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Raycheva R, Kostadinov K, Mitova E, Iskrov G, Stefanov G, Vakevainen M, Elomaa K, Man YS, Gross E, Zschüntzsch J, Röttger R, Stefanov R. Landscape analysis of available European data sources amenable for machine learning and recommendations on usability for rare diseases screening. Orphanet J Rare Dis 2024; 19:147. [PMID: 38582900 PMCID: PMC10998425 DOI: 10.1186/s13023-024-03162-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/30/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Patient registries and databases are essential tools for advancing clinical research in the area of rare diseases, as well as for enhancing patient care and healthcare planning. The primary aim of this study is a landscape analysis of available European data sources amenable to machine learning (ML) and their usability for Rare Diseases screening, in terms of findable, accessible, interoperable, reusable(FAIR), legal, and business considerations. Second, recommendations will be proposed to provide a better understanding of the health data ecosystem. METHODS In the period of March 2022 to December 2022, a cross-sectional study using a semi-structured questionnaire was conducted among potential respondents, identified as main contact person of a health-related databases. The design of the self-completed questionnaire survey instrument was based on information drawn from relevant scientific publications, quantitative and qualitative research, and scoping review on challenges in mapping European rare disease (RD) databases. To determine database characteristics associated with the adherence to the FAIR principles, legal and business aspects of database management Bayesian models were fitted. RESULTS In total, 330 unique replies were processed and analyzed, reflecting the same number of distinct databases (no duplicates included). In terms of geographical scope, we observed 24.2% (n = 80) national, 10.0% (n = 33) regional, 8.8% (n = 29) European, and 5.5% (n = 18) international registries coordinated in Europe. Over 80.0% (n = 269) of the databases were still active, with approximately 60.0% (n = 191) established after the year 2000 and 71.0% last collected new data in 2022. Regarding their geographical scope, European registries were associated with the highest overall FAIR adherence, while registries with regional and "other" geographical scope were ranked at the bottom of the list with the lowest proportion. Responders' willingness to share data as a contribution to the goals of the Screen4Care project was evaluated at the end of the survey. This question was completed by 108 respondents; however, only 18 of them (16.7%) expressed a direct willingness to contribute to the project by sharing their databases. Among them, an equal split between pro-bono and paid services was observed. CONCLUSIONS The most important results of our study demonstrate not enough sufficient FAIR principles adherence and low willingness of the EU health databases to share patient information, combined with some legislation incapacities, resulting in barriers to the secondary use of data.
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Affiliation(s)
- Ralitsa Raycheva
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria.
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria.
| | - Kostadin Kostadinov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Elena Mitova
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Iskrov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Stefanov
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Merja Vakevainen
- Pfizer Biopharmaceuticals Group, Medical Affairs, Helsinki, Finland
| | | | - Yuen-Sum Man
- Global Medical Affairs Rare Disease, Novo Nordisk Health Care AG, Zurich, Switzerland
| | - Edith Gross
- EURORDIS - Rare Diseases Europe, 96 Rue Didot, Paris, 75014, France
| | - Jana Zschüntzsch
- Department of Neurology, University Medical Center, Göttingen, Germany
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
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Iskrov G, Raycheva R, Kostadinov K, Gillner S, Blankart CR, Gross ES, Gumus G, Mitova E, Stefanov S, Stefanov G, Stefanov R. Are the European reference networks for rare diseases ready to embrace machine learning? A mixed-methods study. Orphanet J Rare Dis 2024; 19:25. [PMID: 38273306 PMCID: PMC10809751 DOI: 10.1186/s13023-024-03047-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The delay in diagnosis for rare disease (RD) patients is often longer than for patients with common diseases. Machine learning (ML) technologies have the potential to speed up and increase the precision of diagnosis in this population group. We aim to explore the expectations and experiences of the members of the European Reference Networks (ERNs) for RDs with those technologies and their potential for application. METHODS We used a mixed-methods approach with an online survey followed by a focus group discussion. Our study targeted primarily medical professionals but also other individuals affiliated with any of the 24 ERNs. RESULTS The online survey yielded 423 responses from ERN members. Participants reported a limited degree of knowledge of and experience with ML technologies. They considered improved diagnostic accuracy the most important potential benefit, closely followed by the synthesis of clinical information, and indicated the lack of training in these new technologies, which hinders adoption and implementation in routine care. Most respondents supported the option that ML should be an optional but recommended part of the diagnostic process for RDs. Most ERN members saw the use of ML limited to specialised units only in the next 5 years, where those technologies should be funded by public sources. Focus group discussions concluded that the potential of ML technologies is substantial and confirmed that the technologies will have an important impact on healthcare and RDs in particular. As ML technologies are not the core competency of health care professionals, participants deemed a close collaboration with developers necessary to ensure that results are valid and reliable. However, based on our results, we call for more research to understand other stakeholders' opinions and expectations, including the views of patient organisations. CONCLUSIONS We found enthusiasm to implement and apply ML technologies, especially diagnostic tools in the field of RDs, despite the perceived lack of experience. Early dialogue and collaboration between health care professionals, developers, industry, policymakers, and patient associations seem to be crucial to building trust, improving performance, and ultimately increasing the willingness to accept diagnostics based on ML technologies.
