Systematic reanalysis of genomic data by diagnostic laboratories: a scoping review of ethical, economic, legal and (psycho)social implications.

With the introduction of Next Generation Sequencing (NGS) techniques increasing numbers of disease-associated variants are being identified. This ongoing progress might lead to diagnoses in formerly undiagnosed patients and novel insights in already solved cases. Therefore, many studies suggest introducing systematic reanalysis of NGS data in routine diagnostics. Introduction will, however, also have ethical, economic, legal and (psycho)social (ELSI) implications that Genetic Health Professionals (GHPs) from laboratories should consider before possible implementation of systematic reanalysis. To get a first impression we performed a scoping literature review. Our findings show that for the vast majority of included articles ELSI aspects were not mentioned as such. However, often these issues were raised implicitly. In total, we identified nine ELSI aspects, such as (perceived) professional responsibilities, implications for consent and cost-effectiveness. The identified ELSI aspects brought forward necessary trade-offs for GHPs to consciously take into account when considering responsible implementation of systematic reanalysis of NGS data in routine diagnostics, balancing the various strains on their laboratories and personnel while creating optimal results for new and former patients. Some important aspects are not well explored yet. For example, our study shows GHPs see the values of systematic reanalysis but also experience barriers, often mentioned as being practical or financial only, but in fact also being ethical or psychosocial. Engagement of these GHPs in further research on ELSI aspects is important for sustainable implementation.

On the report of the ASHG "Facing Our History-Building an Equitable Future" initiative.

The American Society of Human Genetics (ASHG)-and the research community it supports-believes in the power of human genetics to advance science, health, and society. However, ASHG and the field have failed to acknowledge, fully and consistently, the misuse of human genetics to serve unjust ends or take action to denounce such use. As the community's oldest and largest professional society, ASHG also has been late in making explicit efforts to integrate equity, diversity, and inclusion into its values, programs, and voice. The Society affirmatively seeks to reckon with, and sincerely apologizes for, its involvement in and silence on the misuse of human genetics research to justify and contribute to injustices in all forms. It commits to sustain and expand its integration of equitable and just principles in the study and use of human genetics research, taking both immediate actions and swiftly determining longer-term goals it will set to realize the benefits of human genetics and genomics research for all.

Ethical Considerations in Research with Genomic Data.

Our ability to generate genomic data is currently well ahead of our ability to understand what they mean, raising challenges about how best to engage with them. This article considers ethical aspects of work with such data, focussing on research contexts that are intertwined with clinical care. We discuss the identifying nature of genomic data, the medical information intrinsic within them, and their linking of people within a biological family. We go on to consider what this means for consent, the importance of thoughtful sharing of genomic data, the challenge of constructing meaningful findings, and the legacy of unequal representation in genomic datasets. We argue that the ongoing success of genomic data research relies on public trust in the enterprise: to justify this trust, we need to ensure robust stewarding, and wide engagement about the ethical issues inherent in such practices.

Beyond inclusion: Enacting team equity in precision medicine research.

PURPOSE: To identify meanings of and challenges to enacting equitable diversification of genomics research, and specifically precision medicine research (PMR), teams. METHODS: We conducted in-depth interviews with 102 individuals involved in three U.S.-based precision medicine research consortia and conducted over 400 observation hours of their working group meetings, consortium-wide meetings, and conference presentations. We also reviewed published reports on genomic workforce diversity (WFD), particularly those relevant to the PMR community. RESULTS: Our study finds that many PMR teams encounter challenges as they strive to achieve equitable diversification on scientific teams. Interviewees articulated that underrepresented team members were often hired to increase the study's capacity to recruit diverse research participants, but are limited to on-the-ground staff positions with little influence over study design. We find existing hierarchies and power structures in the academic research ecosystem compound challenges for equitable diversification. CONCLUSION: Our results suggest that meaningful diversification of PMR teams will only be possible when team equity is prioritized as a core value in academic research communities.

Why sequence all eukaryotes?

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.

Ethical, legal, and social issues in the Earth BioGenome Project.

