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Witte ML, Schoneberg A, Hanss S, Lablans M, Vehreschild J, Krefting D. Adaptability of Existing Feasibility Tools for Clinical Study Research Data Platforms. Stud Health Technol Inform 2023; 307:39-48. [PMID: 37697836 DOI: 10.3233/shti230691] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
INTRODUCTION The increasing need for secondary use of clinical study data requires FAIR infrastructures, i.e. provide findable, accessible, interoperable and reusable data. It is crucial for data scientists to assess the number and distribution of cohorts that meet complex combinations of criteria defined by the research question. This so-called feasibility test is increasingly offered as a self-service, where scientists can filter the available data according to specific parameters. Early feasibility tools have been developed for biosamples or image collections. They are of high interest for clinical study platforms that federate multiple studies and data types, but they pose specific requirements on the integration of data sources and data protection. METHODS Mandatory and desired requirements for such tools were acquired from two user groups - primary users and staff managing a platform's transfer office. Open Source feasibility tools were sought by different literature search strategies and evaluated on their adaptability to the requirements. RESULTS We identified seven feasibility tools that we evaluated based on six mandatory properties. DISCUSSION We determined five feasibility tools to be most promising candidates for adaption to a clinical study research data platform, the Clinical Communication Platform, the German Portal for Medical Research Data, the Feasibility Explorer, Medical Controlling, and the Sample Locator.
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Affiliation(s)
- Marie-Louise Witte
- Department of Medical Informatics, University Medical Center Göttingen, Germany
| | - Anne Schoneberg
- Department of Medical Informatics, University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research, Partner Site Göttingen, Germany
| | - Sabine Hanss
- Department of Medical Informatics, University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research, Partner Site Göttingen, Germany
| | - Martin Lablans
- German Cancer Research Center, Heidelberg, Germany
- CDPMI, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Janne Vehreschild
- Department I of Internal Medicine, University Hospital Cologne, Germany
- German Centre for Infection Research, partner site Bonn-Cologne, Germany
- Department II for Internal Medicine, University Hospital Frankfurt, Germany
| | - Dagmar Krefting
- Department of Medical Informatics, University Medical Center Göttingen, Germany
- German Centre for Cardiovascular Research, Partner Site Göttingen, Germany
- Campus Institute Data Science, Georg-August-University Göttingen, Germany
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Maier D, Vehreschild JJ, Uhl B, Meyer S, Berger-Thürmel K, Boerries M, Braren R, Grünwald V, Hadaschik B, Palm S, Singer S, Stuschke M, Juárez D, Delpy P, Lambarki M, Hummel M, Engels C, Andreas S, Gökbuget N, Ihrig K, Burock S, Keune D, Eggert A, Keilholz U, Schulz H, Büttner D, Löck S, Krause M, Esins M, Ressing F, Schuler M, Brandts C, Brucker DP, Husmann G, Oellerich T, Metzger P, Voigt F, Illert AL, Theobald M, Kindler T, Sudhof U, Reckmann A, Schwinghammer F, Nasseh D, Weichert W, von Bergwelt-Baildon M, Bitzer M, Malek N, Öner Ö, Schulze-Osthoff K, Bartels S, Haier J, Ammann R, Schmidt AF, Guenther B, Janning M, Kasper B, Loges S, Stilgenbauer S, Kuhn P, Tausch E, Runow S, Kerscher A, Neumann M, Breu M, Lablans M, Serve H. Profile of the multicenter cohort of the German Cancer Consortium's Clinical Communication Platform. Eur J Epidemiol 2023; 38:573-586. [PMID: 37017830 PMCID: PMC10073785 DOI: 10.1007/s10654-023-00990-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/09/2023] [Indexed: 04/06/2023]
Abstract
Treatment concepts in oncology are becoming increasingly personalized and diverse. Successively, changes in standards of care mandate continuous monitoring of patient pathways and clinical outcomes based on large, representative real-world data. The German Cancer Consortium's (DKTK) Clinical Communication Platform (CCP) provides such opportunity. Connecting fourteen university hospital-based cancer centers, the CCP relies on a federated IT-infrastructure sourcing data from facility-based cancer registry units and biobanks. Federated analyses resulted in a cohort of 600,915 patients, out of which 232,991 were incident since 2013 and for which a comprehensive documentation is available. Next to demographic data (i.e., age at diagnosis: 2.0% 0-20 years, 8.3% 21-40 years, 30.9% 41-60 years, 50.1% 61-80 years, 8.8% 81+ years; and gender: 45.2% female, 54.7% male, 0.1% other) and diagnoses (five most frequent tumor origins: 22,523 prostate, 18,409 breast, 15,575 lung, 13,964 skin/malignant melanoma, 9005 brain), the cohort dataset contains information about therapeutic interventions and response assessments and is connected to 287,883 liquid and tissue biosamples. Focusing on diagnoses and therapy-sequences, showcase analyses of diagnosis-specific sub-cohorts (pancreas, larynx, kidney, thyroid gland) demonstrate the analytical opportunities offered by the cohort's data. Due to its data granularity and size, the cohort is a potential catalyst for translational cancer research. It provides rapid access to comprehensive patient groups and may improve the understanding of the clinical course of various (even rare) malignancies. Therefore, the cohort may serve as a decisions-making tool for clinical trial design and contributes to the evaluation of scientific findings under real-world conditions.
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Affiliation(s)
- Daniel Maier
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Janne Vehreschild
- University Hospital Frankfurt, Frankfurt, Germany.
- Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany.
- German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.
| | - Barbara Uhl
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandra Meyer
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karin Berger-Thürmel
- University Hospital Munich, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, Medical Center, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rickmer Braren
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- School of Medicine, Technical University Munich, Munich, Germany
| | - Viktor Grünwald
- West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Boris Hadaschik
- West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Palm
- West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susanne Singer
- University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner Site Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Stuschke
- West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Juárez
- German Cancer Research Center (DKFZ), Federated Information Systems, Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pierre Delpy
- German Cancer Research Center (DKFZ), Federated Information Systems, Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohamed Lambarki
- German Cancer Research Center (DKFZ), Federated Information Systems, Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hummel
- Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cäcilia Engels
- Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Andreas
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicola Gökbuget
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristina Ihrig
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Susen Burock
- Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dietmar Keune
- Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ulrich Keilholz
- Charité Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hagen Schulz
- University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Büttner
- University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Steffen Löck
- University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mechthild Krause
- University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mirko Esins
- West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Frank Ressing
- West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Martin Schuler
- West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Brandts
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel P Brucker
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabriele Husmann
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Oellerich
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Metzger
- Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, Medical Center, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederik Voigt
- Faculty of Medicine, Institute of Medical Bioinformatics and Systems Medicine, Medical Center, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna L Illert
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine I, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Matthias Theobald
- University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner Site Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kindler
- University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner Site Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ursula Sudhof
- University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Achim Reckmann
- University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Cancer Consortium (DKTK), Partner Site Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Schwinghammer
- University Hospital Munich, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Nasseh
- University Hospital Munich, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- School of Medicine, Technical University Munich, Munich, Germany
| | - Michael von Bergwelt-Baildon
- University Hospital Munich, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Bitzer
- Center for Personalized Medicine, Eberhard-Karls University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nisar Malek
- Center for Personalized Medicine, Eberhard-Karls University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Öznur Öner
- Center for Personalized Medicine, Eberhard-Karls University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klaus Schulze-Osthoff
- Center for Personalized Medicine, Eberhard-Karls University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Bartels
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jörg Haier
- Comprehensive Cancer Center Hannover (Claudia von Schilling-Zentrum), Hannover Medical School, Hannover, Germany
| | - Raimund Ammann
- Comprehensive Cancer Center Hannover (Claudia von Schilling-Zentrum), Hannover Medical School, Hannover, Germany
| | - Anja Franziska Schmidt
- Comprehensive Cancer Center Hannover (Claudia von Schilling-Zentrum), Hannover Medical School, Hannover, Germany
| | - Bernd Guenther
- Comprehensive Cancer Center Hannover (Claudia von Schilling-Zentrum), Hannover Medical School, Hannover, Germany
| | - Melanie Janning
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
- Mannheim University Medical Center, University of Heidelberg, Mannheim, Germany
- Department of Personalized Medical Oncology (A420), DKFZ German Cancer Research Center, Heidelberg, Germany
| | - Bernd Kasper
- Mannheim University Medical Center, University of Heidelberg, Mannheim, Germany
| | - Sonja Loges
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
- Mannheim University Medical Center, University of Heidelberg, Mannheim, Germany
- Department of Personalized Medical Oncology (A420), DKFZ German Cancer Research Center, Heidelberg, Germany
| | | | - Peter Kuhn
- Neu-Ulm University of Applied Sciences, Neu-Ulm, Germany
| | | | | | | | | | - Martin Breu
- University Hospital of Würzburg, Würzburg, Germany
| | - Martin Lablans
- German Cancer Research Center (DKFZ), Federated Information Systems, Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hubert Serve
- University Hospital Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute, Frankfurt, Germany
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Kussel T, Brenner T, Tremper G, Schepers J, Lablans M, Hamacher K. Record linkage based patient intersection cardinality for rare disease studies using Mainzelliste and secure multi-party computation. Lab Invest 2022; 20:458. [PMID: 36209221 PMCID: PMC9547637 DOI: 10.1186/s12967-022-03671-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The low number of patients suffering from any given rare diseases poses a difficult problem for medical research: With the exception of some specialized biobanks and disease registries, potential study participants' information are disjoint and distributed over many medical institutions. Whenever some of those facilities are in close proximity, a significant overlap of patients can reasonably be expected, further complicating statistical study feasibility assessments and data gathering. Due to the sensitive nature of medical records and identifying data, data transfer and joint computations are often forbidden by law or associated with prohibitive amounts of effort. To alleviate this problem and to support rare disease research, we developed the Mainzelliste Secure EpiLinker (MainSEL) record linkage framework, a secure Multi-Party Computation based application using trusted-third-party-less cryptographic protocols to perform privacy-preserving record linkage with high security guarantees. In this work, we extend MainSEL to allow the record linkage based calculation of the number of common patients between institutions. This allows privacy-preserving statistical feasibility estimations for further analyses and data consolidation. Additionally, we created easy to deploy software packages using microservice containerization and continuous deployment/continuous integration. We performed tests with medical researchers using MainSEL in real-world medical IT environments, using synthetic patient data. RESULTS We show that MainSEL achieves practical runtimes, performing 10 000 comparisons in approximately 5 minutes. Our approach proved to be feasible in a wide range of network settings and use cases. The "lessons learned" from the real-world testing show the need to explicitly support and document the usage and deployment for both analysis pipeline integration and researcher driven ad-hoc analysis use cases, thus clarifying the wide applicability of our software. MainSEL is freely available under: https://github.com/medicalinformatics/MainSEL CONCLUSIONS: MainSEL performs well in real-world settings and is a useful tool not only for rare disease research, but medical research in general. It achieves practical runtimes, improved security guarantees compared to existing solutions, and is simple to deploy in strict clinical IT environments. Based on the "lessons learned" from the real-word testing, we hope to enable a wide range of medical researchers to meet their needs and requirements using modern privacy-preserving technologies.
