Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future
| Autor: | Lennart Martens, Eric W. Deutsch, Oliver Kohlbacher, Nuno Bandeira, Juan Antonio Vizcaíno |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Proteomics
Information privacy Computer science Data management NIST National Institute of Standards and Technology Biochemistry PSM Peptide Spectrum Match Field (computer science) Analytical Chemistry NIH National Institutes of Health HIPAA Health Insurance Portability and Accountability DIA Data Independent Acquisition SMEs Small and Medium-sized Enterprises GEO Gene Expression Omnibus Data Management mass spectrometry media_common 0303 health sciences Variant Call Format 030302 biochemistry & molecular biology EGA European Genome-phenome Archive GA4GH Global Alliance for Genomics and Health 3. Good health DAC Data Access Committee General Data Protection Regulation Perspective CPTAC Clinical Proteome Tumor Analysis Consortium HCD Higher-energy collisional dissociation SAAVs Single Amino Acid Variants Personally identifiable information Confidentiality policy dbGAP database of Genotypes and Phenotypes IRB Institutional Review Board databases JGA Japanese Genotype-phenotype Archive VCF Variant Call Format EBI European Bioinformatics Institute AD Alzheimer’s disease GDPR General Data Protection Regulation 03 medical and health sciences PRM Parallel Reaction Monitoring Humans media_common.cataloged_instance European union Molecular Biology PII Personally Identifiable Information SRM Selected Reaction Monitoring 030304 developmental biology FDR False Discovery Rate MS Mass Spectrometry Information Dissemination business.industry controlled access data ethics Data science PTM Posttranslational Modification ComputingMethodologies_PATTERNRECOGNITION DDA Data-Dependent Acquisition business |
| Zdroj: | Molecular & Cellular Proteomics Molecular & Cellular Proteomics : MCP |
| ISSN: | 1535-9476 |
| Popis: | Today it is the norm that all relevant proteomics data that support the conclusions in scientific publications are made available in public proteomics data repositories. However, given the increase in the number of clinical proteomics studies, an important emerging topic is the management and dissemination of clinical, and thus potentially sensitive, human proteomics data. Both in the United States and in the European Union, there are legal frameworks protecting the privacy of individuals. Implementing privacy standards for publicly released research data in genomics and transcriptomics has led to processes to control who may access the data, so-called “controlled access” data. In parallel with the technological developments in the field, it is clear that the privacy risks of sharing proteomics data need to be properly assessed and managed. In our view, the proteomics community must be proactive in addressing these issues. Yet a careful balance must be kept. On the one hand, neglecting to address the potential of identifiability in human proteomics data could lead to reputational damage of the field, while on the other hand, erecting barriers to open access to clinical proteomics data will inevitably reduce reuse of proteomics data and could substantially delay critical discoveries in biomedical research. In order to balance these apparently conflicting requirements for data privacy and efficient use and reuse of research efforts through the sharing of clinical proteomics data, development efforts will be needed at different levels including bioinformatics infrastructure, policymaking, and mechanisms of oversight. Graphical Abstract Highlights • Availability of proteomics data in public repositories (ProteomeXchange) has become the norm. • There are growing ethical issues and legal requirements related to human clinical proteomics data. • We review the current state of the art and provide our thoughts about some proteomics data types. • We make concrete recommendations to address these issues, summarized in four different points. In Brief Availability of proteomics data in the public domain has become the norm, as it has been the case in genomics and transcriptomics for many years. Analogously to sequencing data, there are increasing ethical issues and legal requirements related to sensitive human clinical proteomics data. We review the current state of the art and make concrete recommendations to address these issues in the proteomics field, which are summarized in four different areas. |
| Databáze: | OpenAIRE |
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