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Foraker RE, Lai AM, Kannampallil TG, Woeltje KF, Trolard AM, Payne PRO. Transmission dynamics: Data sharing in the COVID-19 era. Learn Health Syst 2020; 5:e10235. [PMID: 32838037 PMCID: PMC7323052 DOI: 10.1002/lrh2.10235] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
Problem The current coronavirus disease 2019 (COVID‐19) pandemic underscores the need for building and sustaining public health data infrastructure to support a rapid local, regional, national, and international response. Despite a historical context of public health crises, data sharing agreements and transactional standards do not uniformly exist between institutions which hamper a foundational infrastructure to meet data sharing and integration needs for the advancement of public health. Approach There is a growing need to apply population health knowledge with technological solutions to data transfer, integration, and reasoning, to improve health in a broader learning health system ecosystem. To achieve this, data must be combined from healthcare provider organizations, public health departments, and other settings. Public health entities are in a unique position to consume these data, however, most do not yet have the infrastructure required to integrate data sources and apply computable knowledge to combat this pandemic. Outcomes Herein, we describe lessons learned and a framework to address these needs, which focus on: (a) identifying and filling technology “gaps”; (b) pursuing collaborative design of data sharing requirements and transmission mechanisms; (c) facilitating cross‐domain discussions involving legal and research compliance; and (d) establishing or participating in multi‐institutional convening or coordinating activities. Next steps While by no means a comprehensive evaluation of such issues, we envision that many of our experiences are universal. We hope those elucidated can serve as the catalyst for a robust community‐wide dialogue on what steps can and should be taken to ensure that our regional and national health care systems can truly learn, in a rapid manner, so as to respond to this and future emergent public health crises.
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Heacock ML, Amolegbe SM, Skalla LA, Trottier BA, Carlin DJ, Henry HF, Lopez AR, Duncan CG, Lawler CP, Balshaw DM, Suk WA. Sharing SRP data to reduce environmentally associated disease and promote transdisciplinary research. REVIEWS ON ENVIRONMENTAL HEALTH 2020; 35:111-122. [PMID: 32126018 DOI: 10.1515/reveh-2019-0089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/06/2020] [Indexed: 05/25/2023]
Abstract
The National Institute of Environmental Health Sciences (NIEHS) Superfund Basic Research and Training Program (SRP) funds a wide range of projects that span biomedical, environmental sciences, and engineering research and generate a wealth of data resulting from hypothesis-driven research projects. Combining or integrating these diverse data offers an opportunity to uncover new scientific connections that can be used to gain a more comprehensive understanding of the interplay between exposures and health. Integrating and reusing data generated from individual research projects within the program requires harmonization of data workflows, ensuring consistent and robust practices in data stewardship, and embracing data sharing from the onset of data collection and analysis. We describe opportunities to leverage data within the SRP and current SRP efforts to advance data sharing and reuse, including by developing an SRP dataset library and fostering data integration through Data Management and Analysis Cores. We also discuss opportunities to improve public health by identifying parallels in the data captured from health and engineering research, layering data streams for a more comprehensive picture of exposures and disease, and using existing SRP research infrastructure to facilitate and foster data sharing. Importantly, we point out that while the SRP is in a unique position to exploit these opportunities, they can be employed across environmental health research. SRP research teams, which comprise cross-disciplinary scientists focused on similar research questions, are well positioned to use data to leverage previous findings and accelerate the pace of research. Incorporating data streams from different disciplines addressing similar questions can provide a broader understanding and uncover the answers to complex and discrete research questions.