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Affiliation(s)
- Tobias Kussel
- Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany. .,German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany. .,University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
| | - Torben Brenner
- German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Galina Tremper
- German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Josef Schepers
- Berlin Institute of Health, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
| | - Martin Lablans
- German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Kay Hamacher
- Technische Universität Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
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Mack M, Broche J, George S, Hajjari Z, Janke F, Ranganathan L, Ashouri M, Bleul S, Desuki A, Engels C, Fliedner SM, Hartmann N, Hummel M, Janning M, Kiel A, Köhler T, Koschade S, Lablans M, Lambarki M, Loges S, Lueong S, Meyer S, Ossowski S, Scherer F, Schroeder C, Skowronek P, Thiede C, Uhl B, Vehreschild JJ, von Bubnoff N, Wagner S, Werner TV, Westphalen CB, Fresser P, Sültmann H, Tinhofer I, Winter C. The DKTK EXLIQUID consortium – exploiting liquid biopsies to advance cancer precision medicine for molecular tumor board patients. J LAB MED 2022. [DOI: 10.1515/labmed-2022-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Abstract
Testing for genetic alterations in tumor tissue allows clinicians to identify patients who most likely will benefit from molecular targeted treatment. EXLIQUID – exploiting liquid biopsies to advance cancer precision medicine – investigates the potential of additional non-invasive tools for guiding therapy decisions and monitoring of advanced cancer patients. The term “liquid biopsy” (LB) refers to non-invasive analysis of tumor-derived circulating material such as cell-free DNA in blood samples from cancer patients. Although recent technological advances allow sensitive and specific detection of LB biomarkers, only few LB assays have entered clinical routine to date. EXLIQUID is a German Cancer Consortium (DKTK)-wide joint funding project that aims at establishing LBs as a minimally-invasive tool to analyze molecular changes in circulating tumor DNA (ctDNA). Here, we present the structure, clinical aim, and methodical approach of the new DKTK EXLIQUID consortium. Within EXLIQUID, we will set up a multicenter repository of high-quality LB samples from patients participating in DKTK MASTER and local molecular tumor boards, which use molecular profiles of tumor tissues to guide targeted therapies. We will develop LB assays for monitoring of therapy efficacy by the analysis of tumor mutant variants and tumor-specific DNA methylation patterns in ctDNA from these patients. By bringing together LB experts from all DKTK partner sites and exploiting the diversity of their particular expertise, complementary skills and technologies, the EXLIQUID consortium addresses the challenges of translating LBs into the clinic. The DKTK structure provides EXLIQUID a unique position for the identification of liquid biomarkers even in less common tumor types, thereby extending the group of patients benefitting from non-invasive LB testing. Besides its scientific aims, EXLIQUID is building a valuable precision oncology cohort and LB platform which will be available for future collaborative research studies within the DKTK and beyond.
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Affiliation(s)
- Matthias Mack
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Julian Broche
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephen George
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Zahra Hajjari
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Janke
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Lavanya Ranganathan
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohammadreza Ashouri
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sabine Bleul
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Desuki
- University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg-University Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Cecilia Engels
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephanie M.J. Fliedner
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Michael Hummel
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Melanie Janning
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Alexander Kiel
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Thomas Köhler
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sebastian Koschade
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Martin Lablans
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohamed Lambarki
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sonja Loges
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Smiths Lueong
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sandra Meyer
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Scherer
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrick Skowronek
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christian Thiede
- Department of Medicine I , University Hospital Carl Gustav Carus , Dresden , Germany
- German Cancer Consortium (DKTK), Partner Site Dresden , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Barbara Uhl
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Janne Vehreschild
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Sebastian Wagner
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Tamara V. Werner
- Medical Center, Medical Faculty , Institute for Surgical Pathology, University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - C. Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III , Ludwig Maximilian University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrizia Fresser
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Holger Sültmann
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christof Winter
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
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5
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Löbe M, Bialke M, Bienzeisler J, Drepper J, Ganslandt T, Haderer S, Kraska D, Lablans M, Sax U, Speer R, Stäubert S, Kaulke K. ToolPool Gesundheitsforschung - A Repository for Software and Services Focused on Supporting Clinical and Epidemiological Research. Stud Health Technol Inform 2022; 293:19-27. [PMID: 35592955 DOI: 10.3233/shti220342] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The academic research environment is characterized by self-developed, innovative, customized solutions, which are often free to use for third parties with open-source code and open licenses. On the other hand, they are maintained only to a very limited extent after the end of project funding. The ToolPool Gesundheitsforschung addresses the problem of finding ready to use solutions by building a registry of proven and supported tools, services, concepts and consulting offers. The goal is to provide an up-to-date selection of "relevant" solutions for a given domain that are immediately usable and that are actually used by third parties, rather than aiming at a complete list of all solutions which belong to that domain. Proof of relevance and usage must be provided, for example, by concrete application scenarios, experience reports by uninvolved third parties, references in publications or workshops held. Quality assurance is carried out for new entries by an agreed list of admission criteria, for existing entries at least once a year by a special task force. Currently, 79 solutions are represented, this number is to be significantly expanded by involving of new editors from current national funding initiatives in Germany.
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Affiliation(s)
- Matthias Löbe
- Institut für Medizinische Informatik, Statistik und Epidemiologie (IMISE), Universität Leipzig, Germany
| | - Martin Bialke
- Institut für Community Medicine, Universitätsmedizin Greifswald, Germany
| | - Jonas Bienzeisler
- Institut für Medizinische Informatik, Uniklinik RWTH Aachen, Germany
| | - Johannes Drepper
- TMF - Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V., Berlin, Germany
| | - Thomas Ganslandt
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sophie Haderer
- TMF - Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V., Berlin, Germany
| | - Detlef Kraska
- Medizinisches Zentrum für Informations- und Kommunikationstechnik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Martin Lablans
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- CDPMI, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Ulrich Sax
- Institut für Medizinische Informatik, Universitätsmedizin Göttingen, Germany
| | - Ronald Speer
- LIFE - Leipziger Forschungszentrum für Zivilisationserkrankungen, Germany
| | - Sebastian Stäubert
- Institut für Medizinische Informatik, Statistik und Epidemiologie (IMISE), Universität Leipzig, Germany
| | - Knut Kaulke
- TMF - Technologie- und Methodenplattform für die vernetzte medizinische Forschung e.V., Berlin, Germany
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6
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Ulrich H, Kock-Schoppenhauer AK, Deppenwiese N, Gött R, Kern J, Lablans M, Majeed RW, Stöhr MR, Stausberg J, Varghese J, Dugas M, Ingenerf J. Understanding the Nature of Metadata: Systematic Review. J Med Internet Res 2022; 24:e25440. [PMID: 35014967 PMCID: PMC8790684 DOI: 10.2196/25440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/28/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Background Metadata are created to describe the corresponding data in a detailed and unambiguous way and is used for various applications in different research areas, for example, data identification and classification. However, a clear definition of metadata is crucial for further use. Unfortunately, extensive experience with the processing and management of metadata has shown that the term “metadata” and its use is not always unambiguous. Objective This study aimed to understand the definition of metadata and the challenges resulting from metadata reuse. Methods A systematic literature search was performed in this study following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines for reporting on systematic reviews. Five research questions were identified to streamline the review process, addressing metadata characteristics, metadata standards, use cases, and problems encountered. This review was preceded by a harmonization process to achieve a general understanding of the terms used. Results The harmonization process resulted in a clear set of definitions for metadata processing focusing on data integration. The following literature review was conducted by 10 reviewers with different backgrounds and using the harmonized definitions. This study included 81 peer-reviewed papers from the last decade after applying various filtering steps to identify the most relevant papers. The 5 research questions could be answered, resulting in a broad overview of the standards, use cases, problems, and corresponding solutions for the application of metadata in different research areas. Conclusions Metadata can be a powerful tool for identifying, describing, and processing information, but its meaningful creation is costly and challenging. This review process uncovered many standards, use cases, problems, and solutions for dealing with metadata. The presented harmonized definitions and the new schema have the potential to improve the classification and generation of metadata by creating a shared understanding of metadata and its context.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | | | - Noemi Deppenwiese
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Gött
- Department Epidemiology of Health Care and Community Health, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Raphael W Majeed
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Justus-Liebig-University, Giessen, Germany.,Institute of Medical Informatics, University Hospital RWTH Aachen, Aachen, Germany
| | - Mark R Stöhr
- Universities of Giessen and Marburg Lung Center, German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
| | - Jürgen Stausberg
- Institute of Medical Informatics, Biometry and Epidemiology, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
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7
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Schüttler C, Prokosch HU, Hummel M, Lablans M, Kroll B, Engels C. The journey to establishing an IT-infrastructure within the German Biobank Alliance. PLoS One 2021; 16:e0257632. [PMID: 34551019 PMCID: PMC8457464 DOI: 10.1371/journal.pone.0257632] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/04/2021] [Indexed: 11/19/2022] Open
Abstract
Background Biobanks ensure the long-term storage and accessibility of biospecimens and corresponding data sets. Thus, they form the foundation for many research projects which may contribute to improving medical care. With the establishment of the German Biobank Node and Alliance, expertise in biobanking is bundled and strengthened. An important component within this research infrastructure is the set-up of an information technology (IT) network for allowing feasibility requests across individual biobanks. Objective We aim to describe relevant aspects that have shaped the journey to interconnect biobanks, to enhance their visibility within the research-community, to harmonize data, and to enable feasibility searches to support access to available data and biosamples. Methods To achieve this task, we resorted to a wide variety of methods: we ran a requirement analysis, decided on the mode of operation for the federated team of IT-developers and on the development approach itself, took related national and international initiatives into account, and concluded with evaluations of the developed software artefacts and the operation of the entire chain of applications. Results We drew an IT framework including all heterogeneous data aspects derived from our requirement analysis and developed a comprehensive IT infrastructure. The successful implementation benefited from a smooth interaction of a federated IT team distributed across all participating sites that was even able to manage a major technology change mid-project. Authentication and project management services from associated partners could be integrated and the graphic user interface for an intuitive search tool for biospecimens was designed iteratively. The developed code is open source to ensure sustainability and the local implementation is concluded and functioning. The evaluation of the components was positive. Conclusions The entire project had given ample opportunity for challenges, predictable and unpredictable—from the mode of operation to changing some of the initial ideas. We learned our lessons concerning personnel, budget planning and technical as well as manual monitoring as well as some requirements arising only during the process of the project. Nevertheless, we can here report a success story of a network infrastructure, highly agile and much easier in local installation than initially anticipated.
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Affiliation(s)
- Christina Schüttler
- Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Ulrich Prokosch
- Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Hummel
- German Biobank Node, Charité -Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
- University Medical Center Mannheim, Mannheim, Germany
| | - Björn Kroll
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany
| | - Cäcilia Engels
- German Biobank Node, Charité -Universitätsmedizin Berlin, Berlin, Germany
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8
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Rieder M, Gauchel N, Kaier K, Jakob C, Borgmann S, Classen AY, Schneider J, Eberwein L, Lablans M, Rüthrich M, Dolff S, Wille K, Haselberger M, Heuzeroth H, Bode C, von Zur Mühlen C, Rieg S, Duerschmied D. Pre-medication with oral anticoagulants is associated with better outcomes in a large multinational COVID-19 cohort with cardiovascular comorbidities. Clin Res Cardiol 2021; 111:322-332. [PMID: 34546427 PMCID: PMC8453472 DOI: 10.1007/s00392-021-01939-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/06/2021] [Indexed: 12/15/2022]
Abstract
AIMS Coagulopathy and venous thromboembolism are common findings in coronavirus disease 2019 (COVID-19) and are associated with poor outcome. Timely initiation of anticoagulation after hospital admission was shown to be beneficial. In this study we aim to examine the association of pre-existing oral anticoagulation (OAC) with outcome among a cohort of SARS-CoV-2 infected patients. METHODS AND RESULTS We analysed the data from the large multi-national Lean European Open Survey on SARS-CoV-2 infected patients (LEOSS) from March to August 2020. Patients with SARS-CoV-2 infection were eligible for inclusion. We retrospectively analysed the association of pre-existing OAC with all-cause mortality. Secondary outcome measures included COVID-19-related mortality, recovery and composite endpoints combining death and/or thrombotic event and death and/or bleeding event. We restricted bleeding events to intracerebral bleeding in this analysis to ensure clinical relevance and to limit reporting errors. A total of 1 433 SARS-CoV-2 infected patients were analysed, while 334 patients (23.3%) had an existing premedication with OAC and 1 099 patients (79.7%) had no OAC. After risk adjustment for comorbidities, pre-existing OAC showed a protective influence on the endpoint death (OR 0.62, P = 0.013) as well as the secondary endpoints COVID-19-related death (OR 0.64, P = 0.023) and non-recovery (OR 0.66, P = 0.014). The combined endpoint death or thrombotic event tended to be less frequent in patients on OAC (OR 0.71, P = 0.056). CONCLUSIONS Pre-existing OAC is protective in COVID-19, irrespective of anticoagulation regime during hospital stay and independent of the stage and course of disease.
