Monthly Digest :: Blog Posts

  • Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life
    AM Mc Cartney, J Anderson, L Liggins, et al.
    Perspective, Evolution
    PNAS, January 18, 2022, 119 (4) e2115860119
    Abstract
    The field of genomics has benefited greatly from its “openness” approach to data sharing. However, with the increasing volume of sequence information being created and stored and the growing number of international genomics efforts, the equity of openness is under question. The United Nations Convention of Biodiversity aims to develop and adopt a standard policy on access and benefit-sharing for sequence information across signatory parties. This standardization will have profound implications on genomics research, requiring a new definition of open data sharing. The redefinition of openness is not unwarranted, as its limitations have unintentionally introduced barriers of engagement to some, including Indigenous Peoples. This commentary provides an insight into the key challenges of openness faced by the researchers who aspire to protect and conserve global biodiversity, including Indigenous flora and fauna, and presents immediate, practical solutions that, if implemented, will equip the genomics community with both the diversity and inclusivity required to respectfully protect global biodiversity.

  • Moving from ‘fully’ to ‘appropriately’ informed consent in genomics: The PROMICE framework
    Julian J Koplin, Christopher Gyngell, Julian Savulescu, Danya F Vears
    Bioethics, 7 April 2022
    Abstract
    Genomic sequencing technologies (GS) pose novel challenges not seen in older genetic technologies, making traditional standards for fully informed consent difficult or impossible to meet. This is due to factors including the complexity of the test and the broad range of results it may identify. Meaningful informed consent is even more challenging to secure in contexts involving significant time constraints and emotional distress, such as when rapid genomic testing (RGS) is performed in neonatal intensive care units. In this article, we propose that informed consent matters not for its own sake, but because obtaining it furthers a range of morally important goals, such as promoting autonomy, well-being, and trust in medicine. These goals form the basis of a new framework [PROmoting Morally Important Consent Ends (PROMICE)] for assessing the ethical appropriateness of various informed consent models. We illustrate this framework with two examples: (a) a tiered and layered consent model for obtaining consent for GS, and (b) consent for RGS in critically ill newborns. We conclude that appropriately-rather than fully-informed consent provides the correct standard for genomic medicine and research.

  • Informed consent, genomic research and mental health: A integrative review
    Nina Kilkku, Arja Halkoaho
    Nursing ethics, 4 February 2022
    Open Access
    Abstract
    Background
    Research on genomics has increased while the biobank activities are becoming more common in different countries. In the mental health field, the questions concerning the potential participants’ vulnerability as well as capacity to give the informed consent can cause reluctancy in recruiting persons with mental health problems, although the knowledge and understanding of mental health problems has remarkably changed, and practice is guided with inclusive approaches, such as recovery approach.
    Aim
    The aim of this study was to describe the current knowledge of informed consent practices in the context of genomic research on mental health from the nurses’ viewpoint.
    Methods
    An integrative review was conducted with search from seven international databases. Data consist 14 publications which were analyzed with thematic analysis.
    Ethical considerations
    Ethical requirements were respected in every phase of the research process.
    Findings
    Most of the papers were published in USA and between 2000-2010. Eight reports were categorized as discussion papers, four qualitative studies and one quantitative study. The thematic analysis provided 7 information on five themes: complexity with the capacity to consent, mixed emotions towards participation, factors influencing the decision to participate, nurses’ informed consent process competence and variations between consent procedures.
    Discussion
    In the informed consent practices, there are various aspects which may affect both the willingness to participate in the study and the informed consent process itself. Implications for practice, education, research, and policies are discussed.
    Conclusion
    There is a need for more updated international research on the topic in the context of different international and national guidelines, legislation, and directives. This study provided a viewpoint to the more collaborative research activities with people with lived experiences also in this field of research following the ideas of recovery approach.

