| 1. |
- Spjuth, Ola, 1977-, et al.
(författare)
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Harmonising and linking biomedical and clinical data across disparate data archives to enable integrative cross-biobank research
- 2016
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 24:4, s. 521-528
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Tidskriftsartikel (refereegranskat)abstract
- A wealth of biospecimen samples are stored in modern globally distributed biobanks. Biomedical researchers worldwide need to be able to combine the available resources to improve the power of large-scale studies. A prerequisite for this effort is to be able to search and access phenotypic, clinical and other information about samples that are currently stored at biobanks in an integrated manner. However, privacy issues together with heterogeneous information systems and the lack of agreed-upon vocabularies have made specimen searching across multiple biobanks extremely challenging. We describe three case studies where we have linked samples and sample descriptions in order to facilitate global searching of available samples for research. The use cases include the ENGAGE (European Network for Genetic and Genomic Epidemiology) consortium comprising at least 39 cohorts, the SUMMIT (surrogate markers for micro- and macro-vascular hard endpoints for innovative diabetes tools) consortium and a pilot for data integration between a Swedish clinical health registry and a biobank. We used the Sample avAILability (SAIL) method for data linking: first, created harmonised variables and then annotated and made searchable information on the number of specimens available in individual biobanks for various phenotypic categories. By operating on this categorised availability data we sidestep many obstacles related to privacy that arise when handling real values and show that harmonised and annotated records about data availability across disparate biomedical archives provide a key methodological advance in pre-analysis exchange of information between biobanks, that is, during the project planning phase.
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| 2. |
- van Ommen, Gert-Jan B, et al.
(författare)
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BBMRI-ERIC as a resource for pharmaceutical and life science industries : the development of biobank-based Expert Centres
- 2015
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Ingår i: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 23:7, s. 893-900
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Tidskriftsartikel (refereegranskat)abstract
- Biological resources (cells, tissues, bodily fluids or biomolecules) are considered essential raw material for the advancement of health-related biotechnology, for research and development in life sciences, and for ultimately improving human health. Stored in local biobanks, access to the human biological samples and related medical data for transnational research is often limited, in particular for the international life science industry. The recently established pan-European Biobanking and BioMolecular resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to improve accessibility and interoperability between academic and industrial parties to benefit personalized medicine, disease prevention to promote development of new diagnostics, devices and medicines. BBMRI-ERIC is developing the concept of Expert Centre as public-private partnerships in the precompetitive, not-for-profit field to provide a new structure to perform research projects that would face difficulties under currently established models of academic-industry collaboration. By definition, Expert Centres are key intermediaries between public and private sectors performing the analysis of biological samples under internationally standardized conditions. This paper presents the rationale behind the Expert Centres and illustrates the novel concept with model examples.
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| 3. |
- Wichmann, H-Erich, et al.
(författare)
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Comprehensive catalog of European biobanks
- 2011
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 29:9, s. 795-797
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Yuille, Martin, et al.
(författare)
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Biobanking for Europe
- 2008
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 9:1, s. 14-24
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Biobanks are well-organized resources comprising biological samples and associated information that are accessible to scientific investigation. Across Europe, millions of samples with related data are held in different types of collections. While individual collections can be well organized and accessible, the resources are subject to fragmentation, insecurity of funding and incompleteness. To address these issues, a Biobanking and BioMolecular Resources Infrastructure (BBMRI) is to be developed across Europe, thereby implementing a European roadmap for research infrastructures that was developed by a forum of EU member states and that has been received by the European Commission. In this review, we describe the work involved in preparing for the construction of BBMRI in a European and global context.
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| 5. |
- Almqvist, Catarina, et al.