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Affiliation(s)
- Marina Rieder
- Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Cardiology and Angiology I, Heart Center, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Nadine Gauchel
- Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Department of Cardiology and Angiology I, Heart Center, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany.
| | - Klaus Kaier
- Institute of Medical Biometry and Statistics, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Carolin Jakob
- Department I for Internal Medicine, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Stefan Borgmann
- Department of Infectious Diseases and Infection Control, Ingolstadt Hospital, Ingolstadt, Germany
| | - Annika Y Classen
- Department I for Internal Medicine, Faculty of Medicine, University of Cologne, University Hospital Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jochen Schneider
- School of Medicine, Technical University of Munich, University Hospital Rechts der Isar, Munich, Germany
| | - Lukas Eberwein
- 4Th Department of Internal Medicine, Klinikum Leverkusen, Leverkusen, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,University Medical Center Mannheim, Mannheim, Germany
| | - Maria Rüthrich
- Department for Internal Medicine II, Hematology and Medical Oncology, University Hospital Jena, Jena, Germany.,Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll Institute, Jena, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Duisburg, Germany
| | - Kai Wille
- University Clinic for Haematology, Oncology, Haemostaseology and Palliative Care, Johannes Wesling Medical Center Minden, University of Bochum, Bochum, Germany
| | | | - Hanno Heuzeroth
- Department of Emergency and Intensive Care Medicine, Klinikum Ernst-Von-Bergmann, Potsdam, Germany
| | - Christoph Bode
- Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Cardiology and Angiology I, Heart Center, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Constantin von Zur Mühlen
- Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Cardiology and Angiology I, Heart Center, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Siegbert Rieg
- Division of Infectious Diseases, Department of Medicine II, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Duerschmied
- Department of Medicine III (Interdisciplinary Medical Intensive Care), Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Cardiology and Angiology I, Heart Center, University of Freiburg, Hugstetter Strasse 55, 79106, Freiburg, Germany
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9
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Tremper G, Brenner T, Stampe F, Borg A, Bialke M, Croft D, Schmidt E, Lablans M. MAGICPL: A Generic Process Description Language for Distributed Pseudonymization Scenarios. Methods Inf Med 2021; 60:21-31. [PMID: 34225374 DOI: 10.1055/s-0041-1731387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Pseudonymization is an important aspect of projects dealing with sensitive patient data. Most projects build their own specialized, hard-coded, solutions. However, these overlap in many aspects of their functionality. As any re-implementation binds resources, we would like to propose a solution that facilitates and encourages the reuse of existing components. METHODS We analyzed already-established data protection concepts to gain an insight into their common features and the ways in which their components were linked together. We found that we could represent these pseudonymization processes with a simple descriptive language, which we have called MAGICPL, plus a relatively small set of components. We designed MAGICPL as an XML-based language, to make it human-readable and accessible to nonprogrammers. Additionally, a prototype implementation of the components was written in Java. MAGICPL makes it possible to reference the components using their class names, making it easy to extend or exchange the component set. Furthermore, there is a simple HTTP application programming interface (API) that runs the tasks and allows other systems to communicate with the pseudonymization process. RESULTS MAGICPL has been used in at least three projects, including the re-implementation of the pseudonymization process of the German Cancer Consortium, clinical data flows in a large-scale translational research network (National Network Genomic Medicine), and for our own institute's pseudonymization service. CONCLUSIONS Putting our solution into productive use at both our own institute and at our partner sites facilitated a reduction in the time and effort required to build pseudonymization pipelines in medical research.
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Affiliation(s)
- Galina Tremper
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Torben Brenner
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Florian Stampe
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Borg
- Institute of Medical Biostatistics, Epidemiology and Informatics, Johannes Gutenberg-Universität Mainz, Universitätsmedizin, Mainz, Germany
| | - Martin Bialke
- Department Epidemiology of Health Care and Community Health, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - David Croft
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Esther Schmidt
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
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10
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Reihs R, Proynova R, Maqsood S, Ataian M, Lablans M, Quinlan PR, Lawrence E, Bowman E, van Enckevort E, Bučík DF, Müller H, Holub P. BBMRI-ERIC Negotiator: Implementing Efficient Access to Biobanks. Biopreserv Biobank 2021; 19:414-421. [PMID: 34182766 DOI: 10.1089/bio.2020.0144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various biological resources, such as biobanks and disease-specific registries, have become indispensable resources to better understand the epidemiology and biological mechanisms of disease and are fundamental for advancing medical research. Nevertheless, biobanks and similar resources still face significant challenges to become more findable and accessible by users on both national and global scales. One of the main challenges for users is to find relevant resources using cataloging and search services such as the BBMRI-ERIC Directory, operated by European Research Infrastructure on Biobanking and Biomolecular Resources (BBMRI-ERIC), as these often do not contain the information needed by the researchers to decide if the resource has relevant material/data; these resources are only weakly characterized. Hence, the researcher is typically left with too many resources to explore and investigate. In addition, resources often have complex procedures for accessing holdings, particularly for depletable biological materials. This article focuses on designing a system for effective negotiation of access to holdings, in which a researcher can approach many resources simultaneously, while giving each resource team the ability to implement their own mechanisms to check if the material/data are available and to decide if access should be provided. The BBMRI-ERIC has developed and implemented an access and negotiation tool called the BBMRI-ERIC Negotiator. The Negotiator enables access negotiation to more than 600 biobanks from the BBMRI-ERIC Directory and other discovery services such as GBA/BBMRI-ERIC Locator or RD-Connect Finder. This article summarizes the principles that guided the design of the tool, the terminology used and underlying data model, request workflows, authentication and authorization mechanism(s), and the mechanisms and monitoring processes to stimulate the desired behavior of the resources: to effectively deliver access to biological material and data.
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Affiliation(s)
- Robert Reihs
- BBMRI-ERIC, Graz, Austria.,BBMRI.at and Medical University Graz, Graz, Austria
| | - Rumyana Proynova
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Saher Maqsood
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Maxmilian Ataian
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- BBMRI.de/German Biobank Alliance and German Cancer Research Center, Heidelberg, Germany
| | - Philip R Quinlan
- BBMRI.uk and University of Nottingham, Nottingham, United Kingdom
| | - Emma Lawrence
- BBMRI.uk and University College London, London, United Kingdom
| | - Erinna Bowman
- BBMRI.uk and University College London, London, United Kingdom
| | - Esther van Enckevort
- BBMRI.nl and University of Groningen and University Medical Center Groningen, The Netherlands
| | | | - Heimo Müller
- BBMRI-ERIC, Graz, Austria.,BBMRI.at and Medical University Graz, Graz, Austria
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11
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Lambarki M, Kern J, Croft D, Engels C, Deppenwiese N, Kerscher A, Kiel A, Palm S, Lablans M. Oncology on FHIR: A Data Model for Distributed Cancer Research. Stud Health Technol Inform 2021; 278:203-210. [PMID: 34042895 DOI: 10.3233/shti210070] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
In the field of oncology, a close integration of cancer research and patient care is indispensable. Although an exchange of data between health care providers and other institutions such as cancer registries has already been established in Germany, it does not take advantage of internationally coordinated health data standards. Translational cancer research would also benefit from such standards in the context of secondary data use. This paper employs use cases from the German Cancer Consortium (DKTK) to show how this gap can be closed using a harmonised FHIR-based data model, and how to apply it to an existing federated data platform.
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Affiliation(s)
- Mohamed Lambarki
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jori Kern
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Croft
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cäcilia Engels
- Charité University Medicine Berlin, German Biobank Node, Berlin, Germany
| | - Noemi Deppenwiese
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Alexander Kiel
- Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Stefan Palm
- West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Federated Information Systems, University Medical Center Mannheim, Mannheim, Germany
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12
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Rohde F, Franke M, Sehili Z, Lablans M, Rahm E. Optimization of the Mainzelliste software for fast privacy-preserving record linkage. J Transl Med 2021; 19:33. [PMID: 33451317 PMCID: PMC7809773 DOI: 10.1186/s12967-020-02678-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Data analysis for biomedical research often requires a record linkage step to identify records from multiple data sources referring to the same person. Due to the lack of unique personal identifiers across these sources, record linkage relies on the similarity of personal data such as first and last names or birth dates. However, the exchange of such identifying data with a third party, as is the case in record linkage, is generally subject to strict privacy requirements. This problem is addressed by privacy-preserving record linkage (PPRL) and pseudonymization services. Mainzelliste is an open-source record linkage and pseudonymization service used to carry out PPRL processes in real-world use cases. METHODS We evaluate the linkage quality and performance of the linkage process using several real and near-real datasets with different properties w.r.t. size and error-rate of matching records. We conduct a comparison between (plaintext) record linkage and PPRL based on encoded records (Bloom filters). Furthermore, since the Mainzelliste software offers no blocking mechanism, we extend it by phonetic blocking as well as novel blocking schemes based on locality-sensitive hashing (LSH) to improve runtime for both standard and privacy-preserving record linkage. RESULTS The Mainzelliste achieves high linkage quality for PPRL using field-level Bloom filters due to the use of an error-tolerant matching algorithm that can handle variances in names, in particular missing or transposed name compounds. However, due to the absence of blocking, the runtimes are unacceptable for real use cases with larger datasets. The newly implemented blocking approaches improve runtimes by orders of magnitude while retaining high linkage quality. CONCLUSION We conduct the first comprehensive evaluation of the record linkage facilities of the Mainzelliste software and extend it with blocking methods to improve its runtime. We observed a very high linkage quality for both plaintext as well as encoded data even in the presence of errors. The provided blocking methods provide order of magnitude improvements regarding runtime performance thus facilitating the use in research projects with large datasets and many participants.
