Observational Health Data Sciences and Informatics (OHDSI) open-source stack of tools and the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) to harmonise data from African longitudinal population studies. Operating on Microsoft Azure and Amazon Web Services cloud platforms, and on on-premises servers, the architecture offers adaptability and scalability for other cloud providers and technology infrastructure. The OHDSI-based tools enable a comprehensive suite of services for data pipeline development, profiling, mapping, extraction, transformation, loading, documentation, anonymization, and analysis.

Results

The INSPIRE datahub's "On-ramp" services facilitate the integration of data and metadata from diverse sources into the OMOP CDM. The datahub supports the implementation of OMOP CDM across data producers, harmonizing source data semantically with standard vocabularies and structurally conforming to OMOP table structures. Leveraging OHDSI tools, the datahub performs quality assessment and analysis of the transformed data. It ensures FAIR data by establishing metadata flows, capturing provenance throughout the ETL processes, and providing accessible metadata for potential users. The ETL provenance is documented in a machine- and human-readable Implementation Guide (IG), enhancing transparency and usability.

Conclusion

The pan-African INSPIRE datahub presents a scalable and systematic solution for integrating health data in LMICs. By adhering to FAIR principles and leveraging established standards like OMOP CDM, this architecture addresses the current gap in generating evidence to support policy and decision-making for improving the well-being of LMIC populations. The federated research network provisions allow data producers to maintain control over their data, fostering collaboration while respecting data privacy and security concerns. A use-case demonstrated the pipeline using OHDSI and other open-source tools.

Sharing Medical Big Data While Preserving Patient Confidentiality in Innovative Medicines Initiative: A Summary and Case Report from BigData@Heart

Sharing individual patient data (IPD) is a simple concept but complex to achieve due to data privacy and data security concerns, underdeveloped guidelines, and legal barriers. Sharing IPD is additionally difficult in big data-driven collaborations such as Bigdata@Heart in the Innovative Medicines Initiative, due to competing interests between diverse consortium members. One project within BigData@Heart, case study 1, needed to pool data from seven heterogeneous data sets: five randomized controlled trials from three different industry partners, and two disease registries. Sharing IPD was not considered feasible due to legal requirements and the sensitive medical nature of these data. In addition, harmonizing the data sets for a federated data analysis was difficult due to capacity constraints and the heterogeneity of the data sets. An alternative option was to share summary statistics through contingency tables. Here it is demonstrated that this method along with anonymization methods to ensure patient anonymity had minimal loss of information. Although sharing IPD should continue to be encouraged and strived for, our approach achieved a good balance between data transparency while protecting patient privacy. It also allowed a successful collaboration between industry and academia.

Changes in neonatal morbidity, neonatal care practices, and length of hospital stay of surviving infants born very preterm in the Netherlands in the 1980s and in the 2000s: a comparison analysis with identical characteristics definitions

BACKGROUND

This study evaluates changes in the neonatal morbidity, the neonatal care practices, and the length of hospital stay of surviving very preterm (VP) infants born in the Netherlands in the 1980s and in the 2000s; a period over which historical improvements were introduced into neonatal care. We, herein, also study whether these changes in neonatal morbidity, neonatal care practices and length of hospital stay are associated with sociodemographic, prenatal, and infant characteristics.

METHODS

Two community-based cohorts from 1983 (POPS) and 2002-03 (LOLLIPOP) have provided the perinatal data for our study. The analysis enrolled 1,228 participants born VP (before the 32nd week of gestation) and surviving to 2 years of age without any severe congenital malformation. A rigorous harmonisation protocol ensured a precise comparison of the cohorts by using identical definitions of the perinatal characteristics.

RESULTS

In 2003, mothers were older when giving birth, had higher multiple birth rates, and significantly more parents had received higher education. In 2003, less VP infants had severe intraventricular haemorrhage and sepsis and relatively more received continuous positive airway pressure, mechanical ventilation and caffeine therapy than in 1983. Antenatal corticosteroids and surfactant therapy were provided only in 2003. The length of the stay in the neonatal intensive care unit and in hospital had decreased in 2003 by 22 and 11 days, respectively. Differences persisted after adjustment for sociodemographic, prenatal, and infant characteristics.

CONCLUSIONS

Neonatal morbidities of the surviving VP infants in this study have not increased, and exhibit improvements for various characteristics in two cohorts born 20 years apart with comparable gestational age and birth weight. Our data suggest that the improvements found are associated with more advanced therapeutic approaches and new national protocols in place, and less so with sociodemographic changes. This analysis provides a basis for further comparative analyses of the health and the development of VP children, particularly with regard to long-term outcomes.

Recent Economic Intimate Partner Violence and Posttraumatic Stress Symptoms Among a Racially and Ethnically Diverse Sample of U.S. Women Experiencing Intimate Partner Violence

Posttraumatic stress disorder (PTSD) is a prevalent consequence of physical and sexual intimate partner violence (IPV); however, little is known about the unique contributions of economic IPV. Furthermore, women's economic self-sufficiency may explicate the potential relationship between economic IPV and PTSD symptoms. Guided by the Stress Process Theory and Intersectionality, this study examined associations between economic IPV and women's PTSD symptoms and assessed economic self-sufficiency as a mediator. Participants were 255 adult women experiencing IPV recruited from metropolitan Baltimore, MD, and the state of CT who participated in two different studies. Participants completed surveys on IPV, economic self-sufficiency, and PTSD. Path analyses were conducted to examine direct and indirect associations of economic IPV with economic self-sufficiency and PTSD. Economic IPV was uniquely associated with PTSD symptoms while controlling for other forms of IPV. Economic self-sufficiency significantly partially mediated the association between economic IPV and PTSD symptoms such that economic IPV was associated with PTSD symptoms through economic self-sufficiency. Economic IPV may limit women's ability to make autonomous decisions related to finances, which could be distressing. The mental health impact of economic IPV may be particularly debilitating for women with low economic self-sufficiency as their posttraumatic stress occurs within the context of feeling unable to meet their financial goals and also having a partner control their economic resources. Fostering economic empowerment and asset building may be a strengths-based approach to reduce the PTSD symptomatology among women experiencing IPV.

The successes and challenges of harmonising juvenile idiopathic arthritis (JIA) datasets to create a large-scale JIA data resource

BACKGROUND

CLUSTER is a UK consortium focussed on precision medicine research in JIA/JIA-Uveitis. As part of this programme, a large-scale JIA data resource was created by harmonizing and pooling existing real-world studies. Here we present challenges and progress towards creation of this unique large JIA dataset.

METHODS

Four real-world studies contributed data; two clinical datasets of JIA patients starting first-line methotrexate (MTX) or tumour necrosis factor inhibitors (TNFi) were created. Variables were selected based on a previously developed core dataset, and encrypted NHS numbers were used to identify children contributing similar data across multiple studies.

RESULTS

Of 7013 records (from 5435 individuals), 2882 (1304 individuals) represented the same child across studies. The final datasets contain 2899 (MTX) and 2401 (TNFi) unique patients; 1018 are in both datasets. Missingness ranged from 10 to 60% and was not improved through harmonisation.

CONCLUSIONS

Combining data across studies has achieved dataset sizes rarely seen in JIA, invaluable to progressing research. Losing variable specificity and missingness, and their impact on future analyses requires further consideration.