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403
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Lin C, Braund WE, Auerbach J, Chou JH, Teng JH, Tu P, Mullen J. Policy Decisions and Use of Information Technology to Fight COVID-19, Taiwan. Emerg Infect Dis 2020; 26:1506-1512. [PMID: 32228808 PMCID: PMC7323533 DOI: 10.3201/eid2607.200574] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Because of its proximity to and frequent travelers to and from China, Taiwan faces complex challenges in preventing coronavirus disease (COVID-19). As soon as China reported the unidentified outbreak to the World Health Organization on December 31, 2019, Taiwan assembled a taskforce and began health checks onboard flights from Wuhan. Taiwan’s rapid implementation of disease prevention measures helped detect and isolate the country’s first COVID-19 case on January 20, 2020. Laboratories in Taiwan developed 4-hour test kits and isolated 2 strains of the coronavirus before February. Taiwan effectively delayed and contained community transmission by leveraging experience from the 2003 severe acute respiratory syndrome outbreak, prevalent public awareness, a robust public health network, support from healthcare industries, cross-departmental collaborations, and advanced information technology capacity. We analyze use of the National Health Insurance database and critical policy decisions made by Taiwan’s government during the first 50 days of the COVID-19 outbreak.
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404
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Aguiar ERGR, Navas J, Pacheco LGC. The COVID-19 Diagnostic Technology Landscape: Efficient Data Sharing Drives Diagnostic Development. Front Public Health 2020; 8:309. [PMID: 32626682 PMCID: PMC7314948 DOI: 10.3389/fpubh.2020.00309] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/08/2020] [Indexed: 12/24/2022] Open
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405
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Christley S, Aguiar A, Blanck G, Breden F, Bukhari SAC, Busse CE, Jaglale J, Harikrishnan SL, Laserson U, Peters B, Rocha A, Schramm CA, Taylor S, Vander Heiden JA, Zimonja B, Watson CT, Corrie B, Cowell LG. The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons. Front Big Data 2020; 3:22. [PMID: 33693395 PMCID: PMC7931935 DOI: 10.3389/fdata.2020.00022] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/18/2020] [Indexed: 11/13/2022] Open
Abstract
The Adaptive Immune Receptor Repertoire (AIRR) Community is a research-driven group that is establishing a clear set of community-accepted data and metadata standards; standards-based reference implementation tools; and policies and practices for infrastructure to support the deposit, curation, storage, and use of high-throughput sequencing data from B-cell and T-cell receptor repertoires (AIRR-seq data). The AIRR Data Commons is a distributed system of data repositories that utilizes a common data model, a common query language, and common interoperability formats for storage, query, and downloading of AIRR-seq data. Here is described the principal technical standards for the AIRR Data Commons consisting of the AIRR Data Model for repertoires and rearrangements, the AIRR Data Commons (ADC) API for programmatic query of data repositories, a reference implementation for ADC API services, and tools for querying and validating data repositories that support the ADC API. AIRR-seq data repositories can become part of the AIRR Data Commons by implementing the data model and API. The AIRR Data Commons allows AIRR-seq data to be reused for novel analyses and empowers researchers to discover new biological insights about the adaptive immune system.
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406
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Raisaro JL, Troncoso-Pastoriza JR, Pradervand S, Cuendet M, Misbach M, Sa J, Marino F, Freundler N, Rosat N, Cavin D, Leichtle A, Fellay J, Michielin O, Hubaux JP. SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery. Stud Health Technol Inform 2020; 270:1161-1162. [PMID: 32570563 DOI: 10.3233/shti200345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MedCo is the first operational system that makes sensitive medical-data available for research in a simple, privacy-conscious and secure way. It enables a consortium of clinical sites to collectively protect their data and to securely share them with investigators, without single points of failure. In this short paper, we report on our ongoing effort for the operational deployment of MedCo within the context of the Swiss Personalized Health Network (SPHN) for the Swiss Molecular Tumor Board.
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407
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Gruhl M, Reinecke I, Sedlmayr M. Specification and Distribution of Vocabularies Among Consortial Partners. Stud Health Technol Inform 2020; 270:1393-1394. [PMID: 32570675 DOI: 10.3233/shti200458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Due to the variety of different software systems and disparate observational databases, the need for a uniform data representation rises. Common data models (CDM) support the harmonisation of data. A powerful but compact software setup and a minimum vocabulary set has been composed via Docker to facilitate analysis of data across ten university hospitals. The presented approach also creates the possibility to use a concise database which is easy to deploy.