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Affiliation(s)
- Florens Rohde
- Database Group, University of Leipzig, Leipzig, Germany.
| | - Martin Franke
- Database Group, University of Leipzig, Leipzig, Germany
| | - Ziad Sehili
- Database Group, University of Leipzig, Leipzig, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,Complex Data Processing in Medical Informatics, University Medical Center Mannheim, Mannheim, Germany
| | - Erhard Rahm
- Database Group, University of Leipzig, Leipzig, Germany
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13
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Stammler S, Kussel T, Schoppmann P, Stampe F, Tremper G, Katzenbeisser S, Hamacher K, Lablans M. Mainzelliste SecureEpiLinker (MainSEL): Privacy-Preserving Record Linkage using Secure Multi-Party Computation. Bioinformatics 2020; 38:1657-1668. [PMID: 32871006 PMCID: PMC8896632 DOI: 10.1093/bioinformatics/btaa764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 07/24/2020] [Accepted: 08/25/2020] [Indexed: 11/17/2022] Open
Abstract
Motivation Record Linkage has versatile applications in real-world data analysis contexts, where several datasets need to be linked on the record level in the absence of any exact identifier connecting related records. An example are medical databases of patients, spread across institutions, that have to be linked on personally identifiable entries like name, date of birth or ZIP code. At the same time, privacy laws may prohibit the exchange of this personally identifiable information (PII) across institutional boundaries, ruling out the outsourcing of the record linkage task to a trusted third party. We propose to employ privacy-preserving record linkage (PPRL) techniques that prevent, to various degrees, the leakage of PII while still allowing for the linkage of related records. Results We develop a framework for fault-tolerant PPRL using secure multi-party computation with the medical record keeping software Mainzelliste as the data source. Our solution does not rely on any trusted third party and all PII is guaranteed to not leak under common cryptographic security assumptions. Benchmarks show the feasibility of our approach in realistic networking settings: linkage of a patient record against a database of 10 000 records can be done in 48 s over a heavily delayed (100 ms) network connection, or 3.9 s with a low-latency connection. Availability and implementation The source code of the sMPC node is freely available on Github at https://github.com/medicalinformatics/SecureEpilinker subject to the AGPLv3 license. The source code of the modified Mainzelliste is available at https://github.com/medicalinformatics/MainzellisteSEL. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | | | | | | | | | - Martin Lablans
- German Cancer Research Center, Heidelberg, Germany.,University Medical Centre Mannheim, Germany
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14
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Schüttler C, Huth V, von Jagwitz-Biegnitz M, Lablans M, Prokosch HU, Griebel L. A Federated Online Search Tool for Biospecimens (Sample Locator): Usability Study. J Med Internet Res 2020; 22:e17739. [PMID: 32663150 PMCID: PMC7463387 DOI: 10.2196/17739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/24/2020] [Accepted: 06/14/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The German Biobank Alliance (GBA) aims to establish a cross-site biobank network. For this endeavor, the so-called Sample Locator, a federated search tool for biospecimens and related data, has been developed, forming the heart of its information technology (IT) infrastructure. OBJECTIVE To ensure the sustainable use of such a tool, we included researchers as participants in an end user-based usability evaluation. METHODS To develop a prototype ready for evaluation, we needed input from GBA IT experts. Thus, we conducted a 2-day workshop with 8 GBA IT team members. The focus was on the respective steps of a user-centered design process. With the acquired knowledge, the participants designed low-fidelity mock-ups. The main ideas of these mock-ups were discussed, extracted, and summarized into a comprehensive prototype using Microsoft PowerPoint. Furthermore, we created a questionnaire concerning the usability of the prototype, including the System Usability Scale (SUS), questions on negative and positive aspects, and typical tasks to be fulfilled with the tool. Subsequently, the prototype was pretested on the basis of this questionnaire with researchers who have a biobank background. Based on this preliminary work, the usability analysis was ultimately carried out with researchers and the results were evaluated. RESULTS Altogether, 27 researchers familiar with sample requests evaluated the prototype. The analysis of the feedback certified a good usability, given that the Sample Locator prototype was seen as intuitive and user-friendly by 74% (20/27) of the participants. The total SUS score by the 25 persons that completed the questionnaire was 80.4, indicating good system usability. Still, the evaluation provided useful advice on optimization potential (eg, offering a help function). CONCLUSIONS The findings of this usability analysis indicate that the considerations regarding a user-friendly application that have been made in the development process so far strongly coincide with the perception of the study participants. Nevertheless, it was important to engage prospective end users to ensure that the previous development is going in the desired direction and that the Sample Locator will be used in the future. The user comments and suggestions for improvement will be considered in upcoming iterations for refinement.
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Affiliation(s)
- Christina Schüttler
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Verena Huth
- German Biobank Node, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany.,University Medical Center Mannheim, Mannheim, Germany
| | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lena Griebel
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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15
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Ulrich H, Germer S, Kock-Schoppenhauer AK, Kern J, Lablans M, Ingenerf J. A Smart Mapping Editor for Standardised Data Transformation. Stud Health Technol Inform 2020; 270:1185-1186. [PMID: 32570571 DOI: 10.3233/shti200354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The integration of heterogeneous healthcare data sources is a necessary process to enable the secondary use valuable information in clinical research. Data integration is time-consuming for data stewards. The transformation using predefined rules for data harmonization can reduce the time-consuming and error-prone work and ease the data integration at various sites. In our study, we examined various script(ing) languages to find the most suitable candidate for definition of transformation rules and implement a smart editor which supports the data stewards in selecting rules reusing them. Thereby, it also provides an automatic and seamless documentation to strengthen the reliability of the defined transformation rules.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | | | | | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Germany
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16
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Kock-Schoppenhauer AK, Kroll B, Lambarki M, Ulrich H, Stahl-Toyota S, Habermann JK, Duhm-Harbeck P, Ingenerf J, Lablans M. One Step Away from Technology but One Step Towards Domain Experts-MDRBridge: A Template-Based ISO 11179-Compliant Metadata Processing Pipeline. Methods Inf Med 2019; 58:e72-e79. [PMID: 31853911 DOI: 10.1055/s-0039-3399579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Secondary use of routine medical data relies on a shared understanding of given information. This understanding is achieved through metadata and their interconnections, which can be stored in metadata repositories (MDRs). The necessity of an MDR is well understood, but the local work on metadata is a time-consuming and challenging process for domain experts. OBJECTIVE To support the identification, collection, and provision of metadata in a predefined structured manner to foster consolidation. A particular focus is placed on user acceptance. METHODS We propose a software pipeline MDRBridge as a practical intermediary for metadata capture and processing, based on MDRSheet, an ISO 11179-3 compliant template using popular spreadsheet software. It serves as a practical mediator for metadata acquisition and processing in a broader pipeline. Due to the different origins of the metadata, both manual entry and automatic extractions from application systems are supported. To enable the export of collected metadata into external MDRs, a mapping of ISO 11179 to Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) was developed. RESULTS MDRSheet is embedded in the processing pipeline MDRBridge and delivers metadata in the CDISC ODM format for further use in MDRs. This approach is used to interactively unify core datasets, import existing standard datasets, and automatically extract all defined data elements from source systems. The involvement of clinical domain experts improved significantly due to minimal changes within their usual work routine. CONCLUSION A high degree of acceptance was achieved by adapting the working methods of clinical domain experts. The designed process is capable of transforming all relevant data elements according to the ISO 11179-3 format. MDRSheet is used as an intermediate format to present the information at a glance and to allow editing or supplementing by domain experts.
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Affiliation(s)
| | - B Kroll
- IT Center for Clinical Research, University of Lübeck, Germany
| | - M Lambarki
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - H Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - S Stahl-Toyota
- Medical Informatics for Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - J K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck & University Clinical Center Schleswig-Holstein, Campus Lübeck, Germany.,Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Germany
| | - P Duhm-Harbeck
- IT Center for Clinical Research, University of Lübeck, Germany
| | - J Ingenerf
- Institute of Medical Informatics, University of Lübeck, Germany
| | - M Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
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17
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Lablans M, Schmidt EE, Ückert F. An Architecture for Translational Cancer Research As Exemplified by the German Cancer Consortium. JCO Clin Cancer Inform 2019; 2:1-8. [PMID: 30652543 DOI: 10.1200/cci.17.00062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Networking of medical institutions by means of a capable data infrastructure has the potential to open up vast amounts of routine data to translational cancer research. However, the secondary use of information collected independently in several institutions is a challenging task of data integration. In this review, we discuss the requirements and common challenges involved in the establishment of such a platform. We present methods and tools from the field of medical informatics as solutions to semantic and technical heterogeneity, questions of data protection and record linkage, as well as issues of trust and data ownership. We also describe the architecture of an existing cancer research network as an exemplary application of these methods.
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Affiliation(s)
- Martin Lablans
- All authors: German Cancer Research Center, Heidelberg, Germany
| | | | - Frank Ückert
- All authors: German Cancer Research Center, Heidelberg, Germany
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18
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Juárez D, Schmidt EE, Stahl-Toyota S, Ückert F, Lablans M. A Generic Method and Implementation to Evaluate and Improve Data Quality in Distributed Research Networks. Methods Inf Med 2019; 58:86-93. [PMID: 31514209 DOI: 10.1055/s-0039-1693685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND With the increasing personalization of clinical therapies, translational research is evermore dependent on multisite research cooperations to obtain sufficient data and biomaterial. Distributed research networks rely on the availability of high-quality data stored in local databases operated by their member institutions. However, reusing data documented by independent health providers for the purpose of care, rather than research ("secondary use"), reveal a high variability in terms of data formats, as well as poor data quality, across network sites. OBJECTIVES The aim of this work is the provision of a process for the assessment of data quality with regard to completeness and syntactic accuracy across independently operated data warehouses using common definitions stored in a central (network-wide) metadata repository (MDR). METHODS For assessment of data quality across multiple sites, we employ a framework of so-called bridgeheads. These are federated data warehouses, which allow the sites to participate in a research network. A central MDR is used to store the definitions of the commonly agreed data elements and their permissible values. RESULTS We present the design for a generator of quality reports within a bridgehead, allowing the validation of data in the local data warehouse against a research network's central MDR. A standardized quality report can be produced at each network site, providing a means to compare data quality across sites, as well as to channel feedback to the local data source systems, and local documentation personnel. A reference implementation for this concept has been successfully utilized at 10 sites across the German Cancer Consortium. CONCLUSIONS We have shown that comparable data quality assessment across different partners of a distributed research network is feasible when a central metadata repository is combined with locally installed assessment processes. To achieve this, we designed a quality report and the process for generating such a report. The final step was the implementation in a German research network.
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Affiliation(s)
- D Juárez
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - E E Schmidt
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - S Stahl-Toyota
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - F Ückert
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Lablans
- Federated Information Systems, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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19
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Mate S, Kampf M, Rödle W, Kraus S, Proynova R, Silander K, Ebert L, Lablans M, Schüttler C, Knell C, Eklund N, Hummel M, Holub P, Prokosch HU. Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC. Appl Clin Inform 2019; 10:679-692. [PMID: 31509880 PMCID: PMC6739205 DOI: 10.1055/s-0039-1695793] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background
High-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks.
Objectives
To transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task.
Methods
Based on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application.
Results
The implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients.
Conclusion
A generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.
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Affiliation(s)
- Sebastian Mate
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Marvin Kampf
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Wolfgang Rödle
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Stefan Kraus
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Rumyana Proynova
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Kaisa Silander
- Genomics and Biobank Unit, Finnish National Institute for Health and Welfare, Helsinki, Finland
| | - Lars Ebert
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Christina Schüttler
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Knell
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Niina Eklund
- Genomics and Biobank Unit, Finnish National Institute for Health and Welfare, Helsinki, Finland
| | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria
| | - Petr Holub
- Biobanking and BioMolecular Resources Research Infrastructure (BBMRI-ERIC), Graz, Austria
| | - Hans-Ulrich Prokosch
- Medical Centre for Information and Communication Technology, Universitätsklinikum Erlangen, Erlangen, Germany.,Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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20
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Ulrich H, Kern J, Kock-Schoppenhauer AK, Lablans M, Ingenerf J. Towards a Federation of Metadata Repositories: Addressing Technical Interoperability. Stud Health Technol Inform 2019; 267:74-80. [PMID: 31483257 DOI: 10.3233/shti190808] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The utilisation of metadata repositories increasingly promotes secondary use of routinely collected data. However, this has not yet solved the problem of data exchange across organisational boundaries. The local description of a metadata set must also be exchangeable for flawless data exchange. In previous work, a metadata exchange language QL4MDR was developed. This work aimed to examine the applicability of this exchange language. For this purpose, existing MDR implementations were identified and systematically inspected and roughly divided into two categories to distinguish between data integration and query integration. It has been shown that all the implementations can be adapted to QL4MDR. The integration of metadata is an important first step; it enables the exchange of information, which is so urgently needed for the further processing of instance data, from the metadata mappings to the transformation rules.
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Affiliation(s)
- Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - Jori Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | | | - Martin Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany
- Institute of Medical Informatics, University of Lübeck, Germany
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21
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Schmidt EE, Eichelser C, Ahlborn B, Keune D, Castaños-Vélez E, Juárez D, Lablans M. Automated Reports for Monitoring and Improving Data Quality in a Translational Research Network. Stud Health Technol Inform 2019; 264:1458-1459. [PMID: 31438180 DOI: 10.3233/shti190483] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Standardised, automated quality reports were generated at three pilot locations of the decentralized translational research network DKTK with separated local data warehouses (LDW), for assessing syntactic conformity against common data element definitions deposited in a central metadata repository (MDR). Deviations in the LDW were categorised, and locally corrected. Comparisons of reports from two time points confirm a major improvement in data quality in terms of syntactic conformity, an essential prerequisite for network-wide data integration.