Comparing Decentralized Learning Methods for Health Data Models to Nondecentralized Alternatives: Protocol for a Systematic Review

BACKGROUND

Considering the soaring health-related costs directed toward a growing, aging, and comorbid population, the health sector needs effective data-driven interventions while managing rising care costs. While health interventions using data mining have become more robust and adopted, they often demand high-quality big data. However, growing privacy concerns have hindered large-scale data sharing. In parallel, recently introduced legal instruments require complex implementations, especially when it comes to biomedical data. New privacy-preserving technologies, such as decentralized learning, make it possible to create health models without mobilizing data sets by using distributed computation principles. Several multinational partnerships, including a recent agreement between the United States and the European Union, are adopting these techniques for next-generation data science. While these approaches are promising, there is no clear and robust evidence synthesis of health care applications.

OBJECTIVE

The main aim is to compare the performance among health data models (eg, automated diagnosis and mortality prediction) developed using decentralized learning approaches (eg, federated and blockchain) to those using centralized or local methods. Secondary aims are comparing the privacy compromise and resource use among model architectures.

METHODS

We will conduct a systematic review using the first-ever registered research protocol for this topic following a robust search methodology, including several biomedical and computational databases. This work will compare health data models differing in development architecture, grouping them according to their clinical applications. For reporting purposes, a PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 flow diagram will be presented. CHARMS (Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies)-based forms will be used for data extraction and to assess the risk of bias, alongside PROBAST (Prediction Model Risk of Bias Assessment Tool). All effect measures in the original studies will be reported.

RESULTS

The queries and data extractions are expected to start on February 28, 2023, and end by July 31, 2023. The research protocol was registered with PROSPERO, under the number 393126, on February 3, 2023. With this protocol, we detail how we will conduct the systematic review. With that study, we aim to summarize the progress and findings from state-of-the-art decentralized learning models in health care in comparison to their local and centralized counterparts. Results are expected to clarify the consensuses and heterogeneities reported and help guide the research and development of new robust and sustainable applications to address the health data privacy problem, with applicability in real-world settings.

CONCLUSIONS

We expect to clearly present the status quo of these privacy-preserving technologies in health care. With this robust synthesis of the currently available scientific evidence, the review will inform health technology assessment and evidence-based decisions, from health professionals, data scientists, and policy makers alike. Importantly, it should also guide the development and application of new tools in service of patients' privacy and future research.

TRIAL REGISTRATION

PROSPERO 393126; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=393126.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/45823.

FAIR environmental and health registry (FAIREHR)- supporting the science to policy interface and life science research, development and innovation

The environmental impact on health is an inevitable by-product of human activity. Environmental health sciences is a multidisciplinary field addressing complex issues on how people are exposed to hazardous chemicals that can potentially affect adversely the health of present and future generations. Exposure sciences and environmental epidemiology are becoming increasingly data-driven and their efficiency and effectiveness can significantly improve by implementing the FAIR (findable, accessible, interoperable, reusable) principles for scientific data management and stewardship. This will enable data integration, interoperability and (re)use while also facilitating the use of new and powerful analytical tools such as artificial intelligence and machine learning in the benefit of public health policy, and research, development and innovation (RDI). Early research planning is critical to ensuring data is FAIR at the outset. This entails a well-informed and planned strategy concerning the identification of appropriate data and metadata to be gathered, along with established procedures for their collection, documentation, and management. Furthermore, suitable approaches must be implemented to evaluate and ensure the quality of the data. Therefore, the 'Europe Regional Chapter of the International Society of Exposure Science' (ISES Europe) human biomonitoring working group (ISES Europe HBM WG) proposes the development of a FAIR Environment and health registry (FAIREHR) (hereafter FAIREHR). FAIR Environment and health registry offers preregistration of studies on exposure sciences and environmental epidemiology using HBM (as a starting point) across all areas of environmental and occupational health globally. The registry is proposed to receive a dedicated web-based interface, to be electronically searchable and to be available to all relevant data providers, users and stakeholders. Planned Human biomonitoring studies would ideally be registered before formal recruitment of study participants. The resulting FAIREHR would contain public records of metadata such as study design, data management, an audit trail of major changes to planned methods, details of when the study will be completed, and links to resulting publications and data repositories when provided by the authors. The FAIREHR would function as an integrated platform designed to cater to the needs of scientists, companies, publishers, and policymakers by providing user-friendly features. The implementation of FAIREHR is expected to yield significant benefits in terms of enabling more effective utilization of human biomonitoring (HBM) data.

Ethnic disparities in ambient air and traffic-related pollution exposure and ethnic-specific impacts on clinical biomarker levels

BACKGROUND

Although characterizing the inequality in pollution exposure burden across ethnic groups and the ethnic-specific exposure associations is of great social and public health importance, it has not been systematically investigated in large population studies.

METHODS

The UK Biobank data (N = 485, 806) of individual-level air ambient and traffic-related pollution exposure, biomarkers routinely used in clinical practice, genotype, life-style factors, and socioeconomic status were analyzed. Air pollution exposure estimates were compared among six genetically inferred ethnic groups. We also quantified the association between exposure and biomarkers within and across ethnicities.

RESULTS

Non-European participants (defined by genetics) disproportionately bear a higher burden of exposure than their European counterparts even after adjusting for covariables including socioeconomic status. For example, exposure to NO₂ in people with African ancestry was 30.7 % higher (p = 1.5E-786) than European subjects. Within the genetically defined African group, larger African genetic ancestry proportion (AGAP) was linked to higher ambient air pollutant exposure. Trans-Ethnic analysis identified 32 clinical biomarkers associated with environmental exposure. For 13 biomarkers, the association with exposure was significantly different or even in opposing directions across ethnic groups.

CONCLUSIONS

Substantial disparities in air pollution exposure was observed among genetically-defined ethnic groups. Most importantly, we show that the impact of exposure on biomarkers varies by ethnicity. Reducing the disproportionally high exposure burden on non-European populations and alleviating the adverse consequences in an ethnic-specific manner are of great urgency and significance.

Life course of retrospective harmonization initiatives: key elements to consider

Optimizing research on the developmental origins of health and disease (DOHaD) involves implementing initiatives maximizing the use of the available cohort study data; achieving sufficient statistical power to support subgroup analysis; and using participant data presenting adequate follow-up and exposure heterogeneity. It also involves being able to undertake comparison, cross-validation, or replication across data sets. To answer these requirements, cohort study data need to be findable, accessible, interoperable, and reusable (FAIR), and more particularly, it often needs to be harmonized. Harmonization is required to achieve or improve comparability of the putatively equivalent measures collected by different studies on different individuals. Although the characteristics of the research initiatives generating and using harmonized data vary extensively, all are confronted by similar issues. Having to collate, understand, process, host, and co-analyze data from individual cohort studies is particularly challenging. The scientific success and timely management of projects can be facilitated by an ensemble of factors. The current document provides an overview of the 'life course' of research projects requiring harmonization of existing data and highlights key elements to be considered from the inception to the end of the project.

Harmonizing Ethno-Regionally Diverse Datasets to Advance the Global Epidemiology of Dementia

Understanding dementia and cognitive impairment is a global effort needing data from multiple sources across diverse ethno-regional groups. Methodological heterogeneity means that these data often require harmonization to make them comparable before analysis. We discuss the benefits and challenges of harmonization, both retrospective and prospective, broadly and with a focus on data types that require particular sorts of approaches, including neuropsychological test scores and neuroimaging data. Throughout our discussion, we illustrate general principles and give examples of specific approaches in the context of contemporary research in dementia and cognitive impairment from around the world.

Harmonising electronic health records for reproducible research: challenges, solutions and recommendations from a UK-wide COVID-19 research collaboration

BACKGROUND

The CVD-COVID-UK consortium was formed to understand the relationship between COVID-19 and cardiovascular diseases through analyses of harmonised electronic health records (EHRs) across the four UK nations. Beyond COVID-19, data harmonisation and common approaches enable analysis within and across independent Trusted Research Environments. Here we describe the reproducible harmonisation method developed using large-scale EHRs in Wales to accommodate the fast and efficient implementation of cross-nation analysis in England and Wales as part of the CVD-COVID-UK programme. We characterise current challenges and share lessons learnt.