  • Informed consent practices for exome sequencing: An interview study with clinical geneticists in the Netherlands
    Original Article
    Wendy Bos, Eline M. Bunnik
    Molecular Genetics & Genomic Medicine, 14 January 2022
    Open Access
    Abstract
    Background
    Genomic sequencing is being used more frequently in the clinic, not only by clinical geneticists, but also by other specialists (“mainstreaming”). The use of genomic sequencing gives rise to challenges regarding informed consent, as it can yield more, and more complex results.
    Methods
    This study maps the informed consent process for exome sequencing in the Netherlands by means of semistructured interviews with 14 clinical geneticists. Interviewees were asked about their strategies for informing patients about exome sequencing and supporting patients in their decision making, about what they think of as essential information elements, about the challenges they experience, and about their preferences for future policy and practice.
    Results
    Clinical geneticists typically discuss the following topics: the nature and aim of the test, the possible results (including unsolicited or incidental findings and Variants of Uncertain Significance) of the test and the consequences of those results for the patient and their family members. Some clinical geneticists use a layered approach to informed consent, meaning that they give short and concise information at first, and provide more detailed information depending on the situation or the needs of the patient.
    Conclusion
    During pre-test counseling for genomic sequencing, clinical geneticists use various strategies to enhance patient understanding and personalization of the informed consent process. Going forward, layering information may be part of a solution to ethical challenges of informed consent, also in mainstream settings.

  • Functional genomics data: privacy risk assessment and technological mitigation
    Gamze Gürsoy, Tianxiao Li, Mark B. Gerstein
    Perspective | 10 November 2021
    Nature Reviews Genetics
    Abstract
    The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy challenges, some of which are analogous to those that occur when sharing genetic variant data. However, there are also unique privacy challenges that arise from cryptic information leakage during the processing and summarization of functional genomics data from raw reads to derived quantities, such as gene expression values. Here, we review these challenges and present potential solutions for mitigating privacy risks while allowing broad data dissemination and analysis.

  • Ethical, legal, and social issues in the Earth BioGenome Project
    Jacob S. Sherkow, Katharine B. Barker, Robert Cook-Deegan, Richard Durbin et al.
    Perspective, Evolution
    PNAS, January 18, 2022 | 119 (4) e2115859119
    Abstract
    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.

  • The Human Pangenome Project: a global resource to map genomic diversity
    Ting Wang, Lucinda Antonacci-Fulton, David Haussler
    Perspective | 20 April 2022
    Nature, Volume 604 Issue 7906, 21 April 2022
    The Human Pangenome Reference Consortium aims to offer the highest quality and most complete human pangenome reference that provides diverse genomic representation across human populations.
    Abstract
    The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene–disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.

  • Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa
    Segun Fatumo, Joseph Mugisha, Opeyemi Soremekun, Allan Kalungi, Richard Mayanja, Christopher Kintu, Ronald Makanga, Ayoub Kakande, Andrew Abaasa, Gershim Asiki, Robert Kalyesubula, Robert Newton, Moffat Nyirenda, Manjinder S Sandhu, Pontiano Kaleebu
    medRxiv, 2022.05.05.22274740; doi: https://doi.org/10.1101/2022.05.05.22274740
    Abstract
       The Uganda Genome Resource (UGR) is a well characterised genomic database, with a range of phenotypic communicable and non-communicable diseases and risk factors generated from the Uganda General Population Cohort (GPC) – a population-based open cohort study established in 1989 by the Medical Research Council (MRC) UK in collaboration with the Uganda Virus Research Institute (UVRI).

    In 2011, UGR was launched with genotype data on ∼5000 and whole genome sequence data on ∼2000 Ugandan individuals from 9 ethno-linguistic groups. Leveraging other available platforms at the MRC Uganda such as Biorepository centre for sample storage, Clinical Diagnostic Laboratory Service (CDLS) for sample diagnostic testing, sequencing platform for DNA extraction, Uganda Medical informatics Unit (UMIC) for large-scale data analysis, GPC for additional sample collection, UGR is strategically poised to expand and generate scientific discoveries.

