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Biomedical data warehouses (BDWs) have become an essential tool to facilitate the reuse of health data for both research and decisional applications. Beyond technical issues, the implementation of BDWs requires strong institutional data governance and operational knowledge of the European and national legal framework for the management of research data access and use. In this paper, we describe the compound process of implementation and the contents of a regional university hospital BDW. We present the actions and challenges regarding organizational changes, technical architecture, and shared governance that took place to develop the Nantes BDW. We describe the process to access clinical contents, give details about patient data protection, and use examples to illustrate merging clinical insights. More than 68 million textual documents and 543 million pieces of coded information concerning approximately 1.5 million patients admitted to CHUN between 2002 and 2022 can be queried and transformed to be made available to investigators. Since its creation in 2018, 269 projects have benefited from the Nantes BDW. Access to data is organized according to data use and regulatory requirements. Data use is entirely determined by the scientific question posed. It is the vector of legitimacy of data access for secondary use. Enabling access to a BDW is a game changer for research and all operational situations in need of data. Finally, data governance must prevail over technical issues in institution data strategy vis-à-vis care professionals and patients alike.

Increasing adoption of electronic health records (EHRs) enables research on real-world data. In Germany, this has been limited to university hospitals, and data from acute care hospitals below the university level are lacking. To address this, we used established design patterns to build a data platform that aggregates and standardizes pseudonymized EHR data with patients' consent. We report on the design and implementation of the research platform, as well as patient participation and lessons learned during the scaling of the platform, to incorporate real-world data (with participant consent) from 77 hospitals into a unified data lake. Due to variations in EHR adoption, IT infrastructure, software vendors, interface availability, and regulatory requirements, we used an agile development cycle that involves constant, incremental standardization of data. We implemented a layered lambda infrastructure built on Apache Hadoop. Decentralized connectors ensured data minimization and pseudonymization. We successfully scaled our data model both vertically and horizontally in 77 hospitals. However, we encountered issues during the scaling of real-time data pipelines and IHE (Integrating the Healthcare Enterprise) interfaces. During the first 2 years, patients were asked to consent to secondary data use 1,475,244 times during inpatient admission. We registered 1,023,633 broad instances of consent (consent rate 70.2%). Patients are generally willing to provide consent for secondary use of their data, but obtaining consent requires considerable effort. Building a research data platform is not an end goal, but rather a necessary step in collecting and standardizing longitudinal data to enable research on real-world data. Through the combination of agile development, phased rollouts, and very high levels of automation, we have been able to achieve fast turnaround times for incorporating user feedback and are constantly improving data quality and standardization.

The secondary use of health data is central to biomedical research in the era of data science and precision medicine. National and international initiatives, such as the Global Open Findable, Accessible, Interoperable, and Reusable (GO FAIR) initiative, are supporting this approach in different ways (eg, making the sharing of research data mandatory or improving the legal and ethical frameworks). Preserving patients' privacy is crucial in this context. De-identification and anonymization are the two most common terms used to refer to the technical approaches that protect privacy and facilitate the secondary use of health data. However, it is difficult to find a consensus on the definitions of the concepts or on the reliability of the techniques used to apply them. A comprehensive review is needed to better understand the domain, its capabilities, its challenges, and the ratio of risk between the data subjects' privacy on one side, and the benefit of scientific advances on the other. This work aims at better understanding how the research community comprehends and defines the concepts of de-identification and anonymization. A rich overview should also provide insights into the use and reliability of the methods. Six aspects will be studied: (1) terminology and definitions, (2) backgrounds and places of work of the researchers, (3) reasons for anonymizing or de-identifying health data, (4) limitations of the techniques, (5) legal and ethical aspects, and (6) recommendations of the researchers. Based on a scoping review protocol designed a priori, MEDLINE was searched for publications discussing de-identification or anonymization and published between 2007 and 2017. The search was restricted to MEDLINE to focus on the life sciences community. The screening process was performed by two reviewers independently. After searching 7972 records that matched at least one search term, 135 publications were screened and 60 full-text articles were included. (1) Terminology: Definitions of the terms de-identification and anonymization were provided in less than half of the articles (29/60, 48%). When both terms were used (41/60, 68%), their meanings divided the authors into two equal groups (19/60, 32%, each) with opposed views. The remaining articles (3/60, 5%) were equivocal. (2) Backgrounds and locations: Research groups were based predominantly in North America (31/60, 52%) and in the European Union (22/60, 37%). The authors came from 19 different domains; computer science (91/248, 36.7%), biomedical informatics (47/248, 19.0%), and medicine (38/248, 15.3%) were the most prevalent ones. (3) Purpose: The main reason declared for applying these techniques is to facilitate biomedical research. (4) Limitations: Progress is made on specific techniques but, overall, limitations remain numerous. (5) Legal and ethical aspects: Differences exist between nations in the definitions, approaches, and legal practices. (6) Recommendations: The combination of organizational, legal, ethical, and technical approaches is necessary to protect health data. Interest is growing for privacy-enhancing techniques in the life sciences community. This interest crosses scientific boundaries, involving primarily computer science, biomedical informatics, and medicine. The variability observed in the use of the terms de-identification and anonymization emphasizes the need for clearer definitions as well as for better education and dissemination of information on the subject. The same observation applies to the methods. Several legislations, such as the American Health Insurance Portability and Accountability Act (HIPAA) and the European General Data Protection Regulation (GDPR), regulate the domain. Using the definitions they provide could help address the variable use of these two concepts in the research community.

