Getting genetic ancestry right for science and society

Getting genetic ancestry right for science and society
We must embrace a multidimensional, continuous view of ancestry and move away from continental ancestry categories
Anna C. F. Lewis, et al.
Policy Forum
Science, Volume 376| Issue 6591| 22 Apr 2022

Glaring health disparities have reinvigorated debate about the relevance of race to health, including how race should and should not be used as a variable in research and biomedicine (1). After a long history of race being treated as a biological variable, there is now broad agreement that racial classifications are a product of historically contingent social, economic, and political processes. Many institutions have thus been reexamining their use of race and racism and stating intentions about how race should be used going forward. One common proposal is to use genetic concepts—in particular, genetic ancestry and population categories—as a replacement for race (2). However, the use of ancestry categories has technical limitations, fails to adequately capture human genetic diversity and demographic history, and risks retaining one of the most problematic aspects of race—an essentialist link to biology—by allowing genetic ancestry categories to stand in its place.

Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals
A genome-wide association study in ~3 million individuals identifies 3,952 independent variants associated with educational attainment. A polygenic index explains 12–16% of variance for this trait and contributes to risk prediction for ten diseases.
Aysu Okbay, Yeda Wu, Alexander I. Young
Article | 31 March 2022 | Open Access
Nature Genetics, Volume 54 Issue 4, April 2022
We conduct a genome-wide association study (GWAS) of educational attainment (EA) in a sample of ~3 million individuals and identify 3,952 approximately uncorrelated genome-wide-significant single-nucleotide polymorphisms (SNPs). A genome-wide polygenic predictor, or polygenic index (PGI), explains 12–16% of EA variance and contributes to risk prediction for ten diseases. Direct effects (i.e., controlling for parental PGIs) explain roughly half the PGI’s magnitude of association with EA and other phenotypes. The correlation between mate-pair PGIs is far too large to be consistent with phenotypic assortment alone, implying additional assortment on PGI-associated factors. In an additional GWAS of dominance deviations from the additive model, we identify no genome-wide-significant SNPs, and a separate X-chromosome additive GWAS identifies 57.

Expanding global access to genetic therapies

Expanding global access to genetic therapies
AWT Muigai, School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
World View, Published: 07 January 2022
Nature Biotechnology, 40, pages 20–21 (2022)
…The era of genetic therapies — both gene-editing treatments and gene therapies, several of which are now on the market — has arrived for rare disease. But as more of these therapies come online, it is time to explore how current business models based on patents and restrictive licensing limit access to treatments. It is also time to explore whether there are other ways in which patents can still reward innovators and protect investments while ensuring that the widest number of patients who need these treatments can receive them…

Comparison of public discussions of gene editing on social media between the United States and China

Comparison of public discussions of gene editing on social media between the United States and China
J Ji, M Robbins, JD Featherstone, C Calabrese… –
PloS ONE,  Published: May 2, 2022,
The world’s first gene-edited babies event has stirred controversy on social media over the use of gene editing technology. Understanding public discussions about this controversy will provide important insights about opinions of science and facilitate informed policy decisions. This study compares public discussion topics about gene editing on Twitter and Weibo, as well as the evolution of these topics over four months. Latent Dirichlet allocation (LDA) was used to generate topics for 11,244 Weibo posts and 57,525 tweets from September 25, 2018, to January 25, 2019. Results showed a difference between the topics on Twitter versus Weibo: there were more nuanced discussions on Twitter, and the discussed topics between platforms focused on different areas. Temporal analysis showed that most discussions took place around gene-edited events. Based on our findings, suggestions were provided for policymakers and science communication practitioners to develop more effective communication strategies toward audiences in China and the U.S.

Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life

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
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

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
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

Informed consent, genomic research and mental health: A integrative review
Nina Kilkku, Arja Halkoaho
Nursing ethics, 4 February 2022
Open Access
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.
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.
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.
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.
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.
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

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
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.
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.
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.
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

Functional genomics data: privacy risk assessment and technological mitigation
Gamze Gürsoy, Tianxiao Li, Mark B. Gerstein
Perspective | 10 November 2021
Nature Reviews Genetics
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

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
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.