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408
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Parvanova I, Finkelstein J. Data Integration Approaches for Representing Stem Cell Studies. Stud Health Technol Inform 2020; 270:1235-1236. [PMID: 32570596 DOI: 10.3233/shti200379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to examine existing methods for sharing results of stem cell research via online data repositories. To identify the relevant repositories, a PubMed search was conducted using standard MeSH terms which was followed by a web-based search of relevant databases. The search yielded 16 databases created between 2010 and 2019. The review of databases identified 35 major rubrics and their sub-rubrics organized in a five-module system. Data integration approaches were characterized by three domains (common data elements, data visualization and analysis tools, and ontology mapping) which varied widely across the databases. Current state of stem cell data integration lacks reproducibility and standardization. Standardization of data integration approaches for representing stem cell studies is necessary to facilitate data sharing.
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409
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Danzetta ML, Marenzoni ML, Iannetti S, Tizzani P, Calistri P, Feliziani F. African Swine Fever: Lessons to Learn From Past Eradication Experiences. A Systematic Review. Front Vet Sci 2020; 7:296. [PMID: 32582778 PMCID: PMC7296109 DOI: 10.3389/fvets.2020.00296] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/30/2020] [Indexed: 11/13/2022] Open
Abstract
Prevention, early detection, prompt reaction, and communication play a crucial role in African swine fever (ASF) control. Appropriate surveillance capable of early detection of the disease in both domestic and wild animals, and the implementation of consolidated contingency plans, are currently considered the best means of controlling this disease. The purpose of this study was to understand the lessons to be learned through the global disease eradication history. To establish which strategies were successful for prevention, control, and eradication of ASF, and which errors should not be repeated, we conducted a systematic review. A query was defined to search for surveillance and control strategies applied by countries worldwide for ASF eradication in the past. Inclusion and exclusion criteria were defined. Decisions on study eligibility and data extraction were performed by two independent reviewers and the differences were resolved by consensus or by a third reviewer. From 1,980 papers, 23 were selected and included in the qualitative analysis. Reports from Belgium, Brazil, Cuba, the Dominican Republic and Haiti, France, mainland Italy, Malta, Portugal, and Spain were included. Despite the economic resources allocated and the efforts made, eradication was possible in only eight countries, between the 50s and 90s in the twentieth century, in different epidemiological and cultural contexts, in some instances within <1 year, and in others in about 40 years. Classical surveillance strategies, such as active and passive surveillance, both at farm and slaughterhouse levels, targeted surveillance, together with conventional biosafety and sanitary measures, led to eradication even in countries in which the tick's epidemiological role was demonstrated. Historical surveillance data analysis indicated that eradication was possible even when technological tools either were not available or were used less than they are currently. This emphasizes that data on surveillance and on animal population are crucial for planning effective surveillance, and targeting proper control and intervention strategies. This paper demonstrates that some strategies applied in the past were effective; these could be implemented and improved to confront the current epidemiological wave. This offers encouragement for the efforts made particularly in Europe during the recent epidemics.
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410
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Khurshid A, Rajeswaren V, Andrews S. Using Blockchain Technology to Mitigate Challenges in Service Access for the Homeless and Data Exchange Between Providers: Qualitative Study. J Med Internet Res 2020; 22:e16887. [PMID: 32348278 PMCID: PMC7303832 DOI: 10.2196/16887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND In the homeless population, barriers to housing and supportive services include a lack of control or access to data. Disparate data formats and storage across multiple organizations hinder up-to-date intersystem access to records and a unified view of an individual's health and documentation history. The utility of blockchain to solve interoperability in health care is supported in recent literature, but the technology has yet to be tested in real-life conditions encompassing the complex regulatory standards in the health sector. OBJECTIVE This study aimed to test the feasibility and performance of a blockchain system in a homeless community to securely store and share data across a system of providers in the health care ecosystem. METHODS We performed a series of platform demonstrations and open-ended qualitative feedback interviews to determine the key needs and barriers to user and stakeholder adoption. Account creation and data transactions promoting organizational efficiency and improved health outcomes in this population were tested with homeless users and service providers. RESULTS Persons experiencing homelessness and care organizations could successfully create accounts, grant and revoke data sharing permissions, and transmit documents across a distributed network of providers. However, there were issues regarding the security of shared data, user experience and adoption, and organizational preparedness for service providers as end users. We tested a set of assumptions related to these problems within the project time frame and contractual obligations with an existing blockchain-based platform. CONCLUSIONS Blockchain technology provides decentralized data sharing, validation, immutability, traceability, and integration. These core features enable a secure system for the management and distribution of sensitive information. This study presents a concrete evaluation of the effectiveness of blockchain through an existing platform while revealing limitations from the perspectives of user adoption, cost-effectiveness, scalability, and regulatory frameworks.
