Data harmonization and federated learning for multi-cohort dementia research using the OMOP common data model: A Netherlands consortium of dementia cohorts case study
Journal of Biomedical Informatics, vol. 155, pp. 104661
Abstract
BACKGROUND: Establishing collaborations between cohort studies has been fundamental for progress in health research. However, such collaborations are hampered by heterogeneous data representations across cohorts and legal constraints to data sharing. The first arises from a lack of consensus in standards of data collection and representation across cohort studies and is usually tackled by applying data harmonization processes. The second is increasingly important due to raised awareness for privacy protection and stricter regulations, such as the GDPR. Federated learning has emerged as a privacy-preserving alternative to transferring data between institutions through analyzing data in a decentralized manner. METHODS: In this study, we set up a federated learning infrastructure for a consortium of nine Dutch cohorts with appropriate data available to the etiology of dementia, including an extract, transform, and load (ETL) pipeline for data harmonization. Additionally, we assessed the challenges of transforming and standardizing cohort data using the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) and evaluated our tool in one of the cohorts employing federated algorithms. RESULTS: We successfully applied our ETL tool and observed a complete coverage of the cohorts' data by the OMOP CDM. The OMOP CDM facilitated the data representation and standardization, but we identified limitations for cohort-specific data fields and in the scope of the vocabularies available. Specific challenges arise in a multi-cohort federated collaboration due to technical constraints in local environments, data heterogeneity, and lack of direct access to the data. CONCLUSION: In this article, we describe the solutions to these challenges and limitations encountered in our study. Our study shows the potential of federated learning as a privacy-preserving solution for multi-cohort studies that enhance reproducibility and reuse of both data and analyses.
Authors 17
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Pedro Mateus corresponding
Maastricht University Medical Centre · Maastro Clinic
Affiliation as printed
Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, Netherlands. Electronic address: pedro.mateus@maastro.nl
Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, the Netherlands
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Amsterdam Neuroscience · Vrije Universiteit Amsterdam · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands; Amsterdam Neuroscience, Neurodegeneration, Amsterdam, Netherlands
Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
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Utrecht University · University Medical Center Utrecht · Maastricht University
Affiliation as printed
Department of Internal Medicine, School for Cardiovascular Diseases (CARIM), Maastricht University, Maastricht, Netherlands; Department of Epidemiology and Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
Department of Epidemiology and Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
Department of Internal Medicine, School for Cardiovascular Diseases (CARIM), Maastricht University, Maastricht, the Netherlands
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National Institute for Public Health and the Environment · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Center for Nutrition, Prevention, and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands; Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, Netherlands
Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, Netherlands
Center for Nutrition, Prevention, and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Amsterdam Neuroscience · Vrije Universiteit Amsterdam · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands; Amsterdam Neuroscience, Neurodegeneration, Amsterdam, Netherlands
Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
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Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, Netherlands
Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
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Affiliation as printed
Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, the Netherlands
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Affiliation as printed
Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, the Netherlands
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Affiliation as printed
Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, Netherlands
Biomedical Imaging Group Rotterdam, Dept. Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, the Netherlands
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Affiliation as printed
Erasmus MC - University Medical Centre Rotterdam, Departments of Epidemiology and Radiology & Nuclear Medicine, Netherlands
Erasmus MC – University Medical Centre Rotterdam, Departments of Epidemiology and Radiology & Nuclear Medicine, Netherlands
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Leiden University Medical Center
Affiliation as printed
Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Netherlands
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Leiden University Medical Center
Affiliation as printed
Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Netherlands
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Affiliation as printed
Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Netherlands
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Affiliation as printed
Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Center Limburg, Maastricht University, Netherlands
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Maastricht University Medical Centre · Maastricht University
Affiliation as printed
Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands; Department of Internal Medicine, Maastricht University Medical Centre, Maastricht, Netherlands; MHeNS School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; Heart and Vascular Center, Maastricht University Medical Center+, Maastricht, Netherlands
Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
Department of Internal Medicine, Maastricht University Medical Centre, Maastricht, the Netherlands
Heart and Vascular Center, Maastricht University Medical Center+, Maastricht, the Netherlands
MHeNS School for Mental Health and Neuroscience, Maastricht University, Maastricht, the Netherlands
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Maastricht University Medical Centre · Maastro Clinic
Affiliation as printed
Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, Netherlands
Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, the Netherlands
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Maastricht University Medical Centre · Maastro Clinic
Affiliation as printed
Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, Netherlands
Department of Radiation Oncology (Maastro), GROW School for Oncology and Reproduction, Maastricht University Medical Centre+, Maastricht, the Netherlands
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