    Here, we describe UGR and highlight the important genetic findings thus far including how UGR is providing opportunities to: (1) discover novel disease susceptibility genetic loci; (2) refine association signals at new and existing loci; (3) develop and test Polygenic Risk Score (PRS) to determine individual’s disease risk; 4) assess how some risk factors including infectious diseases are causally related to non-communicable diseases (NCDs) in Africa; (5) develop research capacity for genomics in Africa; and (6) enhance African participation in the global genomics research arena. Leveraging established research infrastructure, expertise, local genomic leadership, global collaboration and strategic funding, we anticipate that UGR can develop further to a comparable level of European and Asian large-scale genomic initiatives.

  • Participant recall and understandings of information on biobanking and future genomic research: experiences from a multi-disease community-based health screening and biobank platform in rural South Africa
    Authors: Manono Luthuli, Nothando Ngwenya, Dumsani Gumede, Resign Gunda, Dickman Gareta, Olivier Koole, Mark J. Siedner, Emily B. Wong and Janet Seeley
    Research  Open Access
    BMC Medical Ethics, 2022 23:43  Published on: 18 April 2022
    Abstract
    Background
    Limited research has been conducted on explanations and understandings of biobanking for future genomic research in African contexts with low literacy and limited healthcare access. We report on the findings of a sub-study on participant understanding embedded in a multi-disease community health screening and biobank platform study known as ‘Vukuzazi’ in rural KwaZulu-Natal, South Africa.
    Methods
    Semi-structured interviews were conducted with research participants who had been invited to take part in the Vukuzazi study, including both participants and non-participants, and research staff that worked on the study. The interviews were transcribed, and themes were identified from the interview transcripts, manually coded, and thematically analysed.
    Results
    Thirty-nine individuals were interviewed. We found that the research team explained biobanking and future genomic research by describing how hereditary characteristics create similarities among individuals. However, recollection and understanding of this explanation seven months after participation was variable. The large volume of information about the Vukuzazi study objectives and procedures presented a challenge to participant recall. By the time of interviews, some participants recalled rudimentary facts about the genetic aspects of the study, but many expressed little to no interest in genetics and biobanking.
    Conclusion
    Participant’s understanding of information related to genetics and biobanking provided during the consent process is affected by the volume of information as well as participant’s interest (or lack thereof) in the subject matter being discussed. We recommend that future studies undertaking biobanking and genomic research treat explanations of this kind of research to participants as an on-going process of communication between researchers, participants and the community and that explanatory imagery and video graphic storytelling should be incorporated into theses explanations as these have previously been found to facilitate understanding among those with low literacy levels. Studies should also avoid having broader research objectives as this can divert participant’s interest and therefore understanding of why their samples are being collected.

  • Gene Editing, Animal Disenhancement and Ethical Debates: A Conundrum for Business Ethics?
    N Thomas, A Langridge
    Animals and Business Ethics
    Book Chapter
    Springer. 25 April 2022
    The Palgrave Macmillan Animal Ethics Series. Palgrave Macmillan, Cham.
    https://doi.org/10.1007/978-3-030-97142-7_10
    Abstract
    Despite the potential of genetic disenhancement to create livestock incapable of pain and thus reduce animal suffering in industrial farming, ethical theorists have rejected disenhancement as intuitively unethical or as part of a broader dismissal of industrial farming. Although criticisms of industrial farming may be valid, the suffering of animals involved still needs to be addressed, and business ethics is specially placed to do so. In this chapter, a brief overview of the related ethical issues of industrial farming and disenhancement are outlined, and practical steps businesses should make to address animal suffering are provided. Explicit Corporate Social Responsibility policies that reflect the interest of animals, workers and consumers as stakeholders should be put in place, which would provide a mechanism to make businesses accountable for genetic modification and animal welfare more generally.