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Affiliation(s)
- Georgi Iskrov
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria.
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002, Plovdiv, Bulgaria.
| | - Ralitsa Raycheva
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002, Plovdiv, Bulgaria
| | - Kostadin Kostadinov
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002, Plovdiv, Bulgaria
| | - Sandra Gillner
- KPM Center for Public Management, University of Bern, Freiburgstr. 3, 3010, Bern, Switzerland
- Swiss Institute for Translational and Entrepreneurial Medicine (Sitem-Insel), Freiburgstr. 3, 3010, Bern, Switzerland
| | - Carl Rudolf Blankart
- KPM Center for Public Management, University of Bern, Freiburgstr. 3, 3010, Bern, Switzerland
- Swiss Institute for Translational and Entrepreneurial Medicine (Sitem-Insel), Freiburgstr. 3, 3010, Bern, Switzerland
| | - Edith Sky Gross
- EURORDIS - Rare Diseases Europe, 96 Rue Didot, 75014, Paris, France
| | - Gulcin Gumus
- EURORDIS - Rare Diseases Europe, 96 Rue Didot, 75014, Paris, France
| | - Elena Mitova
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria
| | - Stefan Stefanov
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria
- Department of Epidemiology and Disaster Medicine, Faculty of Public Health, Medical University, 15A Vasil Aprilov Blvd., 4002, Plovdiv, Bulgaria
| | - Georgi Stefanov
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria
| | - Rumen Stefanov
- Institute for Rare Diseases, 22 Maestro G. Atanasov St., 4017, Plovdiv, Bulgaria
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, 15A Vasil Aprilov Blvd., 4002, Plovdiv, Bulgaria
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Garnier N, Berghout J, Zygmunt A, Singh D, Huang KA, Kantz W, Blankart CR, Gillner S, Zhao J, Roettger R, Saier C, Kirschner J, Schenk J, Atkins L, Ryan N, Zarakowska K, Zschüntzsch J, Zuccolo M, Müllenborn M, Man YS, Goodman L, Trad M, Chalandon AS, Sansen S, Martinez-Fresno M, Badger S, Walther van Olden R, Rothmann R, Lehner P, Tschohl C, Baillon L, Gumus G, Gross E, Stefanov R, Iskrov G, Raycheva R, Kostadinov K, Mitova E, Einhorn M, Einhorn Y, Schepers J, Hübner M, Alves F, Iskandar R, Mayer R, Renieri A, Piperkova A, Gut I, Beltran S, Matthiesen ME, Poetz M, Hansson M, Trollmann R, Agolini E, Ottombrino S, Novelli A, Bertini E, Selvatici R, Farnè M, Fortunato F, Ferlini A. Genetic newborn screening and digital technologies: A project protocol based on a dual approach to shorten the rare diseases diagnostic path in Europe. PLoS One 2023; 18:e0293503. [PMID: 37992053 PMCID: PMC10664952 DOI: 10.1371/journal.pone.0293503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 11/24/2023] Open
Abstract
Since 72% of rare diseases are genetic in origin and mostly paediatrics, genetic newborn screening represents a diagnostic "window of opportunity". Therefore, many gNBS initiatives started in different European countries. Screen4Care is a research project, which resulted of a joint effort between the European Union Commission and the European Federation of Pharmaceutical Industries and Associations. It focuses on genetic newborn screening and artificial intelligence-based tools which will be applied to a large European population of about 25.000 infants. The neonatal screening strategy will be based on targeted sequencing, while whole genome sequencing will be offered to all enrolled infants who may show early symptoms but have resulted negative at the targeted sequencing-based newborn screening. We will leverage artificial intelligence-based algorithms to identify patients using Electronic Health Records (EHR) and to build a repository "symptom checkers" for patients and healthcare providers. S4C will design an equitable, ethical, and sustainable framework for genetic newborn screening and new digital tools, corroborated by a large workout where legal, ethical, and social complexities will be addressed with the intent of making the framework highly and flexibly translatable into the diverse European health systems.
