Addressing the clinical unmet needs in primary Sjögren’s Syndrome through the sharing, harmonization and federated analysis of 21 European cohorts
[Display omitted] •Data sharing can address open issues and clinical unmet needs in rare diseases.•Data curation enhanced the cohort data quality in primary Sjögrens Syndrome (pSS).•Semantic analysis yielded 7,156 harmonized patients across 21 cohorts in pSS.•Federated tree ensembles yield explainab...
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Published in | Computational and structural biotechnology journal Vol. 20; pp. 471 - 484 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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Netherlands
Elsevier B.V
01.01.2022
Research Network of Computational and Structural Biotechnology Elsevier |
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Abstract | [Display omitted]
•Data sharing can address open issues and clinical unmet needs in rare diseases.•Data curation enhanced the cohort data quality in primary Sjögrens Syndrome (pSS).•Semantic analysis yielded 7,156 harmonized patients across 21 cohorts in pSS.•Federated tree ensembles yield explainable AI models for lymphoma development.•Salivary gland swelling & cryoglobulinemia increase the risk for lymphomagenesis.
For many decades, the clinical unmet needs of primary Sjögren’s Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-art data analytics services to address the pSS clinical unmet needs, including the development of lymphoma classification models and the identification of biomarkers for lymphomagenesis. The users of the platform have been able to successfully interlink, curate, and harmonize 21 regional, national, and international European cohorts of 7,551 pSS patients with respect to the ethical and legal issues for data sharing. Federated AI algorithms were trained across the harmonized databases, with reduced execution time complexity, yielding robust lymphoma classification models with 85% accuracy, 81.25% sensitivity, 85.4% specificity along with 5 biomarkers for lymphoma development. To our knowledge, this is the first GDPR compliant platform that provides federated AI services to address the pSS clinical unmet needs. |
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AbstractList | For many decades, the clinical unmet needs of primary Sjögren's Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-art data analytics services to address the pSS clinical unmet needs, including the development of lymphoma classification models and the identification of biomarkers for lymphomagenesis. The users of the platform have been able to successfully interlink, curate, and harmonize 21 regional, national, and international European cohorts of 7,551 pSS patients with respect to the ethical and legal issues for data sharing. Federated AI algorithms were trained across the harmonized databases, with reduced execution time complexity, yielding robust lymphoma classification models with 85% accuracy, 81.25% sensitivity, 85.4% specificity along with 5 biomarkers for lymphoma development. To our knowledge, this is the first GDPR compliant platform that provides federated AI services to address the pSS clinical unmet needs.For many decades, the clinical unmet needs of primary Sjögren's Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-art data analytics services to address the pSS clinical unmet needs, including the development of lymphoma classification models and the identification of biomarkers for lymphomagenesis. The users of the platform have been able to successfully interlink, curate, and harmonize 21 regional, national, and international European cohorts of 7,551 pSS patients with respect to the ethical and legal issues for data sharing. Federated AI algorithms were trained across the harmonized databases, with reduced execution time complexity, yielding robust lymphoma classification models with 85% accuracy, 81.25% sensitivity, 85.4% specificity along with 5 biomarkers for lymphoma development. To our knowledge, this is the first GDPR compliant platform that provides federated AI services to address the pSS clinical unmet needs. For many decades, the clinical unmet needs of primary Sjögren’s Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-art data analytics services to address the pSS clinical unmet needs, including the development of lymphoma classification models and the identification of biomarkers for lymphomagenesis. The users of the platform have been able to successfully interlink, curate, and harmonize 21 regional, national, and international European cohorts of 7,551 pSS patients with respect to the ethical and legal issues for data sharing. Federated AI algorithms were trained across the harmonized databases, with reduced execution time complexity, yielding robust lymphoma classification models with 85% accuracy, 81.25% sensitivity, 85.4% specificity along with 5 biomarkers for lymphoma development. To our knowledge, this is the first GDPR compliant platform that provides federated AI services to address the pSS clinical unmet needs. [Display omitted] •Data sharing can address open issues and clinical unmet needs in rare diseases.