METHODS

Serving the scope and scalability of multiple study protocols, we used linked, anonymised individual-level EHR, demographic and administrative data held within the SAIL Databank for the population of Wales. The harmonisation method was implemented as a four-layer reproducible process, starting from raw data in the first layer. Then each of the layers two to four is framed by, but not limited to, the characterised challenges and lessons learnt. We achieved curated data as part of our second layer, followed by extracting phenotyped data in the third layer. We captured any project-specific requirements in the fourth layer.

RESULTS

Using the implemented four-layer harmonisation method, we retrieved approximately 100 health-related variables for the 3.2 million individuals in Wales, which are harmonised with corresponding variables for > 56 million individuals in England. We processed 13 data sources into the first layer of our harmonisation method: five of these are updated daily or weekly, and the rest at various frequencies providing sufficient data flow updates for frequent capturing of up-to-date demographic, administrative and clinical information.

CONCLUSIONS

We implemented an efficient, transparent, scalable, and reproducible harmonisation method that enables multi-nation collaborative research. With a current focus on COVID-19 and its relationship with cardiovascular outcomes, the harmonised data has supported a wide range of research activities across the UK.

A. Sørensen T, Elhakeem A, Santos AC, Pinot de Moira A, Heude B, Iñiguez C, Pizzi C, Simons E, Voerman E, Corpeleijn E, Zariouh F, Santorelli G, Inskip HM, Barros H, Carson J, Harris JR, Nader JL, Ronkainen J, Strandberg-Larsen K, Santa-Marina L, Calas L, Cederkvist L, Popovic M, Charles MA, Welten M, Vrijheid M, Azad M, Subbarao P, Burton P, Mandhane PJ, Huang RC, Wilson RC, Haakma S, Fernández-Barrés S, Turvey S, Santos S, Tough SC, Sebert S, Moraes TJ, Salika T, Jaddoe VWV, Lawlor DA, Nybo Andersen AM. Gestational age at birth and body size from infancy through adolescence: An individual participant data meta-analysis on 253,810 singletons in 16 birth cohort studies

BACKGROUND

Preterm birth is the leading cause of perinatal morbidity and mortality and is associated with adverse developmental and long-term health outcomes, including several cardiometabolic risk factors and outcomes. However, evidence about the association of preterm birth with later body size derives mainly from studies using birth weight as a proxy of prematurity rather than an actual length of gestation. We investigated the association of gestational age (GA) at birth with body size from infancy through adolescence.

METHODS AND FINDINGS

We conducted a two-stage individual participant data (IPD) meta-analysis using data from 253,810 mother-child dyads from 16 general population-based cohort studies in Europe (Denmark, Finland, France, Italy, Norway, Portugal, Spain, the Netherlands, United Kingdom), North America (Canada), and Australasia (Australia) to estimate the association of GA with body mass index (BMI) and overweight (including obesity) adjusted for the following maternal characteristics as potential confounders: education, height, prepregnancy BMI, ethnic background, parity, smoking during pregnancy, age at child's birth, gestational diabetes and hypertension, and preeclampsia. Pregnancy and birth cohort studies from the LifeCycle and the EUCAN-Connect projects were invited and were eligible for inclusion if they had information on GA and minimum one measurement of BMI between infancy and adolescence. Using a federated analytical tool (DataSHIELD), we fitted linear and logistic regression models in each cohort separately with a complete-case approach and combined the regression estimates and standard errors through random-effects study-level meta-analysis providing an overall effect estimate at early infancy (>0.0 to 0.5 years), late infancy (>0.5 to 2.0 years), early childhood (>2.0 to 5.0 years), mid-childhood (>5.0 to 9.0 years), late childhood (>9.0 to 14.0 years), and adolescence (>14.0 to 19.0 years). GA was positively associated with BMI in the first decade of life, with the greatest increase in mean BMI z-score during early infancy (0.02, 95% confidence interval (CI): 0.00; 0.05, p < 0.05) per week of increase in GA, while in adolescence, preterm individuals reached similar levels of BMI (0.00, 95% CI: -0.01; 0.01, p 0.9) as term counterparts. The association between GA and overweight revealed a similar pattern of association with an increase in odds ratio (OR) of overweight from late infancy through mid-childhood (OR 1.01 to 1.02) per week increase in GA. By adolescence, however, GA was slightly negatively associated with the risk of overweight (OR 0.98 [95% CI: 0.97; 1.00], p 0.1) per week of increase in GA. Although based on only four cohorts (n = 32,089) that reached the age of adolescence, data suggest that individuals born very preterm may be at increased odds of overweight (OR 1.46 [95% CI: 1.03; 2.08], p < 0.05) compared with term counterparts. Findings were consistent across cohorts and sensitivity analyses despite considerable heterogeneity in cohort characteristics. However, residual confounding may be a limitation in this study, while findings may be less generalisable to settings in low- and middle-income countries.

CONCLUSIONS

This study based on data from infancy through adolescence from 16 cohort studies found that GA may be important for body size in infancy, but the strength of association attenuates consistently with age. By adolescence, preterm individuals have on average a similar mean BMI to peers born at term.

HUNT for better public health

Aims:

The Trøndelag Health Study (HUNT) has collected population data through comprehensive decennial surveys over the last four decades and has so far collected data from 240,000 participants. The participants are identified with the unique Norwegian birth number, which enables them to be followed throughout different life stages, from survey to survey, and to endpoint measures in Norwegian national health registers without attrition bias.

Methods:

The study design of HUNT offers several advantages: it provides an overview of the public health development in the population over decades, the data can be used in health services research, clinical epidemiology, studies of causation, trajectories, and consequences of diseases, and to study gene × environment interactions.

Results:

HUNT data have shown major shifts in public health trends, such as decreasing mean blood pressure and resting heart rate among adults, increasing prevalence of obesity, geographical and socioeconomic inequalities in health, increasing mental health distress among adolescents and young adults with an opposite development among the elderly. Data from HUNT have been used in several major international research projects, where data harmonization with several other population cohorts internationally has been done. HUNT has placed great emphasis on safeguarding research ethics, privacy, and data security. The Norwegian authorities established national regulations for the surveys from the time General Data Protection Regulation was introduced in 2018.

Conclusions:

Researchers can apply for HUNT data access from HUNT Research Centre provided they have obtained project approval from the Regional Committee for Medical and Health Research Ethics. Researchers not affiliated to a Norwegian research institution must collaborate with and apply through a Norwegian principal investigator. Information on the application and conditions for data access is available at www.ntnu.edu/hunt/data.

A review of harmonization methods for studying dietary patterns

Data harmonization is the process by which each of the variables from different research studies are standardized to similar units resulting in comparable datasets. These data may be integrated for more powerful and accurate examination and prediction of outcomes for use in the intelligent and smart electronic health software programs and systems. Prospective harmonization is performed when researchers create guidelines for gathering and managing the data before data collection begins. In contrast, retrospective harmonization is performed by pooling previously collected data from various studies using expert domain knowledge to identify and translate variables. In nutritional epidemiology, dietary data harmonization is often necessary to construct the nutrient and food databases necessary to answer complex research questions and develop effective public health policy. In this paper, we review methods for effective data harmonization, including developing a harmonization plan, which common standards already exist for harmonization, and defining variables needed to harmonize datasets. Currently, several large-scale studies maintain harmonized nutrient databases, especially in Europe, and steps have been proposed to inform the retrospective harmonization process. As an example, data harmonization methods are applied to several U.S longitudinal diet datasets. Based on our review, considerations for future dietary data harmonization include user agreements for sharing private data among participating studies, defining variables and data dictionaries that accurately map variables among studies, and the use of secure data storage servers to maintain privacy. These considerations establish necessary components of harmonized data for smart health applications which can promote healthier eating and provide greater insights into the effect of dietary patterns on health.