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Affiliation(s)
- Nicolas Garnier
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Joanne Berghout
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Aldona Zygmunt
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Deependra Singh
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Kui A. Huang
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Waltraud Kantz
- Pfizer Inc., Collegeville, Pennsylvania, United States of America
| | - Carl Rudolf Blankart
- KPM Center for Public Management and Swiss Institute for Translational and Entrepreneurial Medicine, University of Bern, Bern, Switzerland
| | - Sandra Gillner
- KPM Center for Public Management and Swiss Institute for Translational and Entrepreneurial Medicine, University of Bern, Bern, Switzerland
| | - Jiawei Zhao
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Richard Roettger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Christina Saier
- Department of Neuropediatric and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Kirschner
- Department of Neuropediatric and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Joern Schenk
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Leon Atkins
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Nuala Ryan
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Kaja Zarakowska
- Takeda Pharmaceuticals International AG, Opfikon, Switzerland
| | - Jana Zschüntzsch
- Department of Neurology, University Medical Center Goettingen, Göttingen, Germany
| | | | | | - Yuen-Sum Man
- Novo Nordisk Health Care AG, Switzerland &Novo Nordisk A/S, Kloten, Denmark
| | - Liz Goodman
- University College Dublin, National University of Ireland, Dublin, Ireland
| | | | | | | | | | | | | | - Robert Rothmann
- Research Institute AG & Co KG, Digital Human Rights Center, Wien, Austria
| | - Patrick Lehner
- Research Institute AG & Co KG, Digital Human Rights Center, Wien, Austria
| | - Christof Tschohl
- Research Institute AG & Co KG, Digital Human Rights Center, Wien, Austria
| | | | | | | | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Iskrov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Ralitsa Raycheva
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Kostadin Kostadinov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Elena Mitova
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | | | | | - Josef Schepers
- Berlin Institute of Health (at) Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Miriam Hübner
- Berlin Institute of Health (at) Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frauke Alves
- Translational Molecular Imaging, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic of Hematology and Medical Oncology, University Medical Center, Göttingen, Germany
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Göttingen, Germany
| | - Rowan Iskandar
- Swiss Institute for Translational and Entrepreneurial Medicine (sitem-insel), Bern, Switzerland
| | | | | | - Aneta Piperkova
- Bulgarian Association for Personalized Medicine, Sofia, Bulgaria
| | - Ivo Gut
- Centro Nacional de Analisis Genomico, CNAG, Barcelona, Spain
| | - Sergi Beltran
- Centro Nacional de Analisis Genomico, CNAG, Barcelona, Spain
| | | | - Marion Poetz
- Department of Strategy and Innovation, Copenhagen Business School, Copenhagen, Denmark
| | | | | | | | | | | | | | - Rita Selvatici
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marianna Farnè
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Fortunato
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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Raycheva R, Kostadinov K, Mitova E, Bogoeva N, Iskrov G, Stefanov G, Stefanov R. Challenges in mapping European rare disease databases, relevant for ML-based screening technologies in terms of organizational, FAIR and legal principles: scoping review. Front Public Health 2023; 11:1214766. [PMID: 37780450 PMCID: PMC10540868 DOI: 10.3389/fpubh.2023.1214766] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Background Given the increased availability of data sources such as hospital information systems, electronic health records, and health-related registries, a novel approach is required to develop artificial intelligence-based decision support that can assist clinicians in their diagnostic decision-making and shorten rare disease patients' diagnostic odyssey. The aim is to identify key challenges in the process of mapping European rare disease databases, relevant to ML-based screening technologies in terms of organizational, FAIR and legal principles. Methods A scoping review was conducted based on the PRISMA-ScR checklist. The primary article search was conducted in three electronic databases (MEDLINE/Pubmed, Scopus, and Web of Science) and a secondary search was performed in Google scholar and on the organizations' websites. Each step of this review was carried out independently by two researchers. A charting form for relevant study analysis was developed and used to categorize data and identify data items in three domains - organizational, FAIR and legal. Results At the end of the screening process, 73 studies were eligible for review based on inclusion and exclusion criteria with more than 60% (n = 46) of the research published in the last 5 years and originated only from EU/EEA countries. Over the ten-year period (2013-2022), there is a clear cycling trend in the publications, with a peak of challenges reporting every four years. Within this trend, the following dynamic was identified: except for 2016, organizational challenges dominated the articles published up to 2018; legal challenges were the most frequently discussed topic from 2018 to 2022. The following distribution of the data items by domains was observed - (1) organizational (n = 36): data accessibility and sharing (20.2%); long-term sustainability (18.2%); governance, planning and design (17.2%); lack of harmonization and standardization (17.2%); quality of data collection (16.2%); and privacy risks and small sample size (11.1%); (2) FAIR (n = 15): findable (17.9%); accessible sustainability (25.0%); interoperable (39.3%); and reusable (17.9%); and (3) legal (n = 33): data protection by all means (34.4%); data management and ownership (22.9%); research under GDPR and member state law (20.8%); trust and transparency (13.5%); and digitalization of health (8.3%). We observed a specific pattern repeated in all domains during the process of data charting and data item identification - in addition to the outlined challenges, good practices, guidelines, and recommendations were also discussed. The proportion of publications addressing only good practices, guidelines, and recommendations for overcoming challenges when mapping RD databases in at least one domain was calculated to be 47.9% (n = 35). Conclusion Despite the opportunities provided by innovation - automation, electronic health records, hospital-based information systems, biobanks, rare disease registries and European Reference Networks - the results of the current scoping review demonstrate a diversity of the challenges that must still be addressed, with immediate actions on ensuring better governance of rare disease registries, implementing FAIR principles, and enhancing the EU legal framework.
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Affiliation(s)
- Ralitsa Raycheva
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Kostadin Kostadinov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Elena Mitova
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Nataliya Bogoeva
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Iskrov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Georgi Stefanov
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria
- Bulgarian Association for Promotion of Education and Science, Institute for Rare Disease, Plovdiv, Bulgaria
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