•Data curation enhanced the cohort data quality in primary Sjögrens Syndrome (pSS).•Semantic analysis yielded 7,156 harmonized patients across 21 cohorts in pSS.•Federated tree ensembles yield explainable AI models for lymphoma development.•Salivary gland swelling & cryoglobulinemia increase the risk for lymphomagenesis. For many decades, the clinical unmet needs of primary Sjögren’s Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-art data analytics services to address the pSS clinical unmet needs, including the development of lymphoma classification models and the identification of biomarkers for lymphomagenesis. The users of the platform have been able to successfully interlink, curate, and harmonize 21 regional, national, and international European cohorts of 7,551 pSS patients with respect to the ethical and legal issues for data sharing. Federated AI algorithms were trained across the harmonized databases, with reduced execution time complexity, yielding robust lymphoma classification models with 85% accuracy, 81.25% sensitivity, 85.4% specificity along with 5 biomarkers for lymphoma development. To our knowledge, this is the first GDPR compliant platform that provides federated AI services to address the pSS clinical unmet needs. • Data sharing can address open issues and clinical unmet needs in rare diseases. • Data curation enhanced the cohort data quality in primary Sjögrens Syndrome (pSS). • Semantic analysis yielded 7,156 harmonized patients across 21 cohorts in pSS. • Federated tree ensembles yield explainable AI models for lymphoma development. • Salivary gland swelling & cryoglobulinemia increase the risk for lymphomagenesis. For many decades, the clinical unmet needs of primary Sjögren’s Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity of the underlying pathogenic mechanisms, including the pSS-associated lymphomagenesis process. Here, we present the HarmonicSS cloud-computing exemplar which offers beyond the state-of-the-art data analytics services to address the pSS clinical unmet needs, including the development of lymphoma classification models and the identification of biomarkers for lymphomagenesis. The users of the platform have been able to successfully interlink, curate, and harmonize 21 regional, national, and international European cohorts of 7,551 pSS patients with respect to the ethical and legal issues for data sharing. Federated AI algorithms were trained across the harmonized databases, with reduced execution time complexity, yielding robust lymphoma classification models with 85% accuracy, 81.25% sensitivity, 85.4% specificity along with 5 biomarkers for lymphoma development. To our knowledge, this is the first GDPR compliant platform that provides federated AI services to address the pSS clinical unmet needs. |
Author | Jonsson, Roland Torsten, Witte Gandolfo, Saviana De Vita, Salvatore Venetsanopoulou, Aliki Baldini, Chiara A. G. van Roon, Joel Burmeister, Jan Sivils, Kathy Tzioufas, Athanasios G. Filipovic, Nenad Skopouli, Fotini Varvarigou, Theodora Delporte, Christine Dörner, Thomas Fotiadis, Dimitrios I. Kalatzis, Fanis Parisis, Dorian Exarchos, Themis P. Gerli, Roberto Pezoulas, Vasileios C. Bombardieri, Michele Priori, Roberta Andronikou, Vassiliki Bootsma, Hendrika Kourou, Konstantina D. Chondrogiannis, Thymios Soyfoo, Muhammad Shahnawaz Giacomelli, Roberto Goules, Andreas Pers, Jacques-Olivier Chatzis, Luke Tsiknakis, Manolis Bowman, Simon J. Ng, Wan-Fai Votis, Konstantinos May, Thorsten Lishchuk, Iryna Ramos-Casals, Manuel Xavier, Mariette Bartoloni, Elena Marcelino Pérez, Manuel Zampeli, Evi Devauchelle-Pensec, Valérie |
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Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina, Greece – sequence: 6 givenname: Aliki surname: Venetsanopoulou fullname: Venetsanopoulou, Aliki organization: Dept. of Pathophysiology, School of Medicine, University of Athens, Athens, Greece – sequence: 7 givenname: Themis P. surname: Exarchos fullname: Exarchos, Themis P. organization: Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina, Greece – sequence: 8 givenname: Saviana surname: Gandolfo fullname: Gandolfo, Saviana organization: Clinic of Rheumatology, Dept. of Medical and Biological Sciences, Udine University, Udine, Italy – sequence: 9 givenname: Konstantinos surname: Votis fullname: Votis, Konstantinos organization: Centre for Research and Technology Hellas, Thermi, Thessaloniki, Greece – sequence: 10 givenname: Evi surname: Zampeli fullname: Zampeli, Evi organization: Institute for Systemic 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Dept. of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy – sequence: 21 givenname: Michele surname: Bombardieri fullname: Bombardieri, Michele organization: Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts’ Health NHS Trust, London, United Kingdom – sequence: 22 givenname: Hendrika surname: Bootsma fullname: Bootsma, Hendrika organization: Dept. of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, the Netherlands – sequence: 23 givenname: Simon J. surname: Bowman fullname: Bowman, Simon J. organization: Rheumatology Dept., University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK – sequence: 24 givenname: Muhammad Shahnawaz surname: Soyfoo fullname: Soyfoo, Muhammad Shahnawaz organization: Dept. of Rheumatology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium – sequence: 25 givenname: Dorian surname: Parisis fullname: Parisis, Dorian organization: Laboratory of Pathophysiological Biochemistry and Nutrition, Université Libre de Bruxelles, Brussels, Belgium – sequence: 26 givenname: Christine surname: Delporte fullname: Delporte, Christine organization: Laboratory of Pathophysiological Biochemistry and Nutrition, Université Libre de Bruxelles, Brussels, Belgium – sequence: 27 givenname: Valérie surname: Devauchelle-Pensec fullname: Devauchelle-Pensec, Valérie organization: Univ Brest, Inserm, CHU de Brest, UMR1227, Lymphocytes B et Autoimmunité, Brest, France – sequence: 28 givenname: Jacques-Olivier surname: Pers fullname: Pers, Jacques-Olivier organization: Univ Brest, Inserm, CHU de Brest, UMR1227, Lymphocytes B et Autoimmunité, Brest, France – sequence: 29 givenname: Thomas surname: Dörner fullname: Dörner, Thomas organization: Dept. of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany – sequence: 30 givenname: Elena surname: Bartoloni fullname: Bartoloni, Elena organization: Rheumatology Unit, Dept. of Medicine and Surgery, University of Perugia, Perugia, Italy – sequence: 31 givenname: Roberto surname: Gerli fullname: Gerli, Roberto organization: Rheumatology Unit, Dept. of Medicine and Surgery, University of Perugia, Perugia, Italy – sequence: 32 givenname: Roberto surname: Giacomelli fullname: Giacomelli, Roberto organization: Division of Rheumatology, Dept. of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy – sequence: 33 givenname: Roland surname: Jonsson fullname: Jonsson, Roland organization: Dept. of Clinical Science, University of Bergen, Bergen, Norway – sequence: 34 givenname: Wan-Fai surname: Ng fullname: Ng, Wan-Fai organization: Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK – sequence: 35 givenname: Roberta surname: Priori fullname: Priori, Roberta organization: Dept. of Internal Medicine and Medical Specialties, Rheumatology Clinic, Sapienza University of Rome, Rome, Italy – sequence: 36 givenname: Manuel surname: Ramos-Casals fullname: Ramos-Casals, Manuel organization: Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, Barcelona, Spain – sequence: 37 givenname: Kathy surname: Sivils fullname: Sivils, Kathy organization: Oklahoma Medical Research Foundation, OK, US – sequence: 38 givenname: Fotini surname: Skopouli fullname: Skopouli, Fotini organization: Institute for Systemic Autoimmune and Neurological Diseases, Athens, Greece – sequence: 39 givenname: Witte surname: Torsten fullname: Torsten, Witte organization: Dept. of Rheumatology and Immunology, Hanover Medical School, Hanover, Germany – sequence: 40 givenname: Joel surname: A. 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G. van Roon, Joel organization: Dept. of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands – sequence: 41 givenname: Mariette surname: Xavier fullname: Xavier, Mariette organization: Dept. of Rheumatology, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris, Paris, France – sequence: 42 givenname: Salvatore surname: De Vita fullname: De Vita, Salvatore organization: Clinic of Rheumatology, Dept. of Medical and Biological Sciences, Udine University, Udine, Italy – sequence: 43 givenname: Athanasios G. surname: Tzioufas fullname: Tzioufas, Athanasios G. organization: Dept. of Pathophysiology, School of Medicine, University of Athens, Athens, Greece – sequence: 44 givenname: Dimitrios I. surname: Fotiadis fullname: Fotiadis, Dimitrios I. email: fotiadis@uoi.gr organization: Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, Ioannina, Greece |
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Keywords | Data sharing Data curation Biomarkers Data harmonization Federated AI Primary Sjögren’s syndrome Lymphoma classification |
Language | English |
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•Data sharing can address open issues and clinical unmet needs in rare diseases.•Data curation enhanced the cohort data quality in primary... For many decades, the clinical unmet needs of primary Sjögren's Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity... • Data sharing can address open issues and clinical unmet needs in rare diseases. • Data curation enhanced the cohort data quality in primary Sjögrens Syndrome... For many decades, the clinical unmet needs of primary Sjögren’s Syndrome (pSS) have been left unresolved due to the rareness of the disease and the complexity... |
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SubjectTerms | Biomarkers Data curation Data harmonization Data sharing Federated AI Lymphoma classification Primary Sjögren’s syndrome |
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Title | Addressing the clinical unmet needs in primary Sjögren’s Syndrome through the sharing, harmonization and federated analysis of 21 European cohorts |
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