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411
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McLennan S, Celi LA, Buyx A. COVID-19: Putting the General Data Protection Regulation to the Test. JMIR Public Health Surveill 2020; 6:e19279. [PMID: 32449686 PMCID: PMC7265798 DOI: 10.2196/19279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022] Open
Abstract
The coronavirus disease (COVID-19) pandemic is very much a global health issue and requires collaborative, international health research efforts to address it. A valuable source of information for researchers is the large amount of digital health data that are continuously collected by electronic health record systems at health care organizations. The European Union’s General Data Protection Regulation (GDPR) will be the key legal framework with regard to using and sharing European digital health data for research purposes. However, concerns persist that the GDPR has made many organizations very risk-averse in terms of data sharing, even if the regulation permits such sharing. Health care organizations focusing on individual risk minimization threaten to undermine COVID-19 research efforts. In our opinion, there is an ethical obligation to use the research exemption clause of the GDPR during the COVID-19 pandemic to support global collaborative health research efforts. Solidarity is a European value, and here is a chance to exemplify it by using the GDPR regulatory framework in a way that does not hinder but actually fosters solidarity during the COVID-19 pandemic.
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Bell RJ, Haring R. When you are making plans to publish research, you need to plan for data sharing. Climacteric 2020; 23:466-467. [PMID: 32452703 DOI: 10.1080/13697137.2020.1771302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Open data is another step on the pathway of strengthening medical research. Allowing access to data facilitates testing the reproducibility of research findings. It also allows for the testing of new hypotheses, the incorporation of individual level data into meta-analyses and the development of very large data sets in which to develop and test new algorithms. There are now many data repositories that researchers can use to share their protocols, syntax and data. There are strategies both for managing what other researchers do with publically available data and for rewarding researchers who share their data. There is a strong ethical argument for making data publically available and research participants are generally supportive of this approach.
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413
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Du L, Wang M. Genetic Privacy and Data Protection: A Review of Chinese Direct-to-Consumer Genetic Test Services. Front Genet 2020; 11:416. [PMID: 32425986 PMCID: PMC7205185 DOI: 10.3389/fgene.2020.00416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/01/2020] [Indexed: 11/13/2022] Open
Abstract
Background The existing literature has not examined how Chinese direct-to-consumer (DTC) genetic testing providers navigate the issues of informed consent, privacy, and data protection associated with testing services. This research aims to explore these questions by examining the relevant documents and messages published on websites of the Chinese DTC genetic test providers. Methods Using Baidu.com, the most popular Chinese search engine, we compiled the websites of providers who offer genetic testing services and analyzed available documents related to informed consent, the terms of services, and the privacy policy. The analyses were guided by the following inquiries as they applied to each DTC provider: the methods available for purchasing testing products; the methods providers used to obtain informed consent; privacy issues and measures for protecting consumers’ health information; the policy for third-party data sharing; consumers right to their data; and the liabilities in the event of a data breach. Results 68.7% of providers offer multiple channels for purchasing genetic testing products, and that social media has become a popular platform to promote testing services. Informed consent forms are not available on 94% of providers’ websites and a privacy policy is only offered by 45.8% of DTC genetic testing providers. Thirty-nine providers stated that they used measures to protect consumers’ information, of which, 29 providers have distinguished consumers’ general personal information from their genetic information. In 33.7% of the cases examined, providers stated that with consumers’ explicit permission, they could reuse and share the clients’ information for non-commercial purposes. Twenty-three providers granted consumer rights to their health information, with the most frequently mentioned right being the consumers’ right to decide how their data can be used by providers. Lastly, 21.7% of providers clearly stated their liabilities in the event of a data breach, placing more emphasis on the providers’ exemption from any liability. Conclusions Currently, the Chinese DTC genetic testing business is running in a regulatory vacuum, governed by self-regulation. The government should develop a comprehensive legal framework to regulate DTC genetic testing offerings. Regulatory improvements should be made based on periodical reviews of the supervisory strategy to meet the rapid development of the DTC genetic testing industry.