The Earth BioGenome Project (EBP) is an audacious endeavor to obtain whole-genome sequences of representatives from all eukaryotic species on Earth. In addition to the project's technical and organizational challenges, it also faces complicated ethical, legal, and social issues. This paper, from members of the EBP's Ethical, Legal, and Social Issues (ELSI) Committee, catalogs these ELSI concerns arising from EBP. These include legal issues, such as sample collection and permitting; the applicability of international treaties, such as the Convention on Biological Diversity and the Nagoya Protocol; intellectual property; sample accessioning; and biosecurity and ethical issues, such as sampling from the territories of Indigenous peoples and local communities, the protection of endangered species, and cross-border collections, among several others. We also comment on the intersection of digital sequence information and data rights. More broadly, this list of ethical, legal, and social issues for large-scale genomic sequencing projects may be useful in the consideration of ethical frameworks for future projects. While we do not-and cannot-provide simple, overarching solutions for all the issues raised here, we conclude our perspective by beginning to chart a path forward for EBP's work.

CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications.

In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.

Genética, Genómica y COVID-19: implicaciones éticas / Genetics, Genomic and COVID-19: ethical implications

Introducción: La genética y la genómica contribuyen al desarrollo de enfoques personalizados y más efectivos para la prevención y el tratamiento de enfermedades infecciosas. Durante la actual pandemia se realizan estudios genómicos a pacientes con COVID-19 o expuestos no afectados, para delinear los factores del huésped asociados con la variabilidad en la susceptibilidad, la infectividad y gravedad de la enfermedad. Objetivo: Describir las implicaciones éticas de la genética y genómica en la práctica clínica y la salud pública durante la pandemia de la COVID-19. Métodos: Se consultan las bases bibliográficas de PubMed/Medline y Google académico. Se describen las implicaciones éticas, beneficios y perjuicios relacionados con los estudios genéticos y genómicos, en la práctica clínica y la salud pública en la COVID-19. Conclusiones: Los estudios genéticos y genómicos desarrollados durante la pandemia de COVID-19 representan un logro de la coordinación y cooperación global(AU)

Introduction: Genetics and Genomic contribute to the development of personalized approaches and more effective for prevention and treatment of infectious diseases. During the current pandemics, genomic studies have been performed to patients with COVID-19 or expossed, non affected, to trace the factors of the associated host with the variability in the susceptibility, the infectivity and critical condition of the disease. Objective: To describe the ethical implications genetics and genomic in the clinical practice and public health during COVID-19 pandemic. Methods: Bibliographic bases such as PubMed/Medline and Google Scholar were consulted. The ethical implications, benefits and damages related to the genetics and genomic studies are described, in the clinical practice and public health in COVID-19. Conclusions: The genetics and genomic studies developed during COVID-19 pandemic represent an achievement of the global coordination and cooperation (AU)

Australian human research ethics committee members' confidence in reviewing genomic research applications.

Human research ethics committees (HRECs) are evaluating increasing quantities of genomic research applications with complex ethical considerations. Genomic confidence is reportedly low amongst many non-genetics-experts; however, no studies have evaluated genomic confidence levels in HREC members specifically. This study used online surveys to explore genomic confidence levels, predictors of confidence, and genomics resource needs of members from 185 HRECs across Australia. Surveys were fully or partially completed by 145 members. All reported having postgraduate 94 (86%) and/or bachelor 15 (14%) degrees. Participants consisted mainly of researchers (n = 45, 33%) and lay members (n = 41, 30%), affiliated with either public health services (n = 73, 51%) or public universities (n = 31, 22%). Over half had served their HREC [Formula: see text]3 years. Fifty (44%) reviewed genomic studies [Formula: see text]3 times annually. Seventy (60%) had undertaken some form of genomic education. While most (94/103, 91%) had high genomic literacy based on familiarity with genomic terms, average genomic confidence scores (GCS) were moderate (5.7/10, n = 119). Simple linear regression showed that GCS was positively associated with years of HREC service, frequency of reviewing genomic applications, undertaking self-reported genomic education, and familiarity with genomic terms (p < 0.05 for all). Conversely, lay members and/or those relying on others when reviewing genomic studies had lower GCSs (p < 0.05 for both). Most members (n = 83, 76%) agreed further resources would be valuable when reviewing genomic research applications, and online courses and printed materials were preferred. In conclusion, even well-educated HREC members familiar with genomic terms lack genomic confidence, which could be enhanced with additional genomic education and/or resources.

A virtual deliberative public engagement study on heritable genome editing among South Africans: Study protocol.

This article outlines the protocol for a prospective study for virtual deliberative public engagement on heritable genome editing in humans. The study intends to create a platform for a diverse group of 25-30 South Africans to engage with a facilitator and each other on 15 policy questions regarding heritable genome editing, with a focus on: a) the prevention of heritable genetic conditions; b) editing for immunity; and c) editing for enhancement. The aim is to understand the views on these issues so as to inform further research and policy, and to analyse the process and effect of deliberation on opinion. Participants will be expected to study the provided resource materials and pass the entrance exam-aligning with the protocols of the Harvard Personal Genome Project. In this way, the commitment, openness and basic knowledge of the candidates will be tested to ascertain whether they are suitable participants for the deliberative engagement.