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Affiliation(s)
- Esther E Schmidt
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Corinna Eichelser
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Internal Medicine III, Klinikum der Universität München (KUM), Germany.,Department of Medicine III, Klinikum rechts der Isar (MRI), TUM, Germany
| | - Bernd Ahlborn
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Medical Information Sciences, Biometry and Epidemiology (IBE), Ludwig-Maximilians-Universität München (LMU), München, Germany
| | - Dietmar Keune
- Clinical Cancer Registry,Charité Comprehensive Cancer Center, Berlin, Germany
| | | | - David Juárez
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Lablans
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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22
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Ulrich H, Kern J, Tas D, Kock-Schoppenhauer AK, Ückert F, Ingenerf J, Lablans M. QL 4MDR: a GraphQL query language for ISO 11179-based metadata repositories. BMC Med Inform Decis Mak 2019; 19:45. [PMID: 30885183 PMCID: PMC6421684 DOI: 10.1186/s12911-019-0794-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/06/2019] [Indexed: 11/30/2022] Open
Abstract
Background Heterogeneous healthcare instance data can hardly be integrated without harmonizing its schema-level metadata. Many medical research projects and organizations use metadata repositories to edit, store and reuse data elements. However, existing metadata repositories differ regarding software implementation and have shortcomings when it comes to exchanging metadata. This work aims to define a uniform interface with a technical interlingua between the different MDR implementations in order to enable and facilitate the exchange of metadata, to query over distributed systems and to promote cooperation. To design a unified interface for multiple existing MDRs, a standardized data model must be agreed on. The ISO 11179 is an international standard for the representation of metadata, and since most MDR systems claim to be at least partially compliant, it is suitable for defining an interface thereupon. Therefore, each repository must be able to define which parts can be served and the interface must be able to handle highly linked data. GraphQL is a data access layer and defines query techniques designed to navigate easily through complex data structures. Results We propose QL4MDR, an ISO 11179-3 compatible GraphQL query language. The GraphQL schema for QL4MDR is derived from the ISO 11179 standard and defines objects, fields, queries and mutation types. Entry points within the schema define the path through the graph to enable search functionalities, but also the exchange is promoted by mutation types, which allow creating, updating and deleting of metadata. QL4MDR is the foundation for the uniform interface, which is implemented in a modern web-based interface prototype. Conclusions We have introduced a uniform query interface for metadata repositories combining the ISO 11179 standard for metadata repositories and the GraphQL query language. A reference implementation based on the existing Samply.MDR was implemented. The interface facilitates access to metadata, enables better interaction with metadata as well as a basis for connecting existing repositories. We invite other ISO 11179-based metadata repositories to take this approach into account.
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Affiliation(s)
- H Ulrich
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.
| | - J Kern
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - D Tas
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | | | - F Ückert
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - J Ingenerf
- IT Center for Clinical Research, University of Lübeck, Lübeck, Germany.,Institute of Medical Informatics, University of Lübeck, Lübeck, Germany
| | - M Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
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23
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Ahlbrandt J, Lablans M, Glocker K, Stahl-Toyota S, Maier-Hein K, Maier-Hein L, Ückert F. Modern Information Technology for Cancer Research: What's in IT for Me? An Overview of Technologies and Approaches. Oncology 2018; 98:363-369. [PMID: 30439700 DOI: 10.1159/000493638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022]
Abstract
Information technology (IT) can enhance or change many scenarios in cancer research for the better. In this paper, we introduce several examples, starting with clinical data reuse and collaboration including data sharing in research networks. Key challenges are semantic interoperability and data access (including data privacy). We deal with gathering and analyzing genomic information, where cloud computing, uncertainties and reproducibility challenge researchers. Also, new sources for additional phenotypical data are shown in patient-reported outcome and machine learning in imaging. Last, we focus on therapy assistance, introducing tools used in molecular tumor boards and techniques for computer-assisted surgery. We discuss the need for metadata to aggregate and analyze data sets reliably. We conclude with an outlook towards a learning health care system in oncology, which connects bench and bedside by employing modern IT solutions.
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Affiliation(s)
| | | | | | | | | | | | - Frank Ückert
- German Cancer Research Center, Heidelberg, Germany
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Braess J, Amler S, Kreuzer KA, Spiekermann K, Lindemann HW, Lengfelder E, Graeven U, Staib P, Ludwig WD, Biersack H, Ko YD, Uppenkamp MJ, De Wit M, Korsten S, Peceny R, Gaska T, Schiel X, Behringer DM, Kiehl MG, Zinngrebe B, Meckenstock G, Roemer E, Medgenberg D, Spaeth-Schwalbe E, Massenkeil G, Hindahl H, Schwerdtfeger R, Trenn G, Sauerland C, Koch R, Lablans M, Faldum A, Görlich D, Bohlander SK, Schneider S, Dufour A, Buske C, Fiegl M, Subklewe M, Braess B, Unterhalt M, Baumgartner A, Wörmann B, Beelen D, Hiddemann W. Sequential high-dose cytarabine and mitoxantrone (S-HAM) versus standard double induction in acute myeloid leukemia-a phase 3 study. Leukemia 2018; 32:2558-2571. [PMID: 30275528 PMCID: PMC6286323 DOI: 10.1038/s41375-018-0268-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/26/2018] [Accepted: 08/09/2018] [Indexed: 01/17/2023]
Abstract
Dose-dense induction with the S-HAM regimen was compared to standard double induction therapy in adult patients with newly diagnosed acute myeloid leukemia. Patients were centrally randomized (1:1) between S-HAM (2nd chemotherapy cycle starting on day 8 = “dose-dense”) and double induction with TAD-HAM or HAM(-HAM) (2nd cycle starting on day 21 = “standard”). 387 evaluable patients were randomly assigned to S-HAM (N = 203) and to standard double induction (N = 184). The primary endpoint overall response rate (ORR) consisting of complete remission (CR) and incomplete remission (CRi) was not significantly different (P = 0.202) between S-HAM (77%) and double induction (72%). The median overall survival was 35 months after S-HAM and 25 months after double induction (P = 0.323). Duration of critical leukopenia was significantly reduced after S-HAM (median 29 days) versus double induction (median 44 days)—P < 0.001. This translated into a significantly shortened duration of hospitalization after S-HAM (median 37 days) as compared to standard induction (median 49 days)—P < 0.001. In conclusion, dose-dense induction therapy with the S-HAM regimen shows favorable trends but no significant differences in ORR and OS compared to standard double induction. S-HAM significantly shortens critical leukopenia and the duration of hospitalization by 2 weeks.
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Affiliation(s)
- Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany. .,Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany.
| | - Susanne Amler
- Insitute for Biostatistics and Clinical Research, University Hospital, Münster, Germany.,Friedrich Löffler Institute, Federal Research Centre, Greifswald-Insel Riems, Germany
| | - Karl-Anton Kreuzer
- Department of Internal Medicine I, University Hospital, Cologne, Germany
| | - Karsten Spiekermann
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | | | - Eva Lengfelder
- Department of Medicine III, University Hospital, Mannheim, Germany
| | - Ullrich Graeven
- Department of Medicine I, Hospital Maria Hilf, Mönchengladbach, Germany
| | - Peter Staib
- Department of Hematology and Medical Oncology, St. Antonius Hospital, Eschweiler, Germany
| | - Wolf-Dieter Ludwig
- Department of Hematology and Oncology and Tumor Immunology, Helios Hospital, Berlin-Buch, Germany
| | - Harald Biersack
- Department of Medicine I, University Hospital, Lübeck, Germany
| | - Yon-Dschun Ko
- Department of Medicine I, Johanniter Hospital, Bonn, Germany
| | | | - Maike De Wit
- Department of Hematology, Oncology and Palliative Care, Vivantes Klinikum Neukölln, Berlin, Germany
| | - Stefan Korsten
- Department of Medicine, Vinzenz Pallotti Hospital, Bergisch-Gladbach, Germany
| | - Rudolf Peceny
- Department of Hematology and Oncology, Klinikum Osnabrück, Osnabrück, Germany
| | - Tobias Gaska
- Department of Hematology and Oncology, St. Josef Hospital, Paderborn, Germany
| | - Xaver Schiel
- Department of Hematology and Oncology, Klinikum Harlaching, Munich, Germany
| | - Dirk M Behringer
- Department of Hematology, Oncology and Palliative Care, Augusta Hospital, Bochum, Germany
| | - Michael G Kiehl
- Department of Medicine I, Klinikum Frankfurt/Oder, Frankfurt/Oder, Germany
| | - Bettina Zinngrebe
- Department of Hematology, Oncology and Palliative Care, Evangelisches Krankenhaus, Bielefeld, Germany
| | - Gerald Meckenstock
- Department of Medical Oncology, Radiooncology, Hematology and Palliative Care, St. Josef Hospital, Gelsenkirchen, Germany
| | - Eva Roemer
- Department of Hematology and Oncology, Klinikum Idar-Oberstein, Idar-Oberstein, Germany
| | - Dirk Medgenberg
- Department of Medicine III, Klinikum Leverkusen, Leverkusen, Germany
| | | | - Gero Massenkeil
- Department of Medicine II, Klinikum Gütersloh, Gütersloh, Germany
| | - Heidrun Hindahl
- Department of Medicine I, St. Johannes Hospital, Dortmund, Germany
| | - Rainer Schwerdtfeger
- Department for Bone Marrow and Blood Stem Cell Transplantation, DKD Deutsche Klinik für Diagnostik, Wiesbaden, Germany
| | - Guido Trenn
- Department of Medicine I, Knappschaftskrankenhaus, Bottrop, Germany
| | - Cristina Sauerland
- Insitute for Biostatistics and Clinical Research, University Hospital, Münster, Germany
| | - Raphael Koch
- Insitute for Biostatistics and Clinical Research, University Hospital, Münster, Germany
| | - Martin Lablans
- Insitute for Biostatistics and Clinical Research, University Hospital, Münster, Germany.,Division of Medical Informatics in Translational Oncology, DKFZ German Cancer Research Center, Heidelberg, Germany
| | - Andreas Faldum
- Insitute for Biostatistics and Clinical Research, University Hospital, Münster, Germany
| | - Dennis Görlich
- Insitute for Biostatistics and Clinical Research, University Hospital, Münster, Germany
| | - Stefan K Bohlander
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Stephanie Schneider
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | - Annika Dufour
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | - Christian Buske
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany.,Institute of Experimental Cancer Research, University Hospital, Ulm, Germany
| | - Michael Fiegl
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | - Birgit Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany.,Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | - Michael Unterhalt
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | - Anja Baumgartner
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
| | | | - Dietrich Beelen
- Department of Bone Marrow Transplantation, University Hospital, Essen, Germany
| | - Wolfgang Hiddemann
- Department of Medicine III, University Hospital LMU Campus Grosshadern, Munich, Germany
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Bialke M, Bahls T, Geidel L, Rau H, Blumentritt A, Pasewald S, Wolff R, Steinmann J, Bronsch T, Bergh B, Tremper G, Lablans M, Ückert F, Lang S, Idris T, Hoffmann W. MAGIC: once upon a time in consent management-a FHIR ® tale. J Transl Med 2018; 16:256. [PMID: 30217236 PMCID: PMC6137912 DOI: 10.1186/s12967-018-1631-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/06/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The use of medical data for research purposes requires an informed consent of the patient that is compliant with the EU General Data Protection Regulation. In the context of multi-centre research initiatives and a multitude of clinical and epidemiological studies scalable and automatable measures for digital consent management are required. Modular form, structure, and contents render a patient's consent reusable for varying project settings in order to effectively manage and minimise organisational and technical efforts. RESULTS Within the DFG-funded project "MAGIC" (Grant Number HO 1937/5-1) the digital consent management service tool gICS was enhanced to comply with the recommendations published in the TMF data protection guideline for medical research. In addition, a structured exchange format for modular consent templates considering established standards and formats in the area of digital informed consent management was designed. Using the new FHIR standard and the HAPI FHIR library, the first version for an exchange format and necessary import-/export-functionalities were successfully implemented. CONCLUSIONS The proposed exchange format is a "work in progress". It represents a starting point for current discussions concerning digital consent management. It also attempts to improve interoperability between different approaches within the wider IHE-/HL7-/FHIR community. Independent of the exchange format, providing the possibility to export, modify and import templates for consents and withdrawals to be reused in similar clinical and epidemiological studies is an essential precondition for the sustainable operation of digital consent management.
