scholarly journals Privacy, anonymity and subjectivity in genomic research

2016 ◽  
Vol 98 ◽  
Author(s):  
IAN MCGONIGLE ◽  
NOAM SHOMRON
Keyword(s):  
International Law ◽  
Personal Data ◽  
Genetic Data ◽  
Genomic Research ◽  
Genome Data ◽  
Genomic Technologies ◽  
Biology Organization ◽  
Human Genome Data ◽  
European Molecular Biology Organization ◽  
Special Meeting

SummaryThe use of non-anonymized human genome data is becoming increasingly popular in research. Here we review the proceedings of a special meeting on this topic that took place at European Molecular Biology Organization (EMBO) in December 2014. The main points discussed centered on how to achieve ‘anonymity,’ ‘trust,’ and ‘protection of data’ in relation to new genomic technologies and research. Following our report of this meeting, we also raise three further issues for future consideration: the harmonization of international law in relation to genetic data protection; the complex issues around the ‘dividual’ nature of genetic data; and the growing commercial value of personal data. In conclusion, we stress the importance of scientists working in the area of genomic research engaging in interdisciplinary collaborations with humanities and social science scholars and addressing these complicated issues.

scholarly journals A Collection of 2,280 Public Domain (CC0) Curated Human Genotypes

2017 ◽  
Author(s):  
Richard J. Shaw ◽  
Manuel Corpas
Keyword(s):  
Human Genome ◽  
Data Aggregation ◽  
Personal Data ◽  
Public Domain ◽  
Genome Data ◽  
Public Data ◽  
Major Genome ◽  
Indexing Service ◽  
Human Genome Data ◽  
And Control

AbstractCheap sequencing has driven the proliferation of big human genome data aggregation consortiums, providing extensive reference datasets for genome research. These datasets, however, may come with restrictive terms of use, conditioned by the consent frameworks within which individuals donate their data. Having an aggregated genome dataset with unrestricted use, analogous to public domain licensing, is therefore unusually rare. Yet public domain data is tremendously useful because it allows freedom to perform research with it. This comes with the price of donors surrendering their privacy and accepting the associated risks derived from publishing personal data. Using the Repositive platform (https://repositive.io/?23andMe), an indexing service for human genome datasets, we aggregated all deposited files in public data sources under a CC0 license from 23andMe, a leading Direct-to-Consumer genetic testing service. After downloading 3,137 genotypes, we filtered out those that were incomplete, corrupt or duplicated, ending up with a dataset of 2,280 curated files, each one corresponding to a unique individual. Although the size of this dataset is modest compared to current major genome data aggregation projects, its full access and licensing terms, which allows free reuse without attribution, make it a useful reference pool for validation purposes and control experiments.

The protection of genetic information

2010 ◽  
pp. 91-113
Author(s):  
Juri Monducci
Keyword(s):  
Genetic Information ◽  
Personal Data ◽  
Genetic Data ◽  
Case Law ◽  
Genetic Determinism ◽  
Genetic Identity ◽  
Statutory Protection ◽  
Right Not To Know ◽  
Genetic Makeup ◽  
The Right

The law pertaining to personal data has developed in Italy over a thirty-year span that took us from recognition of such data in the case law, in 1975, to its statutory protection, in 2003. This evolution would subsequently come to the point of specifically regulating the processing of genetic data as data revealing an individual's genetic makeup, thereby also revealing the biological future of individuals and their offspring: this information describes an individual at a core level where the deepest, most unchangeable traits are found and can therefore nurture what is nowadays referred to as genetic determinism, which reduces the person to a complex of genetic data and so ignores the whole layer of characteristics that make each of us unique. There is, then, a discriminatory risk inherent in the processing of genetic data, and equally clear are the psychological implications of such processing, so much so that the need has arisen to have rules in place aimed at regulating the biotechnologies and genetics in particular. These rules have given birth to the so-called fourthgeneration rights, inclusive of the right to ones genetic identity and the right not to know ones genetics (although this is something that had been discussed earlier, too), and it is to a discussion of these rights that this essay is devoted.

scholarly journals FDA oversight of NSIGHT genomic research: the need for an integrated systems approach to regulation

2019 ◽  
Author(s):  
Laura V. Milko ◽  
Flavia Chen ◽  
Kee Chan ◽  
Amy M. Brower ◽  
Pankaj B. Agrawal ◽  
...  
Keyword(s):  
Clinical Research ◽  
Systems Approach ◽  
Genomic Sequence ◽  
Clinical Investigation ◽  
Risk Assessments ◽  
Genomic Research ◽  
Institutional Review Boards ◽  
Sequence Information ◽  
Genomic Technologies ◽  
Challenges And Opportunities

