scholarly journals “Who is watching the watchdog?”: ethical perspectives of sharing health-related data for precision medicine in Singapore

2020 ◽  
Author(s):  
Tamra Lysaght ◽  
Angela Ballantyne ◽  
Vicki Xafis ◽  
Serene Ong ◽  
Gerald Owen Schaefer ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Data Sharing ◽  
Data Security ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Public Trust ◽  
International Perspective ◽  
Research Participants ◽  
Related Data ◽  
Trade Offs

Abstract Background We aimed to examine the ethical concerns Singaporeans have about sharing health-data for precision medicine (PM) and identify suggestions for governance strategies. Just as Asian genomes are under-represented in PM, the views of Asian populations about the risks and benefits of data sharing are under-represented in prior attitudinal research.Methods We conducted seven focus groups with 62 participants in Singapore from May to July 2019. They were conducted in three languages (English, Mandarin and Malay) and analysed with qualitative content and thematic analysis. Results Four key themes emerged: nuanced understandings of data security and data sensitivity; trade-offs between data protection and research benefits; trust (and distrust) in the public and private sectors; and governance and control options. Participants were aware of the inherent risks associated with data sharing for research. Participants expressed conditional support for data sharing, including genomic sequence data and information contained within electronic medical records. This support included sharing data with researchers from universities and healthcare institutions, both in Singapore and overseas. Support was conditional on the perceived social value of the research and appropriate de-identification and data security processes. Participants suggested that a data sharing oversight body would help strengthen public trust and comfort in data research for PM in Singapore.Conclusion Maintenance of public trust in data security systems and governance regimes can enhance participation in PM and data sharing for research. Contrary to themes in much prior research, participants demonstrated a sophisticated understanding of the inherent risks of data sharing, analysed trade-offs between risks and potential benefits of PM, and often adopted an international perspective.

scholarly journals “Who is watching the watchdog?”: ethical perspectives of sharing health-related data for precision medicine in Singapore

2020 ◽  
Author(s):  
Tamra Lysaght ◽  
Angela Ballantyne ◽  
Vicki Xafis ◽  
Serene Ong ◽  
Gerald Owen Schaefer ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Data Sharing ◽  
Data Security ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Public Trust ◽  
International Perspective ◽  
Research Participants ◽  
Related Data ◽  
Trade Offs

Abstract Background We aimed to examine the ethical concerns Singaporeans have about sharing health-data for precision medicine (PM) and identify suggestions for governance strategies. Just as Asian genomes are under-represented in PM, the views of Asian populations about the risks and benefits of data sharing are under-represented in prior attitudinal research.Methods We conducted seven focus groups with 62 participants in Singapore from May to July 2019. They were conducted in three languages (English, Mandarin and Malay) and analysed with qualitative content and thematic analysis. Results Four key themes emerged: nuanced understandings of data security and data sensitivity; trades-offs between data protection and research benefits; trust (and distrust) in the public and private sectors; and governance and control options. Participants were aware of the inherent risks associated with data sharing for research. Participants expressed conditional support for data sharing, including genomic sequence data and information contained within electronic medical records. This support included sharing data with researchers from universities and healthcare institutions, both in Singapore and overseas. Support was conditional on the perceived social value of the research and appropriate de-identification and data security processes. Participants suggested that a data sharing oversight body would help strengthen public trust and comfort in data research for PM in Singapore.Conclusion Maintenance of public trust in data security systems and governance regimes can enhance participation in PM and data sharing for research. Contrary to themes in much prior research, participants demonstrated a sophisticated understanding of the inherent risks of data sharing, analysed trade-offs between risks and potential benefits of PM, and often adopted an international perspective.

scholarly journals “Who is watching the watchdog?”: ethical perspectives of sharing health-related data for precision medicine in Singapore

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Tamra Lysaght ◽  
Angela Ballantyne ◽  
Vicki Xafis ◽  
Serene Ong ◽  
Gerald Owen Schaefer ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Data Sharing ◽  
Data Security ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Public Trust ◽  
International Perspective ◽  
Research Participants ◽  
Related Data ◽  
Trade Offs

