Methods and Infrastructure for Networked Medical Research
Methods and Infrastructure for Networked Medical Research
Siddiqui R.A.,Leibniz Institute for Primate Research |
Siddiqui R.A.,Leibniz Institute for Age Research |
Siddiqui R.A.,Methods and Infrastructure for Networked Medical Research |
Krawczak M.,University of Kiel |
And 2 more authors.
PLoS ONE | Year: 2011
In HIV infection, TLR7-triggered IFN-α production exerts a direct antiviral effect through the inhibition of viral replication, but may also be involved in immune pathogenesis leading to AIDS. TLR7 could also be an important mediator of vaccine efficacy. In this study, we analyzed polymorphisms in the X-linked TLR7 gene in the rhesus macaque model of AIDS. Upon resequencing of the TLR7 gene in 36 rhesus macaques of Indian origin, 12 polymorphic sites were detected. Next, we identified three tightly linked single nucleotide polymorphisms (SNP) as being associated with survival time. Genotyping of 119 untreated, simian immunodeficiency virus (SIV)-infected male rhesus macaques, including an 'MHC adjusted' subset, revealed that the three TLR7 SNPs are also significantly associated with set-point viral load. Surprisingly, this effect was not observed in 72 immunized SIV-infected male monkeys. We hypothesize (i) that SNP c.13G>A in the leader peptide is causative for the observed genotype-phenotype association and that (ii) the underlying mechanism is related to RNA secondary structure formation. Therefore, we investigated a fourth SNP (c.-17C>T), located 17 bp upstream of the ATG translation initiation codon, that is also potentially capable of influencing RNA structure. In c.13A carriers, neither set-point viral load nor survival time were related to the c.-17C>T genotype. In c.13G carriers, by contrast, the c.-17C allele was significantly associated with prolonged survival. Again, no such association was detected among immunized SIV-infected macaques. Our results highlight the dual role of TLR7 in immunodeficiency virus infection and vaccination and imply that it may be important to control human AIDS vaccine trials, not only for MHC genotype, but also for TLR7 genotype. © 2011 Siddiqui et al.
Kiehntopf M.,Jena University Hospital |
Kiehntopf M.,Methods and Infrastructure for Networked Medical Research |
Krawczak M.,Methods and Infrastructure for Networked Medical Research |
Krawczak M.,University of Kiel
Human Genetics | Year: 2011
In terms of sample exchange, international collaborations between biobanks, or between biobanks and their research partners, have two important aspects. First, the donors' consent usually implies that the scope and purpose of any sample transfer to third parties is subject to major constraints. Since the legal, ethical and political framework of biobanking may differ substantially, even between countries of comparable jurisdictional systems, general rules for the international sharing of biomaterial are difficult, if not impossible, to define. Issues of uncertainty include the right to transfer the material, the scope of research allowed, and intellectual property rights. Since suitable means of international law enforcement may not be available in the context of biobanking, collaborators are advised to clarify any residual uncertainty by means of bilateral contracts, for example, in the form of material transfer agreements. Second, biobank partners may rightly expect that the biomaterial they receive for further analysis attains a certain level of quality. This implies that a biobank has to implement stringent quality control measures covering, in addition to the material transfer itself, the whole process of material acquisition, transport, pre-analytical handling and storage. Again, it may be advisable for biobank partners to claim contractual warranties for the type and quality of the biomaterial they wish to acquire. © Springer-Verlag 2011.
Ahlbrandt J.,Justus Liebig University |
Brammen D.,Otto Von Guericke University of Magdeburg |
Majeed R.W.,Justus Liebig University |
Lefering R.,Witten/Herdecke University |
And 4 more authors.
Studies in Health Technology and Informatics | Year: 2014
Emergency rooms of hospitals provide care to a lot of patients and have great impact on their outcome, so researching the quality of care seems important. Research using registries has yielded impressive results in other areas of medicine. However centralized data-storage has its pitfalls, especially regarding data privacy. We therefore drafted an IT infrastructure that uses decentralized storage to ensure data privacy, but still enables data transfer between participating hospitals. It implements an independent information broker to ensure anonymity of patients. Still it provides a way for researchers to request data and hospitals to contribute data on an opt-in basis. Although not an entirely new approach, the emphasis on data privacy throughout the design is a novel aspect providing a better balance between the need for big sample sizes and patient privacy. © 2014 European Federation for Medical Informatics and IOS Press.
PubMed | Niederrhein University of Applied Sciences, University Hospital Frankfurt, Otto Von Guericke University of Magdeburg, Justus Liebig University and 2 more.