ABSTRACTThe National Institutes of Health (NIH) funded the Newborn Sequencing In Genomic medicine and public HealTh (NSIGHT) Consortium to investigate the implications, challenges and opportunities associated with the possible use of genomic sequence information in the newborn period. Following announcement of the NSIGHT awardees in 2013, the Food and Drug Administration (FDA) contacted investigators and requested that pre-submissions to investigational device exemptions (IDE) be submitted for the use of genomic sequencing under Title 21 of the Code of Federal Regulations (21 CFR) part 812. IDE regulation permits clinical investigation of medical devices that have not been approved by the FDA. To our knowledge, this marked the first time the FDA determined that NIH-funded clinical genomic research projects are subject to IDE regulation. Here we review the history of and rationale behind FDA oversight of clinical research and the NSIGHT Consortium’s experiences in navigating the IDE process. Overall, NSIGHT investigators found that FDA’s application of existing IDE regulations and medical device definitions aligned imprecisely with the aims of publicly funded exploratory clinical research protocols. IDE risk assessments by the FDA were similar to, but distinct from, protocol risk assessments conducted by local Institutional Review Boards (IRBs), and had the potential to reflect novel oversight of emerging genomic technologies. However, the pre-IDE and IDE process delayed the start of NSIGHT research studies by an average of 10 months, and significantly limited the scope of investigation in two of the four NIH approved projects. Based on the experience of the NSIGHT Consortium, we conclude that policies and practices governing the development and use of novel genomic technologies in clinical research urgently need clarification in order to mitigate potentially conflicting or redundant oversight by IRBs, NIH, FDA, and state authorities.

scholarly journals Role of Legal Principles in Eliminating and Minimizing the Risks of Genomic Technologies

Lex Russica ◽  
2019 ◽  
pp. 121-128 ◽  
Author(s):  
M. N. Maleina
Keyword(s):  
Genetic Information ◽  
Personal Data ◽  
Negative Consequences ◽  
Genetic Characteristics ◽  
Legal Principles ◽  
Genomic Technologies ◽  
Preventive Actions ◽  
The Individual ◽  
Modern Genomic

The use of modern genomic technologies, along with the benefits to the man and society, can lead to negative consequences. Such risks exist both in the process and after the production, isolation, modification, storage of DNA. Prior to detailed legislative regulation of relations regarding the use of genomic technologies for medicinal purposes and not for medical reasons, legal principles become vital.The paper formulates the following basic legal principles of genomic technologies application: the principle of preventive actions of the state to protect citizens from the risks of using genomic technologies; the principle of preserving the human genome as a special species; the principle of guaranteeing the inviolability of the individual of every citizen when using genomic technologies; the principle of priority of life and health of citizens over the interests of science and society; the principle of equality of citizens regardless of genetic characteristics; the principle of protection of genetic information of every citizen as part of personal data; the principle of guaranteeing access to the citizen’s own genetic information. Legal principles can be used to resolve a dispute by analogy of law.

scholarly journals Prawo właściwe dla zobowiązań deliktowych wynikających z naruszenia zasad ochrony danych osobowych przyjętych w RODO

2020 ◽  
pp. 39-59
Author(s):  
Marek Świerczyński
Keyword(s):  
European Union ◽  
International Law ◽  
Personal Data ◽  
Civil Procedure ◽  
Private International Law ◽  
The European Union ◽  
Applicable Law ◽  
National Courts ◽  
International Data ◽  
Conflict Of Law

Disputes arising from international data breaches can be complex. Despite the introduction of new, unified EU regulation on the protection of personal data (GDPR), the European Union failed to amend the Rome II Regulation on the applicable law to non-contractual liability and to extend its scope to the infringements of privacy. GDPR only contains provisions on international civil procedure. However, there are no supplementing conflict-of-law rules. In order to determine the applicable law national courts have to apply divergent and dispersed national codifications of private international law. The aim of this study is to propose an optimal conflict-of-law model for determining the applicable law in case of infringement of the GDPR’s privacy regime.

scholarly journals Accuracy and efficiency of germline variant calling pipelines for human genome data

2020 ◽  
Author(s):  
Sen Zhao ◽  
Oleg Agafonov ◽  
Abdulrahman Azab ◽  
Tomasz Stokowy ◽  
Eivind Hovig
Keyword(s):  
Large Scale ◽  
Variant Calling ◽  
Performance Comparison ◽  
Next Generation Sequencing Technology ◽  
Genome Data ◽  
Germline Variant ◽  
Causal Variants ◽  
Variant Detection ◽  
Variant Analysis ◽  
Human Genome Data

AbstractAdvances in next-generation sequencing technology has enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data, however there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN™ and DeepVariant) using Genome in a Bottle Consortium, “synthetic-diploid” and simulated WGS datasets. DRAGEN™ and DeepVariant show a better accuracy in SNPs and indels calling, with no significant differences in their F1-score. DRAGEN™ platform offers accuracy, flexibility and a highly-efficient running speed, and therefore superior advantage in the analysis of WGS data on a large scale. The combination of DRAGEN™ and DeepVariant also provides a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical application.

scholarly journals Orthology between the genomes of Plasmodium falciparum and rodent malaria parasites: possible practical applications