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414
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Kain M, Bodin M, Loury S, Chi Y, Louis J, Simon M, Lamy J, Barillot C, Dojat M. Small Animal Shanoir (SAS) A Cloud-Based Solution for Managing Preclinical MR Brain Imaging Studies. Front Neuroinform 2020; 14:20. [PMID: 32508612 PMCID: PMC7248267 DOI: 10.3389/fninf.2020.00020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 04/16/2020] [Indexed: 01/28/2023] Open
Abstract
Clinical multicenter imaging studies are frequent and rely on a wide range of existing tools for sharing data and processing pipelines. This is not the case for preclinical (small animal) studies. Animal population imaging is still in infancy, especially because a complete standardization and control of initial conditions in animal models across labs is still difficult and few studies aim at standardization of acquisition and post-processing techniques. Clearly, there is a need of appropriate tools for the management and sharing of data, post-processing and analysis methods dedicated to small animal imaging. Solutions developed for Human imaging studies cannot be directly applied to this specific domain. In this paper, we present the Small Animal Shanoir (SAS) solution for supporting animal population imaging using tools compatible with open data. The integration of automated workflow tools ensures accessibility and reproducibility of research outputs. By sharing data and imaging processing tools, hosted by SAS, we promote data preparation and tools for reproducibility and reuse, and participation in multicenter or replication "open science" studies contributing to the improvement of quality science in preclinical domain. SAS is a first step for promoting open science for small animal imaging and a contribution to the valorization of data and pipelines of reference.
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415
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McWhirter R, Eckstein L, Chalmers D, Critchley C, Nielsen J, Otlowski M, Nicol D. A Scenario-Based Methodology for Analyzing the Ethical, Legal, and Social Issues in Genomic Data Sharing. J Empir Res Hum Res Ethics 2020; 15:355-364. [PMID: 32425102 DOI: 10.1177/1556264620920460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sharing of genomic and associated data is essential to clinical practice and biomedical research, and is increasingly encouraged by journals and funding bodies. Grappling with the range of legal and ethical issues raised by genomic data sharing presents a significant challenge, given the diversity of practices: from defined sharing of individual patient data, to broad-scale public sharing of research data, to uploading of direct-to-consumer test data by community members. Most commentary to date has discussed these issues in broad terms, but the debate can only progress if we engage with more granularity, grounded in jurisdictional and contextual specifics. We developed an empirical approach, creating a set of prototypical scenarios that capture the diversity of current genomic data sharing practices, which allows legal and ethical analysis of key issues at a granular level. The specificity of this approach provides a strong foundation for developing useful and relevant regulatory recommendations.
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416
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Kim H, Kim HR, Kim S, Kim E, Kim SY, Park HY. Public Attitudes Toward Precision Medicine: A Nationwide Survey on Developing a National Cohort Program for Citizen Participation in the Republic of Korea. Front Genet 2020; 11:283. [PMID: 32477396 PMCID: PMC7235362 DOI: 10.3389/fgene.2020.00283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
This nation-wide survey was conducted among Korean adults to examine the public interest in and attitudes toward establishing a citizen participation cohort model and to collect data to support and determine the future policy and research directions of the Resource Collection Project for Precision Medicine Research (RCP-PMR) before the project proceeds. The demographic framework of the survey population was established based on the statistical standards of the Ministry of the Interior and Safety. An online survey was carried out using web panels between 14 May 2018 and 23 May 2018. Sampling was performed using a simple proportional allocation method considering region, gender, and age. From this survey, the RCP-PMR received very high support (94.5%) and the intention to participate was as high as 83.5%. Respondents had a very positive attitude toward providing their samples and information to the study (84.5-89.9%). In terms of incentives to participate, respondents wanted to receive health information (80.2%), monetary compensation (51.4%), and smart devices (41.3%). Most participants responded that it was appropriate to carry out the project at governmental research institutes (66.9%). Respondents also had a positive attitude toward sharing their information and samples as long as it was only shared with the governmental researchers who run the project (88.0%). However, the survey participants expressed concerns about the study being time consuming or a hassle (38.1%), privacy breaches (33.6%), and the lack of returning benefits of participation (25.1%). Participants had a negative attitude toward sharing their data with researchers who are not directly involved in the RCP-PMR. Considering the future use of the database derived from this project, it will be important to communicate with the lay public as well as the RCP-PMR participants to understand their needs in participating in the forthcoming study and to improve their understanding of the goals of the project, and how data sharing can contribute to disease research and prevention. The RCP-PMR should consider building an efficient citizen-participation program and privacy protection for the research participants.