The secondary use of clinical data in data-gathering, non-interventional research or learning activities (SeConts) has great potential for scientific progress and health care improvement. At the same time, it poses relevant risks for the privacy and informational self-determination of patients whose data are used.BACKGROUNDThe secondary use of clinical data in data-gathering, non-interventional research or learning activities (SeConts) has great potential for scientific progress and health care improvement. At the same time, it poses relevant risks for the privacy and informational self-determination of patients whose data are used.Since the current literature lacks a tailored framework for risk assessment in SeConts as well as a clarification of the concept and practical scope of SeConts, we aim to fill this gap.OBJECTIVESince the current literature lacks a tailored framework for risk assessment in SeConts as well as a clarification of the concept and practical scope of SeConts, we aim to fill this gap.In this study, we analyze each element of the concept of SeConts to provide a synthetic definition, investigate the practical relevance and scope of SeConts through a literature review, and operationalize the widespread definition of risk (as a harmful event of a certain magnitude that occurs with a certain probability) to conduct a tailored analysis of privacy risk factors typically implied in SeConts.METHODSIn this study, we analyze each element of the concept of SeConts to provide a synthetic definition, investigate the practical relevance and scope of SeConts through a literature review, and operationalize the widespread definition of risk (as a harmful event of a certain magnitude that occurs with a certain probability) to conduct a tailored analysis of privacy risk factors typically implied in SeConts.We offer a conceptual clarification and definition of SeConts and provide a list of types of research and learning activities that can be subsumed under the definition of SeConts. We also offer a proposal for the classification of SeConts types into the categories non-interventional (observational) clinical research, quality control and improvement, or public health research. In addition, we provide a list of risk factors that determine the probability or magnitude of harm implied in SeConts. The risk factors provide a framework for assessing the privacy-related risks for patients implied in SeConts. We illustrate the use of risk assessment by applying it to a concrete example.RESULTSWe offer a conceptual clarification and definition of SeConts and provide a list of types of research and learning activities that can be subsumed under the definition of SeConts. We also offer a proposal for the classification of SeConts types into the categories non-interventional (observational) clinical research, quality control and improvement, or public health research. In addition, we provide a list of risk factors that determine the probability or magnitude of harm implied in SeConts. The risk factors provide a framework for assessing the privacy-related risks for patients implied in SeConts. We illustrate the use of risk assessment by applying it to a concrete example.In the future, research ethics committees and data use and access committees will be able to rely on and apply the framework offered here when reviewing projects of secondary use of clinical data for learning and research purposes.CONCLUSIONSIn the future, research ethics committees and data use and access committees will be able to rely on and apply the framework offered here when reviewing projects of secondary use of clinical data for learning and research purposes.

BackgroundChanges in well-being of patients with multiple myeloma (MM) before and after diagnosis have not been quantified.AimsExplore the use of secondary data to examine the changes in the well-being of older patients with MM.MethodsWe used the Health and Retirement Study (HRS), linked to Medicare claims to identify older MM patients. We compared patient-reported measures (PRM), including physical impairment, sensory impairment, and patient experience (significant pain, self-rated health, depression) in the interviews before and after MM diagnosis using McNemar’s test. We propensity-matched each MM patient to five HRS participants without MM diagnosis based on baseline characteristics. We compared the change in PRM between the MM patients and their matches.ResultsWe identified 92 HRS patients with MM diagnosis (mean age = 74.6, SD = 8.4). Among the surviving patients, there was a decline in well-being across most measures, including ADL difficulty (23% to 40%, p value = 0.016), poor or fair self-rated health (38% to 61%, p value = 0.004), and depression (15% to 30%, p value = 0.021). Surviving patients reported worse health than participants without MM across most measures, including ADL difficulty (40% vs. 27%, p value = 0.04), significant pain (38% vs. 22%, p value = 0.01), and depression (29% vs. 11%, p value = 0.003).DiscussionSecondary data were used to identify patients with MM diagnosis, and examine changes across multiple measures of well-being. MM diagnosis negatively affects several aspects of patients’ well-being, and these declines are larger than those experienced by similar participants without MM.ConclusionThe results of this study are valuable addition to understanding the experience of patients with MM, despite several data limitations.