(författare)
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LifeGene - A large prospective population-based study of global relevance
- 2011
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Ingår i: European Journal of Epidemiology. - Stockholm : Springer Science and Business Media LLC. - 0393-2990 .- 1573-7284. ; 26:1, s. 67-77
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Tidskriftsartikel (refereegranskat)abstract
- Studying gene-environment interactions requires that the amount and quality of the lifestyle data is comparable to what is available for the corresponding genomic data. Sweden has several crucial prerequisites for comprehensive longitudinal biomedical research, such as the personal identity number, the universally available national health care system, continuously updated population and health registries and a scientifically motivated population. LifeGene builds on these strengths to bridge the gap between basic research and clinical applications with particular attention to populations, through a unique design in a research-friendly setting. LifeGene is designed both as a prospective cohort study and an infrastructure with repeated contacts of study participants approximately every 5 years. Index persons aged 18-45 years old will be recruited and invited to include their household members (partner and any children). A comprehensive questionnaire addressing cutting-edge research questions will be administered through the web with short follow-ups annually. Biosamples and physical measurements will also be collected at baseline, and re-administered every 5 years thereafter. Event-based sampling will be a key feature of LifeGene. The household-based design will give the opportunity to involve young couples prior to and during pregnancy, allowing for the first study of children born into cohort with complete pre-and perinatal data from both the mother and father. Questions and sampling schemes will be tailored to the participants' age and life events. The target of LifeGene is to enrol 500,000 Swedes and follow them longitudinally for at least 20 years.
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| 6. |
- Bexelius, Christin, et al.
(författare)
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Estimation of Physical Activity Levels Using Cell Phone Questionnaires: A Comparison With Accelerometry for Evaluation of Between-Subject and Within-Subject Variations
- 2011
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Ingår i: Journal of Medical Internet Research. - : Journal of Medical Internet Research / Gunther Eysenbach. - 1438-8871. ; 13:3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Physical activity promotes health and longevity. Further elaboration of the role of physical activity for human health in epidemiological studies on large samples requires accurate methods that are easy to use, cheap, and possible to repeat. The use of telecommunication technologies such as cell phones is highly interesting in this respect. In an earlier report, we showed that physical activity level (PAL) assessed using a cell phone procedure agreed well with corresponding estimates obtained using the doubly labeled water method. However, our earlier study indicated high within-subject variation in relation to between-subject variations in PAL using cell phones, but we could not assess if this was a true variation of PAL or an artifact of the cell phone technique. less thanbrgreater than less thanbrgreater thanObjective: Our objective was to compare within-and between-subject variations in PAL by means of cell phones with corresponding estimates using an accelerometer. In addition, we compared the agreement of daily PAL values obtained using the cell phone questionnaire with corresponding data obtained using an accelerometer. less thanbrgreater than less thanbrgreater thanMethods: PAL was measured both with the cell phone questionnaire and with a triaxial accelerometer daily during a 2-week study period in 21 healthy Swedish women (20 to 45 years of age and BMI from 17.7 kg/m(2) to 33.6 kg/m(2)). The results were evaluated by fitting linear mixed effect models and descriptive statistics and graphs. less thanbrgreater than less thanbrgreater thanResults: With the accelerometer, 57% (95% confidence interval [CI] 40%-66%) of the variation was within subjects, while with the cell phone, within-subject variation was 76% (95% CI 59%-83%). The day-to-day variations in PAL observed using the cell phone questions agreed well with the corresponding accelerometer results. less thanbrgreater than less thanbrgreater thanConclusions: Both the cell phone questionnaire and the accelerometer showed high within-subject variations. Furthermore, day-to-day variations in PAL within subjects assessed using the cell phone agreed well with corresponding accelerometer values. Consequently, our cell phone questionnaire is a promising tool for assessing levels of physical activity. The tool may be useful for large-scale prospective studies.
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| 7. |
- Bexelius, Christin, et al.