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417
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neurotic: Neuroscience Tool for Interactive Characterization. eNeuro 2020; 7:ENEURO.0085-20.2020. [PMID: 32332078 PMCID: PMC7215586 DOI: 10.1523/eneuro.0085-20.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/26/2022] Open
Abstract
A software tool for synchronization of video with signals would be of broad general use to behavioral neuroscientists. A new program, called neurotic (NEUROscience Tool for Interactive Characterization), allows users to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, is easy to use, and supports a variety of file formats. The program also facilitates collaborations by using a portable specification for loading and processing data and retrieving data files from online sources. Two examples are shown in which the software is used to explore experimental datasets with extracellular nerve or muscle recordings and simultaneous video of behavior. The configuration specification for controlling how data are located, loaded, processed, and plotted is also summarized. Algorithms for spike detection and burst detection are demonstrated. This new program could be used in many applications in which behavior and signals need to be analyzed together.
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418
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Wallace SE, Kirby E, Knoppers BM. How Can We Not Waste Legacy Genomic Research Data? Front Genet 2020; 11:446. [PMID: 32457803 PMCID: PMC7225345 DOI: 10.3389/fgene.2020.00446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Enabling genomic and biomedical data to be shared for secondary research purposes is not always straightforward for existing “legacy” data sets. Researchers may not know whether their data meet ethical and regulatory requirements for sharing. As a result, these data, collected using public funds and the good will and efforts of the donors and investigators, may not be used beyond their original purpose. Single-use plastics are now being banned in many countries; single-use research should be avoided if possible. This paper describes a filter developed through the driver projects of the Global Alliance for Genomics and Health that can be used by researchers to help them determine the extent of sharing possible for their legacy data and actions to be taken to enable further sharing.
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Franklin EF, Nichols HM, House L, Buzaglo J, Thiboldeaux K. Cancer Patient Perspectives on Sharing of Medical Records and Mobile Device Data for Research Purposes. J Patient Exp 2020; 7:1115-1121. [PMID: 33457553 PMCID: PMC7786788 DOI: 10.1177/2374373520923837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Sharing data is critical to advancing science, improving health, and creating advances in the delivery of health care services. The value of sharing data for cancer research purposes is well established, and there are multiple initiatives under way that address this need. However, there has been less focus on cancer patient perspectives regarding the sharing of their health information for research purposes. This study examined cancer patient perspectives on the sharing of de-identified health data for research purposes including both data from medical records and mobile applications. This cross-sectional study used survey methodology to collect data from cancer patients/survivors (N = 677). Overall, we found that participants were largely willing (71%) to share de-identified medical data and were most motivated (88%) by a desire to help other cancer patients. Patients were less likely to be comfortable sharing mobile application data (34%). It is vital that we understand patient perspectives on data sharing and work with them as partners, valuing their unique contributions, and attending to their preferences.