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Affiliation(s)
- Martin Bialke
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Thomas Bahls
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Lars Geidel
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Henriette Rau
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Arne Blumentritt
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Sandra Pasewald
- Independent Trusted Third Party, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Robert Wolff
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
| | - Jonas Steinmann
- Technology, Methods and Infrastructure for Networked Medical Research (TMF), Charlottenstrasse 42/Dorotheenstrasse, 10117 Berlin, Germany
| | - Tobias Bronsch
- Institute for Medical Informatics and Statistics, Kiel University and University Medical Center Schleswig–Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Björn Bergh
- Institute for Medical Informatics and Statistics, Kiel University and University Medical Center Schleswig–Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Galina Tremper
- Department Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Martin Lablans
- Department Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Frank Ückert
- Department Medical Informatics for Translational Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan Lang
- Technical Committee FHIR, HL7 Deutschland e.V, Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany
| | - Tarik Idris
- InterComponentWare AG (ICW), Altrottstr. 31, 69190 Walldorf, Germany
| | - Wolfgang Hoffmann
- Institute for Community Medicine, Department Epidemiology of Health Care and Community Health, University Medicine Greifswald, Ellernholzstr. 1-2, 17475 Greifswald, Germany
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26
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Schüttler C, Buschhüter N, Döllinger C, Ebert L, Hummel M, Linde J, Prokosch HU, Proynova R, Lablans M. [Erratum to: Requirements for a cross-location biobank IT infrastructure : Survey of stakeholder input on the establishment of a biobank network of the German Biobank Alliance (GBA)]. Pathologe 2018; 39:423. [PMID: 30105610 DOI: 10.1007/s00292-018-0479-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- C Schüttler
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen-Tennenlohe, Deutschland.
| | - N Buschhüter
- Zentralisierte Biomaterialbank der Medizinischen Fakultät der RWTH Aachen University, Aachen, Deutschland
| | - C Döllinger
- BioMaterialBank Heidelberg, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - L Ebert
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
| | - M Hummel
- Zentrale Biomaterialbank (ZeBanC) und German Biobank Node (GBN), Charité-Universitätsmedizin Berlin, Berlin, Deutschland
| | - J Linde
- UMG Biobank, Universitätsmedizin Göttingen, Göttingen, Deutschland
| | - H-U Prokosch
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen-Tennenlohe, Deutschland
| | - R Proynova
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
| | - M Lablans
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland
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Schüttler C, Buschhüter N, Döllinger C, Ebert L, Hummel M, Linde J, Prokosch HU, Proynova R, Lablans M. Anforderungen an eine standortübergreifende Biobanken-IT-Infrastruktur. Pathologe 2018; 39:289-296. [DOI: 10.1007/s00292-018-0435-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Lablans M, Kadioglu D, Muscholl M, Ückert F. Exploiting Distributed, Heterogeneous and Sensitive Data Stocks while Maintaining the Owner’s Data Sovereignty. Methods Inf Med 2018. [PMID: 26196653 DOI: 10.3414/me14-01-0137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
SummaryBackground: To achieve statistical significance in medical research, biological or data samples from several bio- or databanks often need to be complemented by those of other institutions. For that purpose, IT-based search services have been established to locate datasets matching a given set of criteria in databases distributed across several institutions. However, previous approaches require data owners to disclose information about their samples, raising a barrier for their participation in the network.Objective: To devise a method to search distributed databases for datasets matching a given set of criteria while fully maintaining their owner’s data sovereignty.Methods: As a modification to traditional federated search services, we propose the decentral search, which allows the data owner a high degree of control. Relevant data are loaded into local bridgeheads, each under their owner’s sovereignty. Researchers can formulate criteria sets along with a project proposal using a central search broker, which then notifies the bridgeheads. The criteria are, however, treated as an inquiry rather than a query: Instead of responding with results, bridgeheads notify their owner and wait for his/her decision regarding whether and what to answer based on the criteria set, the matching datasets and the specific project proposal. Without the owner’s explicit consent, no data leaves his/ her institution.Results: The decentral search has been deployed in one of the six German Centers for Health Research, comprised of eleven university hospitals. In the process, compliance with German data protection regulations has been confirmed. The decentral search also marks the centerpiece of an open source registry software toolbox aiming to build a national registry of rare diseases in Germany.Conclusions: While the sacrifice of real-time answers impairs some use-cases, it leads to several beneficial side effects: improved data protection due to data parsimony, tolerance for incomplete data schema mappings and flexibility with regard to patient consent. Most importantly, as no datasets ever leave their institution, owners can reject projects without facing potential peer pressure. By its lower barrier for participation, a decentral search service is likely to attract a larger number of partners and to bring a researcher into contact with the right potential partners.
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Affiliation(s)
- M Lablans
- Martin Lablans, University Medical Center Mainz, Obere Zahlbacher Straße 69, 55131 Mainz, Germany, E-mail:
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29
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Kadioglu D, Breil B, Knell C, Lablans M, Mate S, Schlue D, Serve H, Storf H, Ückert F, Wagner T, Weingardt P, Prokosch HU. Samply.MDR - A Metadata Repository and Its Application in Various Research Networks. Stud Health Technol Inform 2018; 253:50-54. [PMID: 30147039] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Collaboration in medical research is becoming common, especially for collecting relevant cases across institutional boundaries. If the data, which is usually very heterogeneously formalized and structured, can be integrated, such a collaboration can facilitate research. An absolute prerequisite for this is an extensive description about the formalization and exact meaning of every data element contained in a dataset. This information is commonly known as metadata. Various research networking projects tackle this challenge with the development of concepts and IT tools. The Samply Metadata Repository (Samply.MDR) is a solution for managing and publishing such metadata in a standardized and reusable way. In this article we present the structure and features of the Samply.MDR as well as its flexible usability by giving an overview about its application in various projects.
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Affiliation(s)
- Dennis Kadioglu
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Bernhard Breil
- Niederrhein University of Applied Sciences, Krefeld, Germany
| | - Christian Knell
- Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany
| | - Martin Lablans
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Mate
- Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany
| | - Danijela Schlue
- Center of Clinical Epidemiology, University Hospital Essen, Essen, Germany
| | - Hubert Serve
- Department of Hematology and Oncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Holger Storf
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Frank Ückert
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Wagner
- Frankfurt Reference Center for Rare Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany
| | | | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Friedrich-Alexander-University Erlangen-Nuernberg, Erlangen, Germany
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Kern J, Tas D, Ulrich H, Schmidt EE, Ingenerf J, Ückert F, Lablans M. A Method to Use Metadata in Legacy Web Applications: The Samply.MDR.Injector. Stud Health Technol Inform 2018; 253:45-49. [PMID: 30147038] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Whenever medical data is integrated from multiple sources, it is regarded good practice to separate data from information about its meaning, such as designations, definitions or permissible values (in short: metadata). However, the ways in which applications work with metadata are imperfect: Many applications do not support fetching metadata from externalized sources such as metadata repositories. In order to display human-readable metadata in any application, we propose not to change the application, but to provide a library that makes a change to the user interface. The goal of this work is to provide a way to "inject" the meaning of metadata keys into the web-based frontend of an application to make it "metadata aware".
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Affiliation(s)
- Jori Kern
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Deniz Tas
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Hannes Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - Esther E Schmidt
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Josef Ingenerf
- IT Center for Clinical Research, University of Lübeck, Germany
| | - Frank Ückert
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Martin Lablans
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
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König J, Kranz B, König S, Schlingmann KP, Titieni A, Tönshoff B, Habbig S, Pape L, Häffner K, Hansen M, Büscher A, Bald M, Billing H, Schild R, Walden U, Hampel T, Staude H, Riedl M, Gretz N, Lablans M, Bergmann C, Hildebrandt F, Omran H, Konrad M. Phenotypic Spectrum of Children with Nephronophthisis and Related Ciliopathies. Clin J Am Soc Nephrol 2017; 12:1974-1983. [PMID: 29146700 PMCID: PMC5718263 DOI: 10.2215/cjn.01280217] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/18/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Genetic heterogeneity and phenotypic variability are major challenges in familial nephronophthisis and related ciliopathies. To date, mutations in 20 different genes (NPHP1 to -20) have been identified causing either isolated kidney disease or complex multiorgan disorders. In this study, we provide a comprehensive and detailed characterization of 152 children with a special focus on extrarenal organ involvement and the long-term development of ESRD. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We established an online-based registry (www.nephreg.de) to assess the clinical course of patients with nephronophthisis and related ciliopathies on a yearly base. Cross-sectional and longitudinal data were collected. Mean observation time was 7.5±6.1 years. RESULTS In total, 51% of the children presented with isolated nephronophthisis, whereas the other 49% exhibited related ciliopathies. Monogenetic defects were identified in 97 of 152 patients, 89 affecting NPHP genes. Eight patients carried mutations in other genes related to cystic kidney diseases. A homozygous NPHP1 deletion was, by far, the most frequent genetic defect (n=60). We observed a high prevalence of extrarenal manifestations (23% [14 of 60] for the NPHP1 group and 66% [61 of 92] for children without NPHP1). A homozygous NPHP1 deletion not only led to juvenile nephronophthisis but also was able to present as a predominantly neurologic phenotype. However, irrespective of the initial clinical presentation, the kidney function of all patients carrying NPHP1 mutations declined rapidly between the ages of 8 and 16 years, with ESRD at a mean age of 11.4±2.4 years. In contrast within the non-NPHP1 group, there was no uniform pattern regarding the development of ESRD comprising patients with early onset and others preserving normal kidney function until adulthood. CONCLUSIONS Mutations in NPHP genes cause a wide range of ciliopathies with multiorgan involvement and different clinical outcomes.