LongITools: Dynamic longitudinal exposome trajectories in cardiovascular and metabolic noncommunicable diseases

The current epidemics of cardiovascular and metabolic noncommunicable diseases have emerged alongside dramatic modifications in lifestyle and living environments. These correspond to changes in our "modern" postwar societies globally characterized by rural-to-urban migration, modernization of agricultural practices, and transportation, climate change, and aging. Evidence suggests that these changes are related to each other, although the social and biological mechanisms as well as their interactions have yet to be uncovered. LongITools, as one of the 9 projects included in the European Human Exposome Network, will tackle this environmental health equation linking multidimensional environmental exposures to the occurrence of cardiovascular and metabolic noncommunicable diseases.

COMETS Analytics: An Online Tool for Analyzing and Meta-Analyzing Metabolomics Data in Large Research Consortia

Consortium-based research is crucial for producing reliable, high-quality findings, but existing tools for consortium studies have important drawbacks with respect to data protection, ease of deployment, and analytical rigor. To address these concerns, we developed COnsortium of METabolomics Studies (COMETS) Analytics to support and streamline consortium-based analyses of metabolomics and other -omics data. The application requires no specialized expertise and can be run locally to guarantee data protection or through a Web-based server for convenience and speed. Unlike other Web-based tools, COMETS Analytics enables standardized analyses to be run across all cohorts, using an algorithmic, reproducible approach to diagnose, document, and fix model issues. This eliminates the time-consuming and potentially error-prone step of manually customizing models by cohort, helping to accelerate consortium-based projects and enhancing analytical reproducibility. We demonstrated that the application scales well by performing 2 data analyses in 45 cohort studies that together comprised measurements of 4,647 metabolites in up to 134,742 participants. COMETS Analytics performed well in this test, as judged by the minimal errors that analysts had in preparing data inputs and the successful execution of all models attempted. As metabolomics gathers momentum among biomedical and epidemiologic researchers, COMETS Analytics may be a useful tool for facilitating large-scale consortium-based research.

Applied machine learning in Alzheimer's disease research: omics, imaging, and clinical data

Alzheimer's disease (AD) remains a devastating neurodegenerative disease with few preventive or curative treatments available. Modern technology developments of high-throughput omics platforms and imaging equipment provide unprecedented opportunities to study the etiology and progression of this disease. Meanwhile, the vast amount of data from various modalities, such as genetics, proteomics, transcriptomics, and imaging, as well as clinical features impose great challenges in data integration and analysis. Machine learning (ML) methods offer novel techniques to address high dimensional data, integrate data from different sources, model the etiological and clinical heterogeneity, and discover new biomarkers. These directions have the potential to help us better manage the disease progression and develop novel treatment strategies. This mini-review paper summarizes different ML methods that have been applied to study AD using single-platform or multi-modal data. We review the current state of ML applications for five key directions of AD research: disease classification, drug repurposing, subtyping, progression prediction, and biomarker discovery. This summary provides insights about the current research status of ML-based AD research and highlights potential directions for future research.

Cohort description: Measures of early-life behaviour and later psychopathology in the LifeCycle Project - EU Child Cohort Network

BACKGROUND

The EU LifeCycle Project was launched in 2017 to combine, harmonise, and analyse data from more than 250,000 participants across Europe and Australia, involving cohorts participating in the EU-funded LifeCycle Project. The purpose of this cohort description is to provide a detailed overview over the major measures within mental health domains that are available in 17 European and Australian cohorts participating in the LifeCycle Project.

METHODS

Data on cognitive, behavioural and psychological development has been collected on participants from birth until adulthood through questionnaire and medical data. We developed an inventory of the available data by mapping individual instruments, domain types, and age groups, providing the basis for statistical harmonization across mental health measures.

RESULTS

The mental health data in LifeCycle contain longitudinal and cross-sectional data for ages 0-18+ years, covering domains across a wide range of behavioural and psychopathology indicators and outcomes (including executive function, depression, ADHD and cognition). These data span a unique combination of qualitative data collected through behavioural/cognitive/mental health questionnaires and examination, as well as data from biological samples and indices in the form of brain imaging (MRI, foetal ultrasound) and DNA methylation data. Harmonized variables on a subset of mental health domains have been developed, providing statistical equivalence of measures required for longitudinal meta-analyses across instruments and cohorts.

CONCLUSION

Mental health data harmonized through the LifeCycle project can be used to study life course trajectories and exposure-outcome models that examine early life risk factors for mental illness and develop predictive markers for later-life disease.

Experiences from the harmonization of Finnish national population-based health survey data

Aims: There are several advantages to pooling survey data from individual studies over time or across different countries. Our aim is to share our experiences on harmonizing data from 13 Finnish health examination surveys covering the years 1972–2017 and to describe the challenges related to harmonizing different variable types using two questionnaire variables – blood pressure measurement and total cholesterol assessment – as examples. Methods: Data from Finnish national population-based health surveys were harmonized as part of the research project ‘Projections of the Burden of Disease and Disability in Finland – Health Policy Prospects’, including variables from questionnaires, objective health measurements and results from the laboratory analysis of biological samples. The process presented in the Maelstrom Research guidelines for data harmonization was followed with minor adjustments. Results: The harmonization of data from objective measurements and biomarkers was reasonably straightforward, but questionnaire items proved more challenging. Some questions and response options had changed during the covered time period. This concerned, for example, questionnaire items on the availability and use of medication and diet. Conclusions: The long time period – 45 years – made harmonization more complicated. The survey questions or response options had changed for some topics due to changes in society. However, common core variables for topics that were especially relevant for the project, such as lifestyle factors and certain diseases or conditions, could be harmonized with sufficient comparability. For future surveys, the use of standardized survey methods and the proper documentation of data collection are recommended to facilitate harmonization.

Pre-statistical harmonization of behavrioal instruments across eight surveys and trials

BACKGROUND

Data harmonization is a powerful method to equilibrate items in measures that evaluate the same underlying construct. There are multiple measures to evaluate dementia related behavioral symptoms. Pre-statistical harmonization of behavioral instruments in dementia research is the first step to develop a statistical crosswalk between measures. Studies that conduct pre-statistical harmonization of behavioral instruments rarely document their methods in a structured, reproducible manner. This is a crucial step which entails careful review, documentation and scrutiny of source data to ensure sufficient comparability between items prior to data pooling. Here, we document the pre-statistical harmonization of items measuring behavioral and psychological symptoms among people with dementia. We provide a box of recommended procedure for future studies.

METHODS

We identified behavioral instruments that are used in clinical practice, a national survey, and randomized trials of dementia care interventions. We rigorously reviewed question content and scoring procedures to establish sufficient comparability across items as well as item quality prior to data pooling. Additionally, we standardized coding to Stata-readable format, which allowed us to automate approaches to identify potential cross-study differences in items and low-quality items. To ensure reasonable model fit for statistical co-calibration, we estimated two-parameter logistic Item Response Theory models within each of the eight studies.

RESULTS

We identified 59 items from 11 behavioral instruments across the eight datasets. We found considerable cross-study heterogeneity in administration and coding procedures for items that measure the same attribute. Discrepancies existed in terms of directionality and quantification of behavioral symptoms for even seemingly comparable items. We resolved item response heterogeneity, missingness and skewness, conditional dependency prior to estimation of item response theory models for statistical co-calibration. We used several rigorous data transformation procedures to address these issues, including re-coding and truncation.