Considerations for Cardiovascular Genetic and Genomic Research With Marginalized Racial and Ethnic Groups and Indigenous Peoples: A Scientific Statement From the American Heart Association.

Historically marginalized racial and ethnic groups and Indigenous peoples are burdened by significant health inequities that are compounded by their underrepresentation in genetic and genomic research. Of all genome-wide association study participants, ≈79% are of European descent, despite this group constituting only 16% of the global population. For underrepresented populations, polygenic risk scores derived from these studies are less accurate in predicting disease phenotypes, novel population-specific genetic variations may be misclassified as potentially pathogenic, and there is a lack of understanding of how different populations metabolize drugs. Although inclusion of marginalized racial and ethnic groups and Indigenous peoples in genetic and genomic research is crucial, scientific studies must be guided by ethical principles of respect, honesty, justice, reciprocity, and care for individuals and communities. Special considerations are needed to support research that benefits the scientific community as well as Indigenous peoples and marginalized groups. Before a project begins, collaboration with community leaders and agencies can lead to successful implementation of the study. Throughout the study, consideration must be given to issues such as implications of informed consent for individuals and communities, dissemination of findings through scientific and community avenues, and implications of community identity for data governance and sharing. Attention to these issues is critical, given historical harms in biomedical research that marginalized groups and Indigenous peoples have suffered. Conducting genetic and genomic research in partnership with Indigenous peoples and marginalized groups guided by ethical principles provides a pathway for scientific advances that will enhance prevention and treatment of cardiovascular disease for everyone.

Thinking about the idea of consent in data science genomics: How 'informed' is it?

In this paper we argue that 'informed' consent in Big Data genomic biobanking is frequently less than optimally informative. This is due to the particular features of genomic biobanking research which render it ethically problematic. We discuss these features together with details of consent models aimed to address them. Using insights from consent theory, we provide a detailed analysis of the essential components of informed consent which includes recommendations to improve consent performance. In addition, and using insights from philosophy of mind and language and psycholinguistics we support our analyses by identifying the nature and function of concepts (ideas) operational in human cognition and language together with an implicit coding/decoding model of human communication. We identify this model as the source of patients/participants poor understanding. We suggest an alternative, explicit model of human communication, namely, that of relevance-theoretic inference which obviates the limitations of the code model. We suggest practical strategies to assist health service professionals to ensure that the specific information they provide concerning the proposed treatment or research is used to inform participants' decision to consent. We do not prescribe a standard, formal approach to decision-making where boxes are ticked; rather, we aim to focus attention towards the sorts of considerations and questions that might usefully be borne in mind in any consent situation. We hope that our theorising will be of real practical benefit to nurses and midwives working on the clinical and research front-line of genomic science.

Has GWAS lost its status as a paragon of open science?

Genomic research led the way in open science, a tradition continued by genome-wide association studies (GWAS)-through the sharing of materials, results, and data. Coordinated quality control procedures also contributed to robust findings. However, recent years have seen declines in GWAS transparency. Here, we assess some shifts away from open science practices with the aim of stimulating a discussion of these issues.

Ethical, Legal, and Social Issues (ELSI) in Clinical Genetics Research.

ELSI (Ethical, Legal, and Social Issues) is a widely used acronym in the bioethics literature that encompasses a broad range of research examining the various impacts of science and technology on society. In Canada, GE3LS (Genetics, Ethical, Economic, Environmental, Legal, Social issues) is the term used to describe ELSI studies in the context of genetics and genomics research. It is intentionally more expansive in that GE3LS explicitly brings economic and environmental issues under its purview. ELSI/GE3LS research is increasingly relevant in recent years as there has been a greater emphasis on "translational research" that moves genomic discoveries from the bench to the clinic. The purpose of this chapter is to outline a range of ELSI-related work that might be conducted as part of a large scale genetics or genomics research project, and to provide some practical insights on how a scientific research team might incorporate a strong and effective ELSI program within its broader research mandate. We begin by describing the historical context of ELSI research and the development of GE3LS research in the Canadian context. We then illustrate how some ELSI research might unfold by outlining a variety of GE3LS research questions or content domains and the methodologies that might be employed in studying them. We conclude with some practical suggestions about how to build an effective ELSI/GE3LS team and focus within a broader scientific research program.