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Affiliation(s)
- Jens König
- Due to the number of contributing authors, the affiliations are provided in the Supplemental Material
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Hinderer M, Boeker M, Wagner SA, Lablans M, Newe S, Hülsemann JL, Neumaier M, Binder H, Renz H, Acker T, Prokosch HU, Sedlmayr M. Integrating clinical decision support systems for pharmacogenomic testing into clinical routine - a scoping review of designs of user-system interactions in recent system development. BMC Med Inform Decis Mak 2017; 17:81. [PMID: 28587608 PMCID: PMC5461630 DOI: 10.1186/s12911-017-0480-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/30/2017] [Indexed: 01/05/2023] Open
Abstract
Background Pharmacogenomic clinical decision support systems (CDSS) have the potential to help overcome some of the barriers for translating pharmacogenomic knowledge into clinical routine. Before developing a prototype it is crucial for developers to know which pharmacogenomic CDSS features and user-system interactions have yet been developed, implemented and tested in previous pharmacogenomic CDSS efforts and if they have been successfully applied. We address this issue by providing an overview of the designs of user-system interactions of recently developed pharmacogenomic CDSS. Methods We searched PubMed for pharmacogenomic CDSS published between January 1, 2012 and November 15, 2016. Thirty-two out of 118 identified articles were summarized and included in the final analysis. We then compared the designs of user-system interactions of the 20 pharmacogenomic CDSS we had identified. Results Alerts are the most widespread tools for physician-system interactions, but need to be implemented carefully to prevent alert fatigue and avoid liabilities. Pharmacogenomic test results and override reasons stored in the local EHR might help communicate pharmacogenomic information to other internal care providers. Integrating patients into user-system interactions through patient letters and online portals might be crucial for transferring pharmacogenomic data to external health care providers. Inbox messages inform physicians about new pharmacogenomic test results and enable them to request pharmacogenomic consultations. Search engines enable physicians to compare medical treatment options based on a patient’s genotype. Conclusions Within the last 5 years, several pharmacogenomic CDSS have been developed. However, most of the included articles are solely describing prototypes of pharmacogenomic CDSS rather than evaluating them. To support the development of prototypes further evaluation efforts will be necessary. In the future, pharmacogenomic CDSS will likely include prediction models to identify patients who are suitable for preemptive genotyping. Electronic supplementary material The online version of this article (doi:10.1186/s12911-017-0480-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc Hinderer
- Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen, Germany.
| | - Martin Boeker
- Medical Informatics, Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Martin Lablans
- Medical Informatics in Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - Stephanie Newe
- Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen, Germany
| | | | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim, Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Harald Renz
- University of Marburg, Institute of Laboratory Medicine, Marburg, Germany
| | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Hans-Ulrich Prokosch
- Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen, Germany
| | - Martin Sedlmayr
- Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Wetterkreuz 13, 91058, Erlangen, Germany
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Mate S, Vormstein P, Kadioglu D, Majeed RW, Lablans M, Prokosch HU, Storf H. On-The-Fly Query Translation Between i2b2 and Samply in the German Biobank Node (GBN) Prototypes. Stud Health Technol Inform 2017; 243:42-46. [PMID: 28883167] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Information retrieval is a major challenge in medical informatics. Various research projects have worked on this task in recent years on an institutional level by developing tools to integrate and retrieve information. However, when it comes down to querying such data across institutions, the challenge persists due to the high heterogeneity of data and differences in software systems. The German Biobank Node (GBN) project faced this challenge when trying to interconnect four biobanks to enable distributed queries for biospecimens. All biobanks had already established integrated data repositories, and some of them were already part of research networks. Instead of developing another software platform, GBN decided to form a bridge between these. This paper describes and discusses a core component from the GBN project, the OmniQuery library, which was implemented to enable on-the-fly query translation between heterogeneous research infrastructures.
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Affiliation(s)
- Sebastian Mate
- Medical Informatics, Univ. of Erlangen-Nürnberg, Erlangen, Germany
| | - Patric Vormstein
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt, Germany; German Cancer Consortium (DKTK), partner site Frankfurt; and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Kadioglu
- Medical Informatics, Univ. of Erlangen-Nürnberg, Erlangen, Germany
| | - Raphael W Majeed
- German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
| | - Martin Lablans
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Holger Storf
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt, Germany; German Cancer Consortium (DKTK), partner site Frankfurt; and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Mate S, Kadioglu D, Majeed RW, Stöhr MR, Folz M, Vormstein P, Storf H, Brucker DP, Keune D, Zerbe N, Hummel M, Senghas K, Prokosch HU, Lablans M. Proof-of-Concept Integration of Heterogeneous Biobank IT Infrastructures into a Hybrid Biobanking Network. Stud Health Technol Inform 2017; 243:100-104. [PMID: 28883179] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cross-institutional biobank networks hold the promise of supporting medicine by enabling the exchange of associated samples for research purposes. Various initiatives, such as BBMRI-ERIC and German Biobank Node (GBN), aim to interconnect biobanks for enabling the compilation of joint biomaterial collections. However, building software platforms to facilitate such collaboration is challenging due to the heterogeneity of existing biobank IT infrastructures and the necessary efforts for installing and maintaining additional software components. As a remedy, this paper presents the concept of a hybrid network for interconnecting already existing software components commonly found in biobanks and a proof-of-concept implementation of two prototypes involving four biobanks of the German Biobank Node. Here we demonstrate the successful bridging of two IT systems found in many German biobanks - Samply and i2b2.
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Affiliation(s)
- Sebastian Mate
- Medical Informatics, Univ. of Erlangen-Nürnberg, Erlangen, Germany
| | - Dennis Kadioglu
- Medical Informatics, Univ. of Erlangen-Nürnberg, Erlangen, Germany
| | - Raphael W Majeed
- UGMLC, German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Mark R Stöhr
- UGMLC, German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Michael Folz
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt, Germany
| | - Patric Vormstein
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt, Germany
| | - Holger Storf
- Medical Informatics Group, University Hospital Frankfurt, Frankfurt, Germany
| | - Daniel P Brucker
- German Cancer Consortium (DKTK), partner site Frankfurt; and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dietmar Keune
- Clinical Cancer Registry, Charité Comprehensive Cancer Center, Berlin, Germany
| | - Norman Zerbe
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany; and Central Biobank Charité (ZeBanC), Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany; and Central Biobank Charité (ZeBanC), Berlin, Germany
| | - Karsten Senghas
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Martin Lablans
- Medical Informatics in Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Proynova R, Alexandre D, Lablans M, Van Enckevort D, Mate S, Eklund N, Silander K, Hummel M, Holub P, Ückert F. A Decentralized IT Architecture for Locating and Negotiating Access to Biobank Samples. Stud Health Technol Inform 2017; 243:75-79. [PMID: 28883174] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
There is a need among researchers for the easy discoverability of biobank samples. Currently, there is no uniform way for finding samples and negotiate access. Instead, researchers have to communicate with each biobank separately. We present the architecture for the BBMRI-CS IT platform, whose goal is to facilitate sample location and access. We chose a decentral approach, which allows for strong data protection and provides the high flexibility needed in the highly heterogeneous landscape of European biobanks. This is the first implementation of a decentral search in the biobank field. With the addition of a Negotiator component, it also allows for easy communication and a follow-through of the lengthy approval process for accessing samples.
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Affiliation(s)
| | | | | | | | - Sebastian Mate
- Friedrich Alexander Universität, Erlangen-Nürnberg & BBMRI.de
| | - Niina Eklund
- Terveyden Ja Hyvinvoinnin Laitos, Helsinki & BBMRI.fi
| | | | | | | | - Frank Ückert
- German Cancer Research Center, Heidelberg.&BBMRI.de
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Schwarting A, Pfeiff B, Amberger C, Pick D, Hesse M, Jendro M, Engels J, Böttger A, Kuhn C, Majdandzic J, Ziese W, Stadelmann ML, Kessler FW, Dinges H, Ultes-Kaiser S, Droste U, Schmalhofer M, Hazenbiller A, Rector M, Weinmann-Menke J, Triantafyllias K, Becker M, Ataian M, Lablans M, Ueckert F, Panholzer T, Blettner M. [The regional network ADAPTHERA : Rheumatology care through coordinated cooperation: comprehensive, trans-sectoral, covering all health insurance. Initial results]. Z Rheumatol 2016; 75:999-1005. [PMID: 27535273 DOI: 10.1007/s00393-016-0132-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of the rheumatology network ADAPTHERA ("risk-adapted rheumatology therapy") is to achieve a comprehensive improvement in rheumatology care by coordinating treatment in a regional, trans-sectoral network. Accompanying biomedical research projects, training concepts, and the construction of a rheumatology register (gathering data and biomaterials) should furthermore ensure the stable and sustainable optimisation of care. In the pilot phase (2012-2015) the focus of the ADAPTHERA network, required as a "regional key project" within the framework of the Initiative on Health Economy of Rheinland-Palatinate (RL-P), Germany, was placed on the optimisation of the early diagnosis of rheumatoid arthritis, where it is well-known that there is a significant care deficit.Through the intensive, stable, and coordinated cooperation of all health care partners in the field of rheumatology (registered general practitioners and orthopaedic specialists, registered core rheumatologists as well as the Association of Rheumatology of RL-P) a unique regional, comprehensive offer with verifiable care optimisation has been established in RL-P. The network is supported by outstanding collaboration with the Association of Statutory Health Insurance Physicians and the self-help organisation Rheumatology League.The aims that were established at the start of the project will be achieved by the end of the pilot phase:- significant improvement in the early diagnosis of rheumatoid arthritis (an average of 23.7 days until diagnosis by rheumatologists)- access covering all health insurance (regardless of the particular scheme the patients belong to)- comprehensive (verifiable participation of general practitioners from all over RL-P)- data and biomaterials collection, established as a basis for biomarker research, and a rheumatology register for RL-P.
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Affiliation(s)
- A Schwarting
- Schwerpunkt Rheumatologie und klinische Immunologie, Universitätsmedizin Mainz, Mainz, Deutschland. .,ACURA Rheumazentrum Rheinland-Pfalz, Bad Kreuznach, Deutschland.
| | - B Pfeiff
- ACURA Rheumazentrum Rheinland-Pfalz, Bad Kreuznach, Deutschland
| | - C Amberger
- Rheumatologische Schwerpunktpraxis, Bad Neuenahr, Deutschland
| | - D Pick
- Rheumatologische Schwerpunktpraxis, Bad Neuenahr, Deutschland
| | - M Hesse
- Rheumatologische Schwerpunktpraxis, Bad Kreuznach, Deutschland
| | - M Jendro
- Rheumatologische Schwerpunktpraxis, Kaiserslautern, Deutschland
| | - J Engels
- Rheumatologische Schwerpunktpraxis, Koblenz, Deutschland
| | - A Böttger
- Rheumatologische Schwerpunktpraxis, Landau, Deutschland
| | - C Kuhn
- Rheumatologische Schwerpunktpraxis, Mainz, Deutschland
| | | | - W Ziese
- Rheumatologische Schwerpunktpraxis, Trier, Deutschland
| | - M-L Stadelmann
- Rheumatologische Schwerpunktpraxis, Wittlich, Deutschland
| | - F W Kessler
- Rheumatologische Schwerpunktpraxis, Niederbrombach, Deutschland
| | - H Dinges
- Rheuma-Orthopädie, Westpfalz-Klinikum, Kusel, Deutschland
| | - S Ultes-Kaiser
- Kassenärztliche Vereinigung Rheinland-Pfalz, Mainz, Deutschland
| | - U Droste
- Deutsche RheumaLiga - Landesverband Rheinland-Pfalz e.V., Bad Kreuznach, Deutschland
| | - M Schmalhofer
- Deutsche RheumaLiga - Landesverband Rheinland-Pfalz e.V., Bad Kreuznach, Deutschland
| | - A Hazenbiller
- Schwerpunkt Rheumatologie und klinische Immunologie, Universitätsmedizin Mainz, Mainz, Deutschland
| | - M Rector
- ACURA Rheumazentrum Rheinland-Pfalz, Bad Kreuznach, Deutschland
| | - J Weinmann-Menke
- Schwerpunkt Rheumatologie und klinische Immunologie, Universitätsmedizin Mainz, Mainz, Deutschland
| | | | - M Becker
- Schwerpunkt Rheumatologie und klinische Immunologie, Universitätsmedizin Mainz, Mainz, Deutschland
| | - M Ataian
- German Cancer Research Center (DKFZ), Department of Medical Informatics in Translational Oncology, Heidelberg, Deutschland
| | - M Lablans
- German Cancer Research Center (DKFZ), Department of Medical Informatics in Translational Oncology, Heidelberg, Deutschland
| | - F Ueckert
- German Cancer Research Center (DKFZ), Department of Medical Informatics in Translational Oncology, Heidelberg, Deutschland
| | - T Panholzer
- Institut für Medizinische Biometrie, Epidemiologie und Informatik, Universitätsmedizin Mainz, Mainz, Deutschland
| | - M Blettner
- Institut für Medizinische Biometrie, Epidemiologie und Informatik, Universitätsmedizin Mainz, Mainz, Deutschland
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Lablans M, Kadioglu D, Mate S, Leb I, Prokosch HU, Ückert F. Strategien zur Vernetzung von Biobanken. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 59:373-8. [DOI: 10.1007/s00103-015-2299-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Zusammenfassung
Hintergrund
Nicht selten benötigt ein medizinisches Forschungsvorhaben mehr biologisches Material, als in einer einzigen Biobank verfügbar ist. Daher unterstützt eine Vielzahl von Strategien das Auffinden potentieller Forschungspartner mit passenden Proben, auch ohne dass diese zuvor in einer zentralisierten Sammlung zusammengeführt werden müssen.