CONCLUSIONS

This study highlights the importance of each aspect involved in the pre-statistical harmonization process of behavioral instruments. We provide guidelines and recommendations for how future research may detect and account for similar issues in pooling behavioral and related instruments.

Individual Data Protected Integrative Regression Analysis of High-Dimensional Heterogeneous Data

Evidence-based decision making often relies on meta-analyzing multiple studies, which enables more precise estimation and investigation of generalizability. Integrative analysis of multiple heterogeneous studies is, however, highly challenging in the ultra high-dimensional setting. The challenge is even more pronounced when the individual-level data cannot be shared across studies, known as DataSHIELD contraint. Under sparse regression models that are assumed to be similar yet not identical across studies, we propose in this paper a novel integrative estimation procedure for data-Shielding High-dimensional Integrative Regression (SHIR). SHIR protects individual data through summary-statistics-based integrating procedure, accommodates between-study heterogeneity in both the covariate distribution and model parameters, and attains consistent variable selection. Theoretically, SHIR is statistically more efficient than the existing distributed approaches that integrate debiased LASSO estimators from the local sites. Furthermore, the estimation error incurred by aggregating derived data is negligible compared to the statistical minimax rate and SHIR is shown to be asymptotically equivalent in estimation to the ideal estimator obtained by sharing all data. The finite-sample performance of our method is studied and compared with existing approaches via extensive simulation settings. We further illustrate the utility of SHIR to derive phenotyping algorithms for coronary artery disease using electronic health records data from multiple chronic disease cohorts.

The EU Child Cohort Network's core data: establishing a set of findable, accessible, interoperable and re-usable (FAIR) variables

The Horizon2020 LifeCycle Project is a cross-cohort collaboration which brings together data from multiple birth cohorts from across Europe and Australia to facilitate studies on the influence of early-life exposures on later health outcomes. A major product of this collaboration has been the establishment of a FAIR (findable, accessible, interoperable and reusable) data resource known as the EU Child Cohort Network. Here we focus on the EU Child Cohort Network's core variables. These are a set of basic variables, derivable by the majority of participating cohorts and frequently used as covariates or exposures in lifecourse research. First, we describe the process by which the list of core variables was established. Second, we explain the protocol according to which these variables were harmonised in order to make them interoperable. Third, we describe the catalogue developed to ensure that the network's data are findable and reusable. Finally, we describe the core data, including the proportion of variables harmonised by each cohort and the number of children for whom harmonised core data are available. EU Child Cohort Network data will be analysed using a federated analysis platform, removing the need to physically transfer data and thus making the data more accessible to researchers. The network will add value to participating cohorts by increasing statistical power and exposure heterogeneity, as well as facilitating cross-cohort comparisons, cross-validation and replication. Our aim is to motivate other cohorts to join the network and encourage the use of the EU Child Cohort Network by the wider research community.

Introduction to the special section on the intergenerational transmission of risk for substance use

Six original research papers were submitted to this Special Section to address questions regarding the intergenerational transmission of risk for cannabis and other substance use. Study teams recruited youth in Iowa, Washington, Oregon, New York, and Arizona in the 1980s-1990s, assessed them into adulthood, and recruited their partners and offspring for another study. All of the studies assessed substance use in 2 or more generations. Other strengths in this section include the strong representation of fathers, the demographic diversity of the samples as a whole, and the demonstrations of varied statistical and replication approaches. The findings highlight features of parental histories of cannabis use during adolescence that are associated with their children's risk for cannabis use and factors that explain or weaken intergenerational similarities. Two groups of prevention scholars also offered commentaries on the implications of these studies for prevention and training, and collaboration. It is hoped that the Special Section will stimulate new hypotheses, replications, and communication among etiological and prevention researchers. Furthermore, the papers highlight that the familial transmission of substance use risk should be taken into account more fully in the design of prevention programs to maximize impacts for youth as well as their future offspring. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD

Combined analysis of multiple, large datasets is a common objective in the health- and biosciences. Existing methods tend to require researchers to physically bring data together in one place or follow an analysis plan and share results. Developed over the last 10 years, the DataSHIELD platform is a collection of R packages that reduce the challenges of these methods. These include ethico-legal constraints which limit researchers' ability to physically bring data together and the analytical inflexibility associated with conventional approaches to sharing results. The key feature of DataSHIELD is that data from research studies stay on a server at each of the institutions that are responsible for the data. Each institution has control over who can access their data. The platform allows an analyst to pass commands to each server and the analyst receives results that do not disclose the individual-level data of any study participants. DataSHIELD uses Opal which is a data integration system used by epidemiological studies and developed by the OBiBa open source project in the domain of bioinformatics. However, until now the analysis of big data with DataSHIELD has been limited by the storage formats available in Opal and the analysis capabilities available in the DataSHIELD R packages. We present a new architecture ("resources") for DataSHIELD and Opal to allow large, complex datasets to be used at their original location, in their original format and with external computing facilities. We provide some real big data analysis examples in genomics and geospatial projects. For genomic data analyses, we also illustrate how to extend the resources concept to address specific big data infrastructures such as GA4GH or EGA, and make use of shell commands. Our new infrastructure will help researchers to perform data analyses in a privacy-protected way from existing data sharing initiatives or projects. To help researchers use this framework, we describe selected packages and present an online book (https://isglobal-brge.github.io/resource_bookdown).

Thigh-worn accelerometry for measuring movement and posture across the 24-hour cycle: a scoping review and expert statement

Introduction

The Prospective Physical Activity Sitting and Sleep consortium (ProPASS) is an international collaboration platform committed to harmonise thigh-worn accelerometry data. The aim of this paper is to (1) outline observational thigh-worn accelerometry studies and (2) summarise key strategic directions arising from the inaugural ProPASS meeting.

Methods

(1) We performed a systematic scoping review for observational studies of thigh-worn triaxial accelerometers in free-living adults (n≥100, 24 hours monitoring protocols). (2)Attendees of the inaugural ProPASS meeting were sent a survey focused on areas related to developing ProPASS: important terminology (Q1); accelerometry constructs (Q2); advantages and distinct contribution of the consortium (Q3); data pooling and harmonisation (Q4); data access and sharing (Q5 and Q6).

Results

(1) Eighty eligible articles were identified (22 primary studies; n~17 685). The accelerometers used most often were the ActivPAL3 and ActiGraph GT3X. The most commonly collected health outcomes were cardiometabolic and musculoskeletal. (2) None of the survey questions elicited the predefined 60% agreement. Survey responses recommended that ProPASS: use the term physical behaviour or movement behaviour rather than 'physical activity' for the data we are collecting (Q1); make only minor changes to ProPASS's accelerometry construct (Q2); prioritise developing standardised protocols/tools (Q4); facilitate flexible methods of data sharing and access (Q5 and Q6).

Conclusions

Thigh-worn accelerometry is an emerging method of capturing movement and posture across the 24 hours cycle. In 2020, the literature is limited to 22 primary studies from high-income western countries. This work identified ProPASS's strategic directions-indicating areas where ProPASS can most benefit the field of research: use of clear terminology, refinement of the measured construct, standardised protocols/tools and flexible data sharing.