Abstract Background We aimed to examine the ethical concerns Singaporeans have about sharing health-data for precision medicine (PM) and identify suggestions for governance strategies. Just as Asian genomes are under-represented in PM, the views of Asian populations about the risks and benefits of data sharing are under-represented in prior attitudinal research. Methods We conducted seven focus groups with 62 participants in Singapore from May to July 2019. They were conducted in three languages (English, Mandarin and Malay) and analysed with qualitative content and thematic analysis. Results Four key themes emerged: nuanced understandings of data security and data sensitivity; trade-offs between data protection and research benefits; trust (and distrust) in the public and private sectors; and governance and control options. Participants were aware of the inherent risks associated with data sharing for research. Participants expressed conditional support for data sharing, including genomic sequence data and information contained within electronic medical records. This support included sharing data with researchers from universities and healthcare institutions, both in Singapore and overseas. Support was conditional on the perceived social value of the research and appropriate de-identification and data security processes. Participants suggested that a data sharing oversight body would help strengthen public trust and comfort in data research for PM in Singapore. Conclusion Maintenance of public trust in data security systems and governance regimes can enhance participation in PM and data sharing for research. Contrary to themes in much prior research, participants demonstrated a sophisticated understanding of the inherent risks of data sharing, analysed trade-offs between risks and potential benefits of PM, and often adopted an international perspective.

scholarly journals "Who is Watching the Watchdog?": Ethical Perspectives of Sharing Health-related Data for Precision Medicine in Singapore

2020 ◽  
Author(s):  
Tamra Lysaght ◽  
Angela Ballantyne ◽  
Vicki Xafis ◽  
Serene Ong ◽  
Gerald Owen Schaefer ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Data Sharing ◽  
Data Security ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Public Trust ◽  
International Perspective ◽  
Research Participants ◽  
Related Data ◽  
Trade Offs

Abstract Background: We aimed to examine the ethical concerns Singaporeans have about sharing health-data for precision medicine (PM) and identify suggestions for governance strategies. Just as Asian genomes are under-represented in PM, the views of Asian populations about the risks and benefits of data sharing are under-represented in prior attitudinal research. Methods: We conducted seven focus groups with 62 participants in Singapore from May to July 2019. They were conducted in three languages (English, Mandarin and Malay) and analysed with qualitative content and thematic analysis. Results: Four key themes emerged: nuanced understandings of data security and data sensitivity; trades-offs between data protection and research benefits; trust (and distrust) in the public and private sectors; and governance and control options. Participants were aware of the inherent risks associated with data sharing for research. Participants expressed conditional support for data sharing, including genomic sequence data and information contained within electronic medical records. This support included sharing data with researchers from universities and healthcare institutions, both in Singapore and overseas. Support was conditional on the perceived social value of the research and appropriate de-identification and data security processes. Participants suggested that a data sharing oversight body would help strengthen public trust and comfort in data research for PM in Singapore. Conclusion: Maintenance of public trust in data security systems and governance regimes can enhance participation in PM and data sharing for research. Contrary to themes in much prior research, participants demonstrated a sophisticated understanding of the inherent risks of data sharing, analysed trade-offs between risks and potential benefits of PM, and often adopted an international perspective.

scholarly journals Artificial intelligence, physiological genomics, and precision medicine

2018 ◽  
Vol 50 (4) ◽  
pp. 237-243 ◽  
Author(s):  
Anna Marie Williams ◽  
Yong Liu ◽  
Kevin R. Regner ◽  
Fabrice Jotterand ◽  
Pengyuan Liu ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Big Data ◽  
Precision Medicine ◽  
Ethical Issues ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Common Diseases ◽  
Powerful Approach ◽  
Genetic And Environmental Factors ◽  
Analytical Approaches

Big data are a major driver in the development of precision medicine. Efficient analysis methods are needed to transform big data into clinically-actionable knowledge. To accomplish this, many researchers are turning toward machine learning (ML), an approach of artificial intelligence (AI) that utilizes modern algorithms to give computers the ability to learn. Much of the effort to advance ML for precision medicine has been focused on the development and implementation of algorithms and the generation of ever larger quantities of genomic sequence data and electronic health records. However, relevance and accuracy of the data are as important as quantity of data in the advancement of ML for precision medicine. For common diseases, physiological genomic readouts in disease-applicable tissues may be an effective surrogate to measure the effect of genetic and environmental factors and their interactions that underlie disease development and progression. Disease-applicable tissue may be difficult to obtain, but there are important exceptions such as kidney needle biopsy specimens. As AI continues to advance, new analytical approaches, including those that go beyond data correlation, need to be developed and ethical issues of AI need to be addressed. Physiological genomic readouts in disease-relevant tissues, combined with advanced AI, can be a powerful approach for precision medicine for common diseases.