(författare)
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Measures of Physical Activity Using Cell Phones: Validation Using Criterion Methods
- 2010
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Ingår i: JOURNAL OF MEDICAL INTERNET RESEARCH. - : JMIR Publications Inc.. - 1438-8871. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Physical activity is associated with reduced risks of many chronic diseases. Data collected on physical activity in large epidemiological studies is often based on paper questionnaires. The validity of these questionnaires is debated, and more effective methods are needed. Objective: This study evaluates repeated measures of physical activity level (PAL) and the feasibility of using a Java-based questionnaire downloaded onto cell phones for collection of such data. The data obtained were compared with reference estimates based on the doubly labeled water method and indirect calorimetry (PAL(ref)). Method: Using a Java-based cell phone application, 22 women reported their physical activity based on two short questions answered daily over a 14-day period (PAL(cell)). Results were compared with reference data obtained from the doubly labeled water method and indirect calorimetry (PAL(ref)). Results were also compared against physical activity levels assessed by two regular paper questionnaires completed by women at the end of the 14-day period (PAL(quest1) and PAL(quest2)). PAL(cell), PAL(quest1), and PAL(quest2) were compared with PAL(ref) using the Bland and Altman procedure. Results: The mean difference between PAL(cell), and PAL(ref) was small (0.014) with narrow limits of agreement (2SD = 0.30) Compared with PAL(ref) the mean difference was also small for PAL(quest1) and PAL(quest2) (0.004 and 0.07, respectively); however, the limits of agreement were wider (PAL(quest), 2SD = 0.50 and PAL(quest2), 2SD = 0.90). The test for trend was statistically significant for PAL(quest1) (slope of regression line = 0.79, P = .04) as well as for PAL(quest2) (slope of regression line = 1.58, P andlt; .001) when compared with PAL(ref). Conclusion: A Java-based physical activity questionnaire administered daily using cell phones produced PAL estimates that agreed well with PAL reference values. Furthermore, the limits of agreement between PAL obtained using cell phones, and reference values were narrower than for corresponding estimates obtained using paper questionnaires. Java-based questionnaires downloaded onto cell phones may be a feasible and cost-effective method of data collection for large-scale prospective studies of physical activity.
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| 8. |
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| 9. |
- Gholami, Ali, et al.
(författare)
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Design and Implementation of the advanced cloud privacy threat modeling
- 2016
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Ingår i: International Journal of Network Security & Its Applications. - 0975-2307 .- 0974-9330. ; 8:2, s. 103-122
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Tidskriftsartikel (refereegranskat)abstract
- Privacy-preservation for sensitive data has become a challenging issue in cloud computing. Threat modeling as a part of requirements engineering in secure software development provides a structured approach for identifying attacks and proposing countermeasures against the exploitation of vulnerabilities in a system. This paper describes an extension of Cloud Privacy Threat Modeling (CPTM) methodology for privacy threat modeling in relation to processing sensitive data in cloud computing environments. It describes the modeling methodology that involved applying Method Engineering to specify characteristics of a cloud privacy threat modeling methodology, different steps in the proposed methodology and corresponding products. In addition, a case study has been implemented as a proof of concept to demonstrate the usability of the proposed methodology. We believe that the extended methodology facilitates the application of a privacy-preserving cloud software development approach from requirements engineering to design.
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| 10. |
- Gholami, Ali, et al.
(författare)
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Privacy Threat Modeling for Emerging BiobankClouds
- 2014
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Ingår i: Procedia Computer Science. - : Elsevier. ; 37, s. 489-496
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Konferensbidrag (refereegranskat)abstract
- There is an increased amount of data produced by next generation sequencing (NGS) machines which demand scalable storage and analysis of genomic data. In order to cope with this huge amount of information, many biobanks are interested in cloud computing capabilities such as on-demand elasticity of computing power and storage capacity. There are several security and privacy requirements mandated by personal data protection legislation which hinder biobanks from migrating big data generated by the NGS machines. This paper describes the privacy requirements of platform-as-service BiobankClouds according to the European Data Protection Directive (DPD). It identifies several key privacy threats which leave BiobankClouds vulnerable to an attack. This study benefits health-care application designers in the requirement elicitation cycle when building privacy-preserving BiobankCloud platforms.
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