CMIID: A comprehensive medical information identifier for clinical search harmonization in Data Safe Havens

Over the last decades clinical research has been driven by informatics changes nourished by distinct research endeavors. Inherent to this evolution, several issues have been the focus of a variety of studies: multi-location patient data access, interoperability between terminological and classification systems and clinical practice and records harmonization. Having these problems in mind, the Data Safe Haven paradigm emerged to promote a newborn architecture, better reasoning and safe and easy access to distinct Clinical Data Repositories. This study aim is to present a novel solution for clinical search harmonization within a safe environment, making use of a hybrid coding taxonomy that enables researchers to collect information from multiple repositories based on a clinical domain query definition. Results show that is possible to query multiple repositories using a single query definition based on clinical domains and the capabilities of the Unified Medical Language System, although it leads to deterioration of the framework response times. Participants of a Focus Group and a System Usability Scale questionnaire rated the framework with a median value of 72.5, indicating the hybrid coding taxonomy could be enriched with additional metadata to further improve the refinement of the results and enable the possibility of using this system as data quality tagging mechanism.

Impact of road traffic noise on obesity measures: Observational study of three European cohorts

BACKGROUND

Environmental stressors such as transport noise may contribute to development of obesity through increased levels of stress hormones, sleep deprivation and endocrine disruption. Epidemiological evidence supporting an association of road traffic noise with obesity markers is still relatively scant and confined to certain geographical regions. We aimed to examine the cross-sectional associations between road traffic noise and obesity markers in three large European cohorts involving nearly 500,000 individuals.

METHODS

Three population-based cohorts (UK Biobank, Lifelines, HUNT3) were established between 2006 and 2013 in the UK, the Netherlands and Norway respectively. For all three cohorts, residential 24-h road traffic noise (Lden) for 2009 was modelled from a standardised European noise assessment framework. Residential exposures to NO2 for 2007 and PM2.5 for 2010 were estimated from Europe-wide land use regression models. Obesity markers including body mass index and waist circumference were measured at recruitment. Obesity and central obesity status were subsequently derived. Regression models were fitted in each cohort, adjusting for a harmonised set of demographic and lifestyle covariates, with further adjustments for air pollution in the main model.

RESULTS

The main analyses included 412,934 participants of UK Biobank, 61,032 of Lifelines and 30,305 of HUNT3, with a mean age of 43-56 years and Lden ranging 42-89 dB(A) across cohorts. In UK Biobank, per 10 dB(A) higher of Lden: BMI was higher by 0.14kg/m2 (95%CI: 0.11-0.18), waist circumference higher by 0.27 cm (95%CI: 0.19-0.35), odds of obesity was 1.06 (95%CI: 1.04-1.08) and of central obesity was 1.05 (95%CI: 1.04-1.07). These associations were robust to most other sensitivity analyses but attenuated by further adjustment of PM2.5 or area-level socioeconomic status. Associations were more pronounced among women, those with low physical activity, higher household income or hearing impairment. In HUNT3, associations were observed for obesity or central obesity status among those exposed to Lden greater than 55 dB(A). In contrast, no or negative associations were observed in the Lifelines cohort.

CONCLUSIONS

This largest study to date providing mixed findings on impacts of long-term exposure to road traffic noise on obesity, which necessitates future analyses using longitudinal data to further investigate this potentially important epidemiological link.

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

Background

The MINDMAP project implemented a multinational data infrastructure to investigate the direct and interactive effects of urban environments and individual determinants of mental well-being and cognitive function in ageing populations. Using a rigorous process involving multiple teams of experts, longitudinal data from six cohort studies were harmonised to serve MINDMAP objectives. This article documents the retrospective data harmonisation process achieved based on the Maelstrom Research approach and provides a descriptive analysis of the harmonised data generated.

Methods

A list of core variables (the DataSchema) to be generated across cohorts was first defined, and the potential for cohort-specific data sets to generate the DataSchema variables was assessed. Where relevant, algorithms were developed to process cohort-specific data into DataSchema format, and information to be provided to data users was documented. Procedures and harmonisation decisions were thoroughly documented.

Results

The MINDMAP DataSchema (v2.0, April 2020) comprised a total of 2841 variables (993 on individual determinants and outcomes, 1848 on environmental exposures) distributed across up to seven data collection events. The harmonised data set included 220 621 participants from six cohorts (10 subpopulations). Harmonisation potential, participant distributions and missing values varied across data sets and variable domains.

Conclusion

The MINDMAP project implemented a collaborative and transparent process to generate a rich integrated data set for research in ageing, mental well-being and the urban environment. The harmonised data set supports a range of research activities and will continue to be updated to serve ongoing and future MINDMAP research needs.

The LifeCycle Project-EU Child Cohort Network: a federated analysis infrastructure and harmonized data of more than 250,000 children and parents

Early life is an important window of opportunity to improve health across the full lifecycle. An accumulating body of evidence suggests that exposure to adverse stressors during early life leads to developmental adaptations, which subsequently affect disease risk in later life. Also, geographical, socio-economic, and ethnic differences are related to health inequalities from early life onwards. To address these important public health challenges, many European pregnancy and childhood cohorts have been established over the last 30 years. The enormous wealth of data of these cohorts has led to important new biological insights and important impact for health from early life onwards. The impact of these cohorts and their data could be further increased by combining data from different cohorts. Combining data will lead to the possibility of identifying smaller effect estimates, and the opportunity to better identify risk groups and risk factors leading to disease across the lifecycle across countries. Also, it enables research on better causal understanding and modelling of life course health trajectories. The EU Child Cohort Network, established by the Horizon2020-funded LifeCycle Project, brings together nineteen pregnancy and childhood cohorts, together including more than 250,000 children and their parents. A large set of variables has been harmonised and standardized across these cohorts. The harmonized data are kept within each institution and can be accessed by external researchers through a shared federated data analysis platform using the R-based platform DataSHIELD, which takes relevant national and international data regulations into account. The EU Child Cohort Network has an open character. All protocols for data harmonization and setting up the data analysis platform are available online. The EU Child Cohort Network creates great opportunities for researchers to use data from different cohorts, during and beyond the LifeCycle Project duration. It also provides a novel model for collaborative research in large research infrastructures with individual-level data. The LifeCycle Project will translate results from research using the EU Child Cohort Network into recommendations for targeted prevention strategies to improve health trajectories for current and future generations by optimizing their earliest phases of life.

The challenges in data integration - heterogeneity and complexity in clinical trials and patient registries of Systemic Lupus Erythematosus

Background

Individual clinical trials and cohort studies are a useful source of data, often under-utilised once a study has ended. Pooling data from multiple sources could increase sample sizes and allow for further investigation of treatment effects; even if the original trial did not meet its primary goals. Through the MASTERPLANS (MAximizing Sle ThERapeutic PotentiaL by Application of Novel and Stratified approaches) national consortium, focused on Systemic Lupus Erythematosus (SLE), we have gained valuable real-world experiences in aligning, harmonising and combining data from multiple studies and trials, specifically where standards for data capture, representation and documentation, were not used or were unavailable. This was not without challenges arising both from the inherent complexity of the disease and from differences in the way data were captured and represented across different studies.

Main body

Data were, unavoidably, aligned by hand, matching up equivalent or similar patient variables across the different studies. Heterogeneity-related issues were tackled and data were cleaned, organised and combined, resulting in a single large dataset ready for analysis. Overcoming these hurdles, often seen in large-scale data harmonization and integration endeavours of legacy datasets, was made possible within a realistic timescale and limited resource by focusing on specific research questions driven by the aims of MASTERPLANS. Here we describe our experiences tackling the complexities in the integration of large, diverse datasets, and the lessons learned.

Conclusions

Harmonising data across studies can be complex, and time and resource consuming. The work carried out here highlights the importance of using standards for data capture, recording, and representation, to facilitate both the integration of large datasets and comparison between studies. Where standards are not implemented at the source harmonisation is still possible by taking a flexible approach, with systematic preparation, and a focus on specific research questions.