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Matamoros S, Hendriksen RS, Pataki BÁ, Pakseresht N, Rossello M, Silvester N, Amid C, Aarestrup FM, Koopmans M, Cochrane G, Csabai I, Lund O, Schultsz C. Accelerating surveillance and research of antimicrobial resistance - an online repository for sharing of antimicrobial susceptibility data associated with whole-genome sequences. Microb Genom 2020; 6:e000342. [PMID: 32255760 PMCID: PMC7371118 DOI: 10.1099/mgen.0.000342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/31/2020] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is an emerging threat to modern medicine. Improved diagnostics and surveillance of resistant bacteria require the development of next-generation analysis tools and collaboration between international partners. Here, we present the 'AMR Data Hub', an online infrastructure for storage and sharing of structured phenotypic AMR data linked to bacterial whole-genome sequences. Leveraging infrastructure built by the European COMPARE Consortium and structured around the European Nucleotide Archive (ENA), the AMR Data Hub already provides an extensive data collection of more than 2500 isolates with linked genome and AMR data. Representing these data in standardized formats, we provide tools for the validation and submission of new data and services supporting search, browse and retrieval. The current collection was created through a collaboration by several partners from the European COMPARE Consortium, demonstrating the capacities and utility of the AMR Data Hub and its associated tools. We anticipate growth of content and offer the hub as a basis for future research into methods to explore and predict AMR.
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421
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Azzariti DR, Hamosh A. Genomic Data Sharing for Novel Mendelian Disease Gene Discovery: The Matchmaker Exchange. Annu Rev Genomics Hum Genet 2020; 21:305-326. [PMID: 32339034 DOI: 10.1146/annurev-genom-083118-014915] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the last decade, exome and/or genome sequencing has become a common test in the diagnosis of individuals with features of a rare Mendelian disorder. Despite its success, this test leaves the majority of tested individuals undiagnosed. This review describes the Matchmaker Exchange (MME), a federated network established to facilitate the solving of undiagnosed rare-disease cases through data sharing. MME supports genomic matchmaking, the act of connecting two or more parties looking for cases with similar phenotypes and variants in the same candidate genes. An application programming interface currently connects six matchmaker nodes-the Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER), GeneMatcher, PhenomeCentral, seqr, MyGene2, and the Initiative on Rare and Undiagnosed Diseases (IRUD) Exchange-resulting in a collective data set spanning more than 150,000 cases from more than 11,000 contributors in 88 countries. Here, we describe the successes and challenges of MME, its individual matchmaking nodes, plans for growing the network, and considerations for future directions.
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422
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Hulsen T. Sharing Is Caring- Data Sharing Initiatives in Healthcare. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17093046. [PMID: 32349396 PMCID: PMC7246891 DOI: 10.3390/ijerph17093046] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/17/2020] [Accepted: 04/24/2020] [Indexed: 02/05/2023]
Abstract
In recent years, more and more health data are being generated. These data come not only from professional health systems, but also from wearable devices. All these 'big data' put together can be utilized to optimize treatments for each unique patient ('precision medicine'). For this to be possible, it is necessary that hospitals, academia and industry work together to bridge the 'valley of death' of translational medicine. However, hospitals and academia often are reluctant to share their data with other parties, even though the patient is actually the owner of his/her own health data. Academic hospitals usually invest a lot of time in setting up clinical trials and collecting data, and want to be the first ones to publish papers on this data. There are some publicly available datasets, but these are usually only shared after study (and publication) completion, which means a severe delay of months or even years before others can analyse the data. One solution is to incentivize the hospitals to share their data with (other) academic institutes and the industry. Here, we show an analysis of the current literature around data sharing, and we discuss five aspects of data sharing in the medical domain: publisher requirements, data ownership, growing support for data sharing, data sharing initiatives and how the use of federated data might be a solution. We also discuss some potential future developments around data sharing, such as medical crowdsourcing and data generalists.
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423
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Marks DF. Increasing the transparency, openness and replicability of psychological research: Mandatory data sharing for empirical studies in the Journal of Health Psychology. J Health Psychol 2020; 25:729-732. [PMID: 32330082 DOI: 10.1177/1359105320916858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This editorial announces this journal's policy on transparency, openness and replication. From 1 July 2020, authors of manuscripts submitted to Journal of Health Psychology (JHP) are required to make the raw data fully accessible to all readers. JHP will only consider manuscripts which follow an open publication model defined as follows: M = Mandatory, I = Inclusion (of), R = Raw, D = Data (MIRD). All data and analytical procedures must be sufficiently well described to enable a third party with the appropriate expertise to replicate the data analyses. It is expected that findings and analyses in the JHP will be fully capable of being accurately reproduced.