2002 ◽  
Vol 357 (1417) ◽  
pp. 55-63 ◽  
Author(s):  
A. P. Waters
Keyword(s):  
Plasmodium Falciparum ◽  
Gene Function ◽  
Proteome Analysis ◽  
Experimental System ◽  
Genomic Research ◽  
Experimental Investigations ◽  
Practical Applications ◽  
Genome Data ◽  
Entire Sequence ◽  
Regulated Gene Expression

The work of the consortium that has been formed to complete the entire sequence of the genome of a selected clone of the human malaria parasite, Plasmodium falciparum , is almost finished. Already huge tracts of the genome are available as fully assembled chromosomes or large contigs and the work of initial annotation is in an advanced state. Post–genomic research is in one sense the process of furthering the process of annotation, creating biological atlases and preliminary attempts to make global descriptions of gene transcription and proteome analysis are underway. Comparison between significant amounts of genome data from both closely, and more distantly related organisms, can facilitate the identification of genes themselves, coordinately regulated gene expression groups, gene function and genome organization. Models of malaria can fulfil these functions and in addition provide an experimental system wherein predictions can be tested and basic experimental investigations performed within numerous aspects of disease, pathology, parasite–host and parasite–vector interactions. Comparative genomics in Plasmodium has already been shown to have informative roles in the completion of annotation and the elucidation of gene function. These roles will be illustrated by example and used as the basis for a discussion of the utility of genome information and malaria models in realizing the desired product of Plasmodium genomics, the development of malaria therapies.

Consent for Use of Genetic Data among US Hispanics/Latinos: Results from the Hispanic Community Health Study/ Study of Latinos

2021 ◽  
Vol 31 (4) ◽  
pp. 547-558
Author(s):  
Sara Gonzalez ◽  
Garrett Strizich ◽  
Carmen R. Isasi ◽  
Simin Hua ◽  
Betsy Comas ◽  
...  
Keyword(s):  
Community Health ◽  
Data Sharing ◽  
Genetic Data ◽  
Genomic Research ◽  
Health Study ◽  
Medicine Research ◽  
For Profit ◽  
Hispanic Community ◽  
Precision Medicine Research

Inclusion of historically underrepresented populations in biomedical research is critical for large precision medicine research initia­tives. Among 13,721 Hispanic Community Health Study/Study of Latinos (HCHS/SOL) enrollees, we used multivariable-adjusted prevalence ratios to describe characteristics associated with participants’ willingness to consent to different levels of biospecimen and genetic data analysis and sharing. At baseline (2008-2011), HCHS/SOL par­ticipants almost universally consented to the use of biospecimens and genetic data by study investigators and their collabora­tors (97.6%; 95%CI: 97.1, 98.0). Fewer consented to biospecimen and genetic data sharing with investigators not affiliated with the HCHS/SOL research team (81%, 95%CI: 80, 82) or any data sharing with commer­cial/for-profit entities (75%, 95%CI: 74, 76). Those refusing to share their data beyond the study investigators group were more often females, Spanish language-speakers and non-US born individuals. As expected, participants who were retained and recon­sented at the six-year follow up visit tended to embrace broader data sharing, although this varied by group. Over time, Puerto Ricans and Dominicans were more likely to convert to broader data sharing than individuals of a Mexican background. Our analysis suggests that acculturation and im­migration status of specific Hispanic/Latino communities may influence decisions about participation in genomic research projects and biobanks. Ethn Dis. 2021;31(4):547- 558; doi:10.18865/ed.31.4.547

Article 9 Processing of special categories of personal data

2020 ◽  
Author(s):  
Ludmila Georgieva ◽  
Christopher Kuner
Keyword(s):  
Decision Making ◽  
Data Protection ◽  
Personal Data ◽  
Genetic Data ◽  
Biometric Data ◽  
Individual Decision Making ◽  
Vital Interest ◽  
Data Portability ◽  
Definition Of ◽  
Data Subject

Article 4(1) (Definition of personal data); Article 4(2) (Definition of processing); Article 4(11) (Definition of consent); Article 4(13) (Definition of genetic data, see also recital 34); Article 4(14) (Definition of biometric data); Article 4(15) (Definition of data concerning health, see also recital 35); Article 6(4)(c) (Lawfulness of processing, compatibility test) (see too recital 46 on vital interest); Article 13(2)(c) (Information to be provided where personal data are collected from the data subject); Article 17(1)(b), (3)(c) (Right to erasure (‘right to be forgotten’)); Article 20(1)(a) (Right to data portability); Article 22(4) (Automated individual decision-making, including profiling); Article 27(2)(a) (Representatives of controllers or processors not established in the Union); Article 30(5) (Records of processing activities); Article 35(3)(b) (Data protection impact assessment) (see too recital 91); Article 37(1)(c) (Designation of the data protection officer) (see too recital 97); Article 83(5)(a) (General conditions for imposing administrative fines).

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