Ziel
Der vorliegende Beitrag beschreibt die Klassifizierung verschiedener Strategien zur Vernetzung von Biomaterialbanken, speziell zur Probensuche, sowie eine IT-Infrastruktur, die diese Ansätze kombiniert.
Material und Methoden
Bestehende Strategien lassen sich nach drei Kriterien klassifizieren: a) Granularität der Probendaten: grobe Daten auf Bankebene (Katalog) vs. feingranulare Daten auf Probenebene, b) Speicherort der Probendaten: zentrale (zentraler Suchdienst) vs. dezentrale Datenhaltung (föderierte Suchdienste) und c) Automatisierungsgrad: automatisch (abfragebasiert, föderierter Suchdienst) vs. halbautomatisch (anfragebasiert, dezentrale Suche). Alle genannten Suchdienste setzen eine Datenintegration voraus; dabei helfen Metadaten bei der Überwindung semantischer Heterogenität.
Ergebnisse
Der „Common Service IT“ in BBMRI-ERIC („Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium“) vereint einen Katalog, die dezentrale Suche und Metadaten in einer integrierten Plattform, um Forschern vielseitige Werkzeuge zur Suche nach passendem Probenmaterial zu geben und bei den Biobankern gleichzeitig ein hohes Maß an Datenhoheit zu bewahren.
Diskussion
Trotz ihrer Unterschiede schließen sich die vorgestellten Strategien zur Vernetzung von Biomaterialbanken gegenseitig nicht aus. Vielmehr lassen sie sich in gemeinsamen Forschungsinfrastrukturen sinnvoll ergänzen und sie können sogar voneinander profitieren.
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Affiliation(s)
- Martin Lablans
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Deutschland.
| | - Dennis Kadioglu
- Institut für medizinische Biometrie, Epidemiologie und Informatik (IMBEI), Universitätsmedizin Mainz, 55101, Mainz, Deutschland
| | - Sebastian Mate
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Ines Leb
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Hans-Ulrich Prokosch
- Lehrstuhl für Medizinische Informatik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Deutschland
| | - Frank Ückert
- Medizinische Informatik in der Translationalen Onkologie, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Deutschland
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Werner C, Lablans M, Ataian M, Raidt J, Wallmeier J, Große-Onnebrink J, Kuehni CE, Haarman EG, Leigh MW, Quittner AL, Lucas JS, Hogg C, Witt M, Priftis KN, Yiallouros P, Nielsen KG, Santamaria F, Ückert F, Omran H. An international registry for primary ciliary dyskinesia. Eur Respir J 2015; 47:849-59. [PMID: 26659107 DOI: 10.1183/13993003.00776-2015] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/07/2015] [Indexed: 11/05/2022]
Abstract
Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disorder leading to chronic upper and lower airway disease. Fundamental data on epidemiology, clinical presentation, course and treatment strategies are lacking in PCD. We have established an international PCD registry to realise an unmet need for an international platform to systematically collect data on incidence, clinical presentation, treatment and disease course.The registry was launched in January 2014. We used internet technology to ensure easy online access using a web browser under www.pcdregistry.eu. Data from 201 patients have been collected so far. The database is comprised of a basic data form including demographic and diagnostic information, and visit forms designed to monitor the disease course.To establish a definite PCD diagnosis, we used strict diagnostic criteria, which required two to three diagnostic methods in addition to classical clinical symptoms. Preliminary analysis of lung function data demonstrated a mean annual decline of percentage predicted forced expiratory volume in 1 s of 0.59% (95% CI 0.98-0.22).Here, we present the development of an international PCD registry as a new promising tool to advance the understanding of this rare disorder, to recruit candidates for research studies and ultimately to improve PCD care.
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Affiliation(s)
- Claudius Werner
- Dept of General Paediatrics, Paediatric Pulmonology Unit, University Children's Hospital Muenster, Münster, Germany
| | - Martin Lablans
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maximilian Ataian
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Johanna Raidt
- Dept of General Paediatrics, Paediatric Pulmonology Unit, University Children's Hospital Muenster, Münster, Germany
| | - Julia Wallmeier
- Dept of General Paediatrics, Paediatric Pulmonology Unit, University Children's Hospital Muenster, Münster, Germany
| | - Jörg Große-Onnebrink
- Dept of General Paediatrics, Paediatric Pulmonology Unit, University Children's Hospital Muenster, Münster, Germany
| | - Claudia E Kuehni
- Institute of Social and Preventive Medicine (ISPM), Paediatric Respiratory Epidemiology, University of Bern, Bern, Switzerland
| | - Eric G Haarman
- Dept of Paediatric Pulmonology, VU University Medical Center, Amsterdam, The Netherlands
| | - Margaret W Leigh
- Dept of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | | | - Jane S Lucas
- University of Southampton Faculty of Medicine and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Claire Hogg
- Dept of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| | - Michal Witt
- Dept of Molecular and Clinical Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan and International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Kostas N Priftis
- Paediatric Pulmonology, 3rd Dept of Paediatrics, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital, Athens, Greece
| | - Panayiotis Yiallouros
- Cyprus International Institute for Environmental & Public Health in Association with Harvard School of Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Kim G Nielsen
- Danish PCD Centre, Paediatric Pulmonary Service, Dept of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Frank Ückert
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heymut Omran
- Dept of General Paediatrics, Paediatric Pulmonology Unit, University Children's Hospital Muenster, Münster, Germany
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Lablans M, Borg A, Ückert F. A RESTful interface to pseudonymization services in modern web applications. BMC Med Inform Decis Mak 2015; 15:2. [PMID: 25656224 PMCID: PMC4350982 DOI: 10.1186/s12911-014-0123-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/12/2014] [Indexed: 12/02/2022] Open
Abstract
Background Medical research networks rely on record linkage and pseudonymization to determine which records from different sources relate to the same patient. To establish informational separation of powers, the required identifying data are redirected to a trusted third party that has, in turn, no access to medical data. This pseudonymization service receives identifying data, compares them with a list of already reported patient records and replies with a (new or existing) pseudonym. We found existing solutions to be technically outdated, complex to implement or not suitable for internet-based research infrastructures. In this article, we propose a new RESTful pseudonymization interface tailored for use in web applications accessed by modern web browsers. Methods The interface is modelled as a resource-oriented architecture, which is based on the representational state transfer (REST) architectural style. We translated typical use-cases into resources to be manipulated with well-known HTTP verbs. Patients can be re-identified in real-time by authorized users’ web browsers using temporary identifiers. We encourage the use of PID strings for pseudonyms and the EpiLink algorithm for record linkage. As a proof of concept, we developed a Java Servlet as reference implementation. Results The following resources have been identified: Sessions allow data associated with a client to be stored beyond a single request while still maintaining statelessness. Tokens authorize for a specified action and thus allow the delegation of authentication. Patients are identified by one or more pseudonyms and carry identifying fields. Relying on HTTP calls alone, the interface is firewall-friendly. The reference implementation has proven to be production stable. Conclusion The RESTful pseudonymization interface fits the requirements of web-based scenarios and allows building applications that make pseudonymization transparent to the user using ordinary web technology. The open-source reference implementation implements the web interface as well as a scientifically grounded algorithm to generate non-speaking pseudonyms.
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Affiliation(s)
- Martin Lablans
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 69, Mainz, 55131, Germany.
| | - Andreas Borg
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 69, Mainz, 55131, Germany.
| | - Frank Ückert
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher Straße 69, Mainz, 55131, Germany.
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Mallidis C, Cooper TG, Hellenkemper B, Lablans M, Uckert F, Nieschlag E. Ten years' experience with an external quality control program for semen analysis. Fertil Steril 2012; 98:611-616.e4. [PMID: 22633256 DOI: 10.1016/j.fertnstert.2012.05.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/26/2012] [Accepted: 05/03/2012] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To gauge the performance of laboratories and impact of the German semen analysis external quality control program (QuaDeGA) over its first 10 years. DESIGN Retrospective analysis of QuaDeGA's twice yearly distribution of fixed semen samples and electronic material documenting sperm motility. Ranking of each participant's responses was determined according to their relation to a "target window." SETTING Multicenter. PAITENT(S): Healthy donors. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Laboratory performance, World Health Organization (WHO) adherence. RESULT(S) Over 19 runs, there was a steady increase of participants (280 laboratories), the largest group being private urologic practices. Although use of WHO-recommended Neubauer chamber (from 33% to 55%) and diluent (from 11% to 32%) increased, the opposite occurred with morphology staining protocols (from 41% to 19%). Overall, <8% of laboratories truly followed WHO guidelines. Median-based comparisons, replacing reference laboratories, resulted in a merging of performance rankings regardless of the protocols used. CONCLUSION(S) Adherence to WHO recommendations is low, with the majority of laboratories using methods expressly opposed by the guidelines. Participation in QuaDeGA was found to improve the performance of the laboratories involved in the program. However, the use of median-based ranking, while decreasing the extent of variance between laboratories, brings into question the significance of the rankings.
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Affiliation(s)
- Con Mallidis
- Center of Reproductive Medicine and Andrology, University of Münster, Münster, Germany.
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Steffens M, Husmann G, Koca M, Lablans M, Komor M, Zeissig S, Emrich K, Brandts C, Serve H, Blettner M, Uckert F. IT behind a platform for Translational Cancer Research - concept and objectives. Stud Health Technol Inform 2012; 180:1135-1137. [PMID: 22874378] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The German Consortium for Translational Cancer Research (DKTK) and the Rhine-Main Translational Cancer Research Network (RM-TCRN) are designed to exploit large population cohorts of cancer patients for the purpose of bio-banking, clinical trials, and clinical cancer registration. Hence, the success of these platforms is heavily dependent on the close interlinking of clinical data from cancer patients, information from study registries, and data from bio-banking systems of different laboratories and scientific institutions. This article referring to the poster discusses the main challenges of the platforms from an information technology point of view, legal and data security issues, and outlines an integrative IT-concept concerning a decentralized, distributed search approach where data management and search is in compliance with existing legislative rules.
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Lablans M, Bartholomäus S, Uckert F. Providing trust and interoperability to federate distributed biobanks. Stud Health Technol Inform 2011; 169:644-648. [PMID: 21893827] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biomedical research requires large numbers of well annotated, quality-assessed samples which often cannot be provided by a single biobank. Connecting biobanks, researchers and service providers raises numerous challenges including trust among partners and towards the infrastructure as well as interoperability problems. Therefore we develop a holistic, open-source and easy-to-use IT infrastructure. Our federated approach allows partners to reflect their organizational structures and protect their data sovereignty. The search service and the contact arrangement processes increase data sovereignty without stigmatizing for rejecting a specific cooperation. The infrastructure supports daily processes with an integrated basic sample manager and user-definable electronic case report forms. Interfaces for existing IT systems avoid re-entering of data. Moreover, resource virtualization is supported to make underutilized resources of some partners accessible to those with insufficient equipment for mutual benefit. The functionality of the resulting infrastructure is outlined in a use-case to demonstrate collaboration within a translational research network. Compared to other existing or upcoming infrastructures, our approach has ultimately the same goals, but relies on gentle incentives rather than top-down imposed progress.
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Affiliation(s)
- Martin Lablans
- Institute of Medical Informatics, University of Münster, Germany
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