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424
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Baker BT, Damaraju E, Silva RF, Plis SM, Calhoun VD. Decentralized dynamic functional network connectivity: State analysis in collaborative settings. Hum Brain Mapp 2020; 41:2909-2925. [PMID: 32319193 PMCID: PMC7336163 DOI: 10.1002/hbm.24986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/17/2020] [Accepted: 03/04/2020] [Indexed: 11/11/2022] Open
Abstract
As neuroimaging data increase in complexity and related analytical problems follow suite, more researchers are drawn to collaborative frameworks that leverage data sets from multiple data‐collection sites to balance out the complexity with an increased sample size. Although centralized data‐collection approaches have dominated the collaborative scene, a number of decentralized approaches—those that avoid gathering data at a shared central store—have grown in popularity. We expect the prevalence of decentralized approaches to continue as privacy risks and communication overhead become increasingly important for researchers. In this article, we develop, implement and evaluate a decentralized version of one such widely used tool: dynamic functional network connectivity. Our resulting algorithm, decentralized dynamic functional network connectivity (ddFNC), synthesizes a new, decentralized group independent component analysis algorithm (dgICA) with algorithms for decentralized k‐means clustering. We compare both individual decentralized components and the full resulting decentralized analysis pipeline against centralized counterparts on the same data, and show that both provide comparable performance. Additionally, we perform several experiments which evaluate the communication overhead and convergence behavior of various decentralization strategies and decentralized clustering algorithms. Our analysis indicates that ddFNC is a fine candidate for facilitating decentralized collaboration between neuroimaging researchers, and stands ready for the inclusion of privacy‐enabling modifications, such as differential privacy.
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425
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Marovic B, Curcin V. Impact of the European General Data Protection Regulation (GDPR) on Health Data Management in a European Union Candidate Country: A Case Study of Serbia. JMIR Med Inform 2020; 8:e14604. [PMID: 32301736 PMCID: PMC7195664 DOI: 10.2196/14604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/27/2019] [Accepted: 10/06/2019] [Indexed: 12/04/2022] Open
Abstract
As of May 2018, all relevant institutions within member countries of the European Economic Area are required to comply with the European General Data Protection Regulation (GDPR) or face significant fines. This regulation has also had a notable effect on the European Union (EU) candidate countries, which are undergoing the process of harmonizing their legislature with the EU as part of the accession process. The Republic of Serbia is an example of such a candidate country, and its 2018 Personal Data Protection Act mirrors the majority of provisions in the GDPR. This paper presents the impact of the GDPR on health data management and Serbia’s capability to conduct international health data research projects. Data protection incidents reported in Serbia are explored to identify common underlying causes using a novel taxonomy of contributing factors across aspects and health system levels. The GDPR has an extraterritorial application for the non-EU data controllers who process the data of EU citizens and residents, which mainly affects private practices used by medical tourists from the EU, public health care institutions frequented by foreigners, as well as expatriates, dual citizens, tourists, and other visitors. Serbia generally does not have well-established procedures to support international research collaborations around its health data. For smaller projects, contractual arrangements can be made with health data providers and their ethics committees. Even then, organizations that have not previously participated in similar ventures may require approval or support from health authorities. Extensive studies that involve multisite data typically require the support of central health system institutions and relevant research data aggregators or electronic health record vendors. The lack of a framework for preparation, anonymization, and assurance of privacy preservation forces researchers to rely heavily on local expertise and support. Given the current limitation and potential issues with the legislation, it remains to be seen whether the move toward the GDPR will be beneficial for the Serbian health system, medical research, protection of personal data and privacy rights, and research capacity. Although significant progress has been made so far, a strategic approach is needed at the national level to address insufficient resources in the area of data protection and develop the personal data protection environment further. This will also require a targeted educational effort among health workers and decision makers, aiming to improve awareness and develop skills and knowledge necessary for the workforce.
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