Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data

Type-2 diabetes epigenetic biomarkers: present status and future directions for global and Indigenous health

Type-2 diabetes is a systemic condition with rising global prevalence, disproportionately affecting Indigenous communities worldwide. Recent advances in epigenomics methods, particularly in DNA methylation detection, have enabled the discovery of associations between epigenetic changes and Type-2 diabetes. In this review, we summarise DNA methylation profiling methods, and discuss how these technologies can facilitate the discovery of epigenomic biomarkers for Type-2 diabetes. We critically evaluate previous DNA methylation biomarker studies, particularly those using microarray platforms, and advocate for a shift towards sequencing-based approaches to improve genome-wide coverage. Furthermore, we emphasise the need for biomarker studies that include genetically diverse populations, especially Indigenous communities who are significantly impacted by Type-2 diabetes. We discuss research approaches and ethical considerations that can better facilitate Type-2 diabetes biomarker development to ensure that future genomics-based precision medicine efforts deliver equitable health outcomes. We propose that by addressing these gaps, future research can better capture the genetic and environmental complexities of Type-2 diabetes among populations at disproportionate levels of risk, ultimately leading to more effective diagnostic and therapeutic strategies.

The accuracy of polygenic score models for BMI and Type II diabetes in the Native Hawaiian population

Polygenic scores (PGS) are promising in stratifying individuals based on the genetic susceptibility to complex diseases or traits. However, the accuracy of PGS models, typically trained in European- or East Asian-ancestry populations, tend to perform poorly in other ethnic minority populations and their accuracies have not been evaluated for Native Hawaiians. In particular, for body mass index (BMI) and type-2 diabetes (T2D), Polynesian-ancestry individuals such as Native Hawaiians or Samoans exhibit varied distribution from other continental populations, but are understudied, particularly in the context of PGS. Using BMI and T2D as examples of metabolic traits of importance to Polynesian populations (along with height as a comparison of a similarly highly polygenic trait), here we examine the prediction accuracies of PGS models in a large Native Hawaiian sample from the Multiethnic Cohort with up to 5300 individuals. We find evidence of lowered prediction accuracies for the PGS models in some cases, particularly for height. We also find that using the Native Hawaiian samples as an optimization cohort during training does not consistently improve PGS performance. Moreover, even the best-performing PGS models among Native Hawaiians have lowered prediction accuracy among the subset of individuals most enriched with Polynesian ancestry. Our findings indicate that factors such as admixture histories, sample size, and diversity in GWAS can influence PGS performance for complex traits among Native Hawaiian samples. This study provides an initial survey of PGS performance among Native Hawaiians and exposes the current gaps and challenges associated with improving polygenic prediction models for underrepresented minority populations.

Towards an inclusive Open Science: examining EDI and public participation in policy documents across Europe and the Americas

National, international and organizational Open Science (OS) policies are being formulated to improve and accelerate research through increased transparency, collaboration and better access to scientific knowledge. Yet, there is mounting concern that OS policies do not effectively capture the ethos of OS, and particularly its goal of making science more collaborative, inclusive and socially engaged. This study explores how OS is conceptualized in emerging OS policies and to what extent notions of equity, diversity and inclusion (EDI), as well as public participation are reflected in policy guidelines and recommendations. We use a qualitative document research approach to critically analyse 52 OS policy documents published between January 2020 and December 2022 in Europe and the Americas. Our results show that OS policies overwhelmingly focus on making research outputs publicly accessible, neglecting to advance the two aspects of OS that hold the key to achieving an equitable and inclusive scientific culture-namely, EDI and public participation. While these concepts are often mentioned and even embraced in OS policy documents, concrete guidance on how they can be promoted in practice is overwhelmingly lacking. Rather than advancing the openness of scientific findings first and promoting EDI and public participation efforts second, we argue that incentives and guidelines must be provided and implemented concurrently to advance the OS movement's stated goal of making science open to all.

Microbiomes in action: multifaceted benefits and challenges across academic disciplines

Microbiomes combine the species and activities of all microorganisms living together in a specific habitat. They comprise unique ecological niches with influences that scale from local to global ecosystems. Understanding the connectivity of microbiomes across academic disciplines is important to help mitigate global climate change, reduce food insecurity, control harmful diseases, and ensure environmental sustainability. However, most publications refer to individual microbiomes, and those integrating two or more related disciplines are rare. This review examines the multifaceted benefits of microbiomes across agriculture, food manufacturing and preservation, the natural environment, human health, and biocatalyst processes. Plant microbiomes, by improving plant nutrient cycling and increasing plant abiotic and biotic stress resilience, have increased crop yields by over 20%. Food microbiomes generate approximately USD 30 billion to the global economy through the fermented food industry alone. Environmental microbiomes help detoxify pollutants, absorb more than 90% of heavy metals, and facilitate carbon sequestration. For human microbiomes, an adult person can carry up to 38 trillion microbes which regulate well being, immune functionality, reproductive function, and disease prevention. Microbiomes are used to optimize biocatalyst processes which produce bioenergy and biochemicals; bioethanol production alone is valued at over USD 83 billion p.a. However, challenges, including knowledge gaps, engaging indigenous communities, technical limitations, regulatory considerations, the need for interdisciplinary collaboration, and ethical issues, must be overcome before the potential for microbiomes can be more effectively realized.

Trusted partners, community priorities, and data protections: requirements for precision medicine research with Alaska Native peoples

Precision medicine holds promise for improving health care by tailoring disease treatment and prevention efforts to the needs of individual patients. It also raises ethical questions related to equitable distribution of the benefits of precision medicine; data management, including the terms of data ownership, sharing, and security; and, the nature and extent of community engagement in and oversight of research. These questions are particularly salient for minoritized communities that have been harmed by unethical research practices and often deprived the full benefit of advances in medical science. Understanding the perspectives of these communities is essential to the design and conduct of ethical and effective precision medicine research. This study explored perspectives on the acceptability, feasibility, value, and benefits and harms of precision medicine research among Alaska Native and American Indian (ANAI) peoples. We conducted four focus groups with ANAI individuals who receive primary care from a Tribal health organization in Anchorage, Alaska. Participants were willing to engage in precision medicine research provided specific requirements were met. Research must be conducted by the Tribal health organization or another trusted partner, community health priorities must drive the research agenda, and researchers must employ robust data protections to guard against loss of data security and maintain control over data use and access. These requirements work collectively to ensure research benefits and respects Tribal sovereignty. These findings could help inform efforts to design and implement precision medicine research programs tailored to concerns of ANAI peoples.

A call to action to scale up research and clinical genomic data sharing

Genomic data from millions of individuals have been generated worldwide to drive discovery and clinical impact in precision medicine. Lowering the barriers to using these data collectively is needed to equitably realize the benefits of the diversity and scale of population data. We examine the current landscape of global genomic data sharing, including the evolution of data sharing models from data aggregation through to data visiting, and for certain use cases, cross-cohort analysis using federated approaches across multiple environments. We highlight emerging examples of best practice relating to participant, patient and community engagement; evolution of technical standards, tools and infrastructure; and impact of research and health-care