Extending the Minimum Information About BIobank Data Sharing Terminology to Describe Samples, Sample Donors, and Events

Introduction: The Minimum Information About BIobank data Sharing (MIABIS) was initiated in 2012. MIABIS aims to create a common biobank terminology to facilitate data sharing in biobanks and sample collections. The MIABIS Core terminology consists of three components describing biobanks, sample collections, and studies, in which information on samples and sample donors is provided at aggregated form. However, there is also a need to describe samples and sample donors at an individual level to allow more elaborate queries on available biobank samples and data. Therefore the MIABIS terminology has now been extended with components describing samples and sample donors at an individual level. Materials and Methods: The components were defined according to specific scope and use cases by a large group of experts, and through several cycles of reviews, according to the new MIABIS governance model of BBMRI-ERIC (Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium). The guiding principles applied in developing these components included the following terms: model should consider only samples of human origin, model should be applicable to all types of samples and all sample donors, and model should describe the current status of samples stored in a given biobank. Results: A minimal set of standard attributes for defining samples and sample donors is presented here. We added an "event" component to describe attributes that are not directly describing samples or sample donors but are tightly related to them. To better utilize the generic data model, we suggest a procedure by which interoperability can be promoted, using specific MIABIS profiles. Discussion: The MIABIS sample and donor component extensions and the new generic data model complement the existing MIABIS Core 2.0 components, and substantially increase the potential usability of this terminology for better describing biobank samples and sample donors. They also support the use of individual level data about samples and sample donors to obtain accurate and detailed biobank availability queries.

Associations of self-reported physical activity and anxiety symptoms and status among 7,874 Irish adults across harmonised datasets: a DEDIPAC-study

BACKGROUND

Anxiety is an adaptive response to an objective or perceived threat; however, when symptoms become severe and chronic it that can become a maladaptive anxiety disorder. Limited evidence suggests that physical activity may be associated with prevention against anxiety. This study uses data from The Irish Longitudinal Study on Ageing (TILDA) and The Mitchelstown Cohort Study to investigate cross-sectional associations between physical activity and anxiety symptoms and status among Irish adults.

METHODS

Both datasets were harmonized (n = 7874). The short form International Physical Activity Questionnaire measured physical activity. Participants were classified as meeting World Health Organization physical activity guidelines (≥150 min weekly of moderate intensity physical activity, ≥75 min weekly of vigorous intensity physical activity, or ≥ 600 MET-minutes) or not. They were also divided into three groups based on weekly MET-minutes of moderate-to-vigorous physical activity (Low: 0-599; Moderate: 600-1199; High: ≥1200), and three groups based on weekly minutes of walking (Low: 0-209; Moderate: 210-419; High: 420+). Anxiety symptoms were measured by the Hospital Anxiety and Depression Scale with a score of ≥8 indicating anxiety. Binomial logistic regression, adjusted for relevant confounders examined physical activity-anxiety associations.

RESULTS

Females had higher rates of anxiety than males (28.0% vs 20.0%; p < 0.001). Following adjustment for relevant covariates, meeting physical activity guidelines was associated with 13.5% (95% CI: 2.0-23.7; p = 0.023) lower odds of anxiety. Moderate and High physical activity were associated with 13.5% (- 11.0-32.6; p = 0.254) and 13.6% (1.4-4.2; p = 0.030) lower odds of anxiety compared to Low physical activity, respectively. Moderate and High walking were associated with 2.1% (- 14.5-16.3; p = 0.789) and 5.1% (- 9.3-17.6; p = 0.467) lower odds of anxiety compared to Low walking, respectively.

CONCLUSION

Meeting physical activity guidelines is associated with lower odds of anxiety, but the strength of associations did not increase considerably with increased physical activity levels.

Machine-learning-based patient-specific prediction models for knee osteoarthritis

Osteoarthritis (OA) is an extremely common musculoskeletal disease. However, current guidelines are not well suited for diagnosing patients in the early stages of disease and do not discriminate patients for whom the disease might progress rapidly. The most important hurdle in OA management is identifying and classifying patients who will benefit most from treatment. Further efforts are needed in patient subgrouping and developing prediction models. Conventional statistical modelling approaches exist; however, these models are limited in the amount of information they can adequately process. Comprehensive patient-specific prediction models need to be developed. Approaches such as data mining and machine learning should aid in the development of such models. Although a challenging task, technology is now available that should enable subgrouping of patients with OA and lead to improved clinical decision-making and precision medicine.

Leveraging real-world data to investigate multiple sclerosis disease behavior, prognosis, and treatment

Randomized controlled clinical trials and real-world observational studies provide complementary information but with different validity. Some clinical questions (disease behavior, prognosis, validation of outcome measures, comparative effectiveness, and long-term safety of therapies) are often better addressed using real-world data reflecting larger, more representative populations. Integration of disease history, clinician-reported outcomes, performance tests, and patient-reported outcome measures during patient encounters; imaging and biospecimen analyses; and data from wearable devices increase dataset utility. However, observational studies utilizing these data are susceptible to many potential sources of bias, creating barriers to acceptance by regulatory agencies and the medical community. Therefore, data standardization and validation within datasets, harmonization across datasets, and application of appropriate analysis methods are important considerations. We review approaches to improve the scope, quality, and analyses of real-world data to advance understanding of multiple sclerosis and its treatment, as an example of opportunities to better support patient care and research.

Incorporating neurophysiological measures into clinical assessments: Fundamental challenges and a strategy for addressing them

Recent scientific initiatives have called for increased use of neurobiological variables in clinical and other applied assessments. However, the task of incorporating neural measures into psychological assessments entails significant methodological challenges that have not been effectively addressed to date. As a result, neurophysiological measures remain underutilized in clinical and applied assessments, and formal procedures for integrating such measures with report-based measures are lacking. In this article, we discuss major methodological issues that have impeded progress in this direction, and propose a systematic research strategy for integrating neurophysiological measures into psychological assessment protocols. The strategy we propose is an iterative psychoneurometric approach that provides a means to establish multimethod (MM) measurement models for core biobehavioral traits that influence functioning across diverse areas of life. We provide a detailed illustration of a MM model for one such trait, inhibitory control (inhibition-disinhibition), and highlight work being done to develop counterpart models for other biobehavioral traits (i.e., threat sensitivity, reward sensitivity, affiliative capacity). We discuss how these measurement models can be refined and extended through use of already existing data sets, and outline steps that can be taken to establish norms for MM assessments and optimize the feasibility of their use in everyday practice. We believe this model-oriented strategy can provide a viable pathway toward effective use of neurophysiological measures in routine clinical assessments. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Overview of Federated Facility to Harmonize, Analyze and Management of Missing Data in Cohorts

Cohorts are instrumental for epidemiologically oriented observational studies. Cohort studies usually observe large groups of individuals for a specific period of time to identify the contributing factors to a specific outcome (for instance an illness) and create associations between risk factors and the outcome under study. In collaborative projects, federated data facilities are meta-database systems that are distributed across multiple locations that permit to analyze, combine, or harmonize data from different sources making them suitable for mega- and meta-analyses. The harmonization of data can increase the statistical power of studies through maximization of sample size, allowing for additional refined statistical analyses, which ultimately lead to answer research questions that could not be addressed while using a single study. Indeed, harmonized data can be analyzed through mega-analysis of raw data or fixed effects meta-analysis. Other types of data might be analyzed by e.g., random-effects meta-analyses or Bayesian evidence synthesis. In this article, we describe some methodological aspects related to the construction of a federated facility to optimize analyses of multiple datasets, the impact of missing data, and some methods for handling missing data in cohort studies.