Type: | Journal: Studies in health technology and informatics | Year: 2014
Emergency rooms of hospitals provide care to a lot of patients and have great impact on their outcome, so researching the quality of care seems important. Research using registries has yielded impressive results in other areas of medicine. However centralized data-storage has its pitfalls, especially regarding data privacy. We therefore drafted an IT infrastructure that uses decentralized storage to ensure data privacy, but still enables data transfer between participating hospitals. It implements an independent information broker to ensure anonymity of patients. Still it provides a way for researchers to request data and hospitals to contribute data on an opt-in basis. Although not an entirely new approach, the emphasis on data privacy throughout the design is a novel aspect providing a better balance between the need for big sample sizes and patient privacy.
Stausberg J.,Ludwig Maximilians University of Munich |
Altmann U.,Justus Liebig University |
Antony G.,Kompetenznetz Parkinson |
Drepper J.,Methods and Infrastructure for Networked Medical Research |
And 2 more authors.
Applied Clinical Informatics | Year: 2010
Background: Several disease specific registers are operated by members of the 'TMF - Technology, Methods, and Infrastructure for Networked Medical Research', an umbrella organization of research networks in Germany. Objective: To describe the coverage and the current state as well as financial and organizational issues of registers operated by member networks of the TMF, to identify their requirements and needs, and to recommend best practice models. Methods: A survey with a self-completion questionnaire including all 55 TMF member networks was carried out in winter 2007/2008. Interviews focusing on technological issues were conducted and analyzed in summer 2009 with a convenience sample of 10 registers. Results: From 55 TMF member networks, 11 provided information about 14 registers. Six registers address diseases of the circulatory system with more than 150,000 registered patients. The interviews revealed a typical setting of "research registers". Research registers are an important mean to generate hypotheses for clinical research, to identify eligible patients, and to share data with clinical trials. Concerning technical solutions, we found a remarkable heterogeneity. The analysis of the most efficient registers revealed a structure with five levels as best practice model of register management: executive, operations, IT-management, software, hardware. Conclusion: In the last ten years, the TMF member networks established disease specific registers in Germany mainly to support clinical research. The heterogeneity of organizational and technical solutions as well as deficits in register planning motivated the development of respective recommendations. The TMF will continue to assist the registers in quality improvement. © Schattauer 2010.
Bauer C.R.K.D.,University of Gottingen |
Ganslandt T.,Friedrich - Alexander - University, Erlangen - Nuremberg |
Baum B.,University of Gottingen |
Christoph J.,Friedrich - Alexander - University, Erlangen - Nuremberg |
And 8 more authors.
Methods of Information in Medicine | Year: 2016
Background: In recent years, research data warehouses moved increasingly into the focus of interest of medical research. Nevertheless, there are only a few center-independent infrastructure solutions available. They aim to provide a consolidated view on medical data from various sources such as clinical trials, electronic health records, epidemiological registries or longitudinal cohorts. The i2b2 framework is a well-established solution for such repositories, but it lacks support for importing and integrating clinical data and metadata. Objectives: The goal of this project was to develop a platform for easy integration and administration of data from heterogeneous sources, to provide capabilities for linking them to medical terminologies and to allow for transforming and mapping of data streams for user-specific views. Methods: A suite of three tools has been developed: the i2b2 Wizard for simplifying administration of i2b2, the IDRT Import and Mapping Tool for loading clinical data from various formats like CSV, SQL, CDISC ODM or biobanks and the IDRT i2b2 Web Client Plugin for advanced export options. The Import and Mapping Tool also includes an ontology editor for rearranging and mapping patient data and structures as well as annotating clinical data with medical terminologies, primarily those used in Germany (ICD-10-GM, OPS, ICD-O, etc.). Results: With the three tools functional, new i2b2-based research projects can be created, populated and customized to researcher’s needs in a few hours. Amalgamating data and metadata from different databases can be managed easily. With regards to data privacy a pseudonymization service can be plugged in. Using common ontologies and reference terminologies rather than projectspecific ones leads to a consistent understanding of the data semantics. Conclusions: i2b2’s promise is to enable clinical researchers to devise and test new hypothesis even without a deep knowledge in statistical programing. The approach pre-sented here has been tested in a number of scenarios with millions of observations and tens of thousands of patients. Initially mostly observant, trained researchers were able to construct new analyses on their own. Early feedback indicates that timely and extensive access to their “own” data is appreciated most, but it is also lowering the barrier for other tasks, for instance checking data quality and completeness (missing data, wrong coding). © Schattauer 2016.
PubMed | Friedrich - Alexander - University, Erlangen - Nuremberg, University of Leipzig, Methods and Infrastructure for Networked Medical Research and University of Gottingen
Type: | Journal: Studies in health technology and informatics | Year: 2016
Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.