With new technologies, health data can be collected in a variety of different clinical, research, and public health contexts, and then can be used for a range of new purposes. Establishing the public's views about digital health data sharing is essential for policy makers to develop effective harmonization initiatives for digital health data governance at the European level. This study investigated public preferences for digital health data sharing. A discrete choice experiment survey was administered to a sample of European residents in 12 European countries (Austria, Denmark, France, Germany, Iceland, Ireland, Italy, the Netherlands, Norway, Spain, Sweden, and the United Kingdom) from August 2020 to August 2021. Respondents answered whether hypothetical situations of data sharing were acceptable for them. Each hypothetical scenario was defined by 5 attributes (\"data collector,\" \"data user,\" \"reason for data use,\" \"information on data sharing and consent,\" and \"availability of review process\"), which had 3 to 4 attribute levels each. A latent class model was run across the whole data set and separately for different European regions (Northern, Central, and Southern Europe). Attribute relative importance was calculated for each latent class's pooled and regional data sets. A total of 5015 completed surveys were analyzed. In general, the most important attribute for respondents was the availability of information and consent during health data sharing. In the latent class model, 4 classes of preference patterns were identified. While respondents in 2 classes strongly expressed their preferences for data sharing with opposing positions, respondents in the other 2 classes preferred not to share their data, but attribute levels of the situation could have had an impact on their preferences. Respondents generally found the following to be the most acceptable: a national authority or academic research project as the data user; being informed and asked to consent; and a review process for data transfer and use, or transfer only. On the other hand, collection of their data by a technological company and data use for commercial communication were the least acceptable. There was preference heterogeneity across Europe and within European regions. This study showed the importance of transparency in data use and oversight of health-related data sharing for European respondents. Regional and intraregional preference heterogeneity for \"data collector,\" \"data user,\" \"reason,\" \"type of consent,\" and \"review\" calls for governance solutions that would grant data subjects the ability to control their digital health data being shared within different contexts. These results suggest that the use of data without consent will demand weighty and exceptional reasons. An interactive and dynamic informed consent model combined with oversight mechanisms may be a solution for policy initiatives aiming to harmonize health data use across Europe.

Procedural coding presents a taxing challenge for clinicians. However, recent advances in natural language processing offer a promising avenue for developing applications that assist clinicians, thereby alleviating their administrative burdens. This study seeks to create an application capable of predicting procedure codes by analysing clinicians’ operative notes, aiming to streamline their workflow and enhance efficiency. We downstreamed an existing and a native German medical BERT model in a secondary use scenario, utilizing already coded surgery notes to model the coding procedure as a multi-label classification task. In comparison to the transformer-based architecture, we were levering the non-contextual model fastText, a convolutional neural network, a support vector machine and logistic regression for a comparative analysis of possible coding performance. About 350,000 notes were used for model adaption. By considering the top five suggested procedure codes from medBERT.de, surgeryBERT.at, fastText, a convolutional neural network, a support vector machine and a logistic regression, the mean average precision achieved was 0.880, 0.867, 0.870, 0.851, 0.870 and 0.805 respectively. Support vector machines performed better for surgery reports with a sequence length greater than 512, achieving a mean average precision of 0.872 in comparison to 0.840 for fastText, 0.837 for medBERT.de and 0.820 for surgeryBERT.at. A prototypical front-end application for coding support was additionally implemented. The problem of predicting procedure codes from a given operative report can be successfully modelled as a multi-label classification task, with a promising performance. Support vector machines as a classical machine learning method outperformed the non-contextual fastText approach. FastText with less demanding hardware resources has reached a similar performance to BERT-based models and has shown to be more suitable for explaining the predictions efficiently.

Background Large-scale linkage of international clinical datasets could lead to unique insights into disease aetiology and facilitate treatment evaluation and drug development. Hereto, multi-stakeholder consortia are currently designing several disease-specific translational research platforms to enable international health data sharing. Despite the recent adoption of the EU General Data Protection Regulation (GDPR), the procedures for how to govern responsible data sharing in such projects are not at all spelled out yet. In search of a first, basic outline of an ethical governance framework, we set out to explore relevant ethical principles and norms. Methods We performed a systematic review of literature and ethical guidelines for principles and norms pertaining to data sharing for international health research. Results We observed an abundance of principles and norms with considerable convergence at the aggregate level of four overarching themes: societal benefits and value; distribution of risks, benefits and burdens; respect for individuals and groups; and public trust and engagement. However, at the level of principles and norms we identified substantial variation in the phrasing and level of detail, the number and content of norms considered necessary to protect a principle, and the contextual approaches in which principles and norms are used. Conclusions While providing some helpful leads for further work on a coherent governance framework for data sharing, the current collection of principles and norms prompts important questions about how to streamline terminology regarding de-identification and how to harmonise the identified principles and norms into a coherent governance framework that promotes data sharing while securing public trust.

The European Health Data Space (EHDS) aspires to enable secure, interoperable, and decentralized health data usage across Europe. This paper explores legal and technical challenges in implementing EHDS goals, particularly for secondary data use. It highlights federated and swarm learning as promising yet complex solutions, requiring robust infrastructure, standardization, and regulatory clarity. We emphasize the need for coordinated legislative and technological advances to realize EHDS ambitions.