The Finnish psychiatric birth cohort consortium (PSYCOHORTS) - content, plans and perspectives

Background: Psychiatric disorders tend to be developmental, and longitudinal settings are required to examine predictors of psychiatric phenomena. Replicating and combining data and results from different birth cohorts, which are a source of reliable data, can make research even more valuable. The Finnish Psychiatric Birth Cohort Consortium (PSYCOHORTS) project combines birth cohorts in Finland. Aim: The aim of this paper is to introduce content, plans and perspectives of the PSYCOHORTS project that brings together researchers from Finland. In addition, we illustrate an example of data harmonization using available data on causes of death. Content: PSYCOHORTS includes eight Finnish birth cohorts. The project has several plans: to harmonize different data from birth cohorts, to incorporate biobanks into psychiatric birth cohort research, to apply multigenerational perspectives, to integrate longitudinal patterns of marginalization and inequality in mental health, and to utilize data in health economics research. Data on causes of death, originally obtained from Finnish Cause of Death register, were harmonized across the six birth cohorts using SAS macro facility. Results: Harmonization of the cause of death data resulted in a total of 21,993 observations from 1965 to 2015. For example, the percentage of deaths due to suicide and the sequelae of intentional self-harm was 14% and alcohol-related diseases, including accidental poisoning by alcohol, was 13%. Conclusions: PSYCOHORTS lays the foundation for complex examinations of psychiatric disorders that is based on compatible datasets, use of biobanks and multigenerational approach to risk factors, and extensive data on marginalization and inequality.

Comparison of reproductive history gathered by interview and by vital records linkage after 40 years of follow-up: Bogalusa Babies

Background

To examine the consistency and likely degree of bias in a study of cardiovascular health, linked with reproductive data over 40 years.

Methods

Linkage of vital statistics data of births to female Bogalusa Heart Study participants was compared to interviewing of female participants. The characteristics of participants, the agreement, and demographic, study-related, and medical predictors of discrepancy were analyzed, using kappa statistics, mean and median differences, and logistic regression.

Results

Overall, 3944 (66.7%) of participants were located by one or both sources. The strongest predictor of either linkage or interview was recent and/or frequent participation in the parent study. Agreement between the two sources was generally good (kappa > 0.9 for birthweight and 0.8 for gestational age). Black race, older age, and time since pregnancy were associated with greater discrepancy in reporting of outcomes, but cardiovascular risk factors generally were not.

Conclusions

Combining information from multiple sources to increase sample size and outcome ascertainment may be valid, which will increase population health sciences’ ability to leverage the many existing, large-scale sources to answer previously unexplored questions, even those that the data were not initially collected to answer.

Electronic supplementary material

The online version of this article (10.1186/s12874-019-0758-0) contains supplementary material, which is available to authorized users.

Transnational access to large prospective cohorts in Europe: Current trends and unmet needs

Biobank samples and data from studies of large prospective cohorts (LPC) represent an invaluable resource for health research. Efficient sharing and pooling of samples and data is a central pre-requisite for new advances in biomedical science. This requirement, however, is not compatible with the present scattered and traditional access governance structures, where legal and ethical frameworks often form an obstacle for effective sharing. Moreover, the EU General Data Protection Regulation (GDPR) is demanding increasingly rigorous administration from all those organisations processing personal data. The BBMRI-LPC project (Biobanking and Biomolecular Research Infrastructure - Large Prospective Cohorts) assembled 21 LPCs from 10 countries and two EU-wide multinational cohort networks with a key objective to promote collaborative innovative transnational research proposed by external researchers on the broad field of common chronic diseases, and analyze the gaps and needs involved. BBMRI-LPC organized three scientific calls to offer European investigators an opportunity to gain free of charge transnational access to research material available in the participating cohorts. A total of 11 high-quality research proposals involving multiple prospective cohorts were granted, and the access process in the individual projects carefully monitored. Divergent access governance structures, complex legal and ethical frameworks and heterogeneous procedures were identified as currently constituting substantial obstacles for sample and data transfer in Europe. To optimize the scientific value and use of these research resources, practical solutions for more streamlined access governance in collaborative projects are urgently needed. A number of infrastructure developments could be made to improve time-efficiency in access provision.

Integrating Clinical and Epidemiologic Data on Allergic Diseases Across Birth Cohorts: A Harmonization Study in the Mechanisms of the Development of Allergy Project

The numbers of international collaborations among birth cohort studies designed to better understand asthma and allergies have increased in the last several years. However, differences in definitions and methods preclude direct pooling of original data on individual participants. As part of the Mechanisms of the Development of Allergy (MeDALL) Project, we harmonized data from 14 birth cohort studies (each with 3-20 follow-up periods) carried out in 9 European countries during 1990-1998 or 2003-2009. The harmonization process followed 6 steps: 1) organization of the harmonization panel; 2) identification of variables relevant to MeDALL objectives (candidate variables); 3) proposal of a definition for each candidate variable (reference definition); 4) assessment of the compatibility of each cohort variable with its reference definition (inferential equivalence) and classification of this inferential equivalence as complete, partial, or impossible; 5) convocation of a workshop to agree on the reference definitions and classifications of inferential equivalence; and 6) preparation and delivery of data through a knowledge management portal. We agreed on 137 reference definitions. The inferential equivalence of 3,551 cohort variables to their corresponding reference definitions was classified as complete, partial, and impossible for 70%, 15%, and 15% of the variables, respectively. A harmonized database was delivered to MeDALL investigators. In asthma and allergy birth cohorts, the harmonization of data for pooled analyses is feasible, and high inferential comparability may be achieved. The MeDALL harmonization approach can be used in other collaborative projects.

Towards the Establishment of a Biomedical Ontology for the Primary Sjögren's Syndrome

Primary Sjögren's Syndrome (pSS) has been characterized as a hypersensitivity reaction type II systemic autoimmune chronic disease causing exocrine gland dysfunction mainly affecting women near the menopausal age. pSS patients exhibit dryness of the main mucosal surfaces and are highly prone to lymphoma development. This paper presents a first biomedical ontology for pSS based on a reference model which was determined by pSS clinical experts. The ensuing ontology constitutes the fundamental basis for mapping pSS-related ontologies from international cohorts to a common ontology. The ontology mapping (i.e., schematic interlinking) procedure is, in fact, a preliminary step to harmonize heterogeneous medical data obtained from various cohorts.

Observational health research in Europe: understanding the General Data Protection Regulation and underlying debate

Insights into the incidence and survival of cancer, the influence of lifestyle and environmental factors and the interaction of treatment regimens with outcomes are hugely dependent on observational research, patient data derived from the healthcare system and from volunteers participating in cohort studies, often non-selective. Since 25th May 2018, the European General Data Protection Regulation (GDPR) applies to such data. The GDPR focusses on more individual control for data subjects of 'their' data. Yet, the GDPR was preceded by a long debate. The research community participated actively in that debate, and as a result, the GDPR has research exemptions as well. Some of those apply directly; other exemptions need to be implemented into national law. Those exemptions will be discussed together with a general outline of the GDPR. I propose a substantive definition of research-absent in the GDPR-which can warrant its special status in the GDPR. The debate is not over yet. Most legal texts exhibit ambiguity and are interpreted against a background of values. In this case, those could be subsumed under informational self-determination versus solidarity and the deeper meaning of autonomy. Values will also guide national implementation and their interpretation. The value of individual control or informational self-determination should be balanced by nuanced visions about our mutual dependency in healthcare, as an ever-learning system, especially in the European solidarity-based healthcare systems. Good research governance might be a way forward to escape the consent or anonymise dichotomy.