scholarly journals Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

2017 ◽  
Author(s):  
Gil Alterovitz ◽  
Dennis Dean ◽  
Carole Goble ◽  
Michael R. Crusoe ◽  
Stian Soiland-Reyes ◽  
...  
Keyword(s):  
Precision Medicine ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Data Provenance ◽  
Provenance Analysis ◽  
Link Type ◽  
Sequencing Studies ◽  
Standardized Reporting ◽  
Personalized Approach

AbstractA personalized approach based on a patient’s or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to FAIR guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet lab procedures to computational methods. The BioCompute framework (https://osf.io/zm97b/) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCO) offer that standard, and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development”. By communication of high-throughput sequencing studies using a BCO, regulatory agencies (e.g., FDA), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next generation sequencing workflow exchange, reporting, and regulatory reviews.

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

A New User-controlled and Efficient Encrypted Data Sharing Model in Cloud Storage

2019 ◽  
Vol 13 (4) ◽  
pp. 356-363
Author(s):  
Yuezhong Wu ◽  
Wei Chen ◽  
Shuhong Chen ◽  
Guojun Wang ◽  
Changyun Li
Keyword(s):  
Data Sharing ◽  
Data Security ◽  
Cloud Storage ◽  
Screening Program ◽  
Original Data ◽  
Third Party ◽  
Active System ◽  
Encrypted Data ◽  
Active User ◽  
User Data

Background: Cloud storage is generally used to provide on-demand services with sufficient scalability in an efficient network environment, and various encryption algorithms are typically applied to protect the data in the cloud. However, it is non-trivial to obtain the original data after encryption and efficient methods are needed to access the original data. Methods: In this paper, we propose a new user-controlled and efficient encrypted data sharing model in cloud storage. It preprocesses user data to ensure the confidentiality and integrity based on triple encryption scheme of CP-ABE ciphertext access control mechanism and integrity verification. Moreover, it adopts secondary screening program to achieve efficient ciphertext retrieval by using distributed Lucene technology and fine-grained decision tree. In this way, when a trustworthy third party is introduced, the security and reliability of data sharing can be guaranteed. To provide data security and efficient retrieval, we also combine active user with active system. Results: Experimental results show that the proposed model can ensure data security in cloud storage services platform as well as enhance the operational performance of data sharing. Conclusion: The proposed security sharing mechanism works well in an actual cloud storage environment.

scholarly journals Special Issue: Genetic Basis of Phenotypic Variation in Drosophila and Other Insects

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1212
Author(s):  
J. Spencer Johnston ◽  
Carl E. Hjelmen
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Basis ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Complete Genomic Sequence ◽  
Special Issue ◽  
Model Species ◽  
Road Map ◽  
Generation Sequencing ◽  
Complete Genomic

Next-generation sequencing provides a nearly complete genomic sequence for model and non-model species alike; however, this wealth of sequence data includes no road map [...]

scholarly journals Data Dentistry: How Data Are Changing Clinical Care and Research

2021 ◽  
pp. 002203452110202
Author(s):  
F. Schwendicke ◽  
J. Krois
Keyword(s):  
Health Care ◽  
Data Sharing ◽  
Clinical Care ◽  
Open Data ◽  
User Interaction ◽  
Data Availability ◽  
Related Data ◽  
Data User ◽  
Regulatory Data ◽  
Consumer Data

Data are a key resource for modern societies and expected to improve quality, accessibility, affordability, safety, and equity of health care. Dental care and research are currently transforming into what we term data dentistry, with 3 main applications: 1) medical data analysis uses deep learning, allowing one to master unprecedented amounts of data (language, speech, imagery) and put them to productive use. 2) Data-enriched clinical care integrates data from individual (e.g., demographic, social, clinical and omics data, consumer data), setting (e.g., geospatial, environmental, provider-related data), and systems level (payer or regulatory data to characterize input, throughput, output, and outcomes of health care) to provide a comprehensive and continuous real-time assessment of biologic perturbations, individual behaviors, and context. Such care may contribute to a deeper understanding of health and disease and a more precise, personalized, predictive, and preventive care. 3) Data for research include open research data and data sharing, allowing one to appraise, benchmark, pool, replicate, and reuse data. Concerns and confidence into data-driven applications, stakeholders’ and system’s capabilities, and lack of data standardization and harmonization currently limit the development and implementation of data dentistry. Aspects of bias and data-user interaction require attention. Action items for the dental community circle around increasing data availability, refinement, and usage; demonstrating safety, value, and usefulness of applications; educating the dental workforce and consumers; providing performant and standardized infrastructure and processes; and incentivizing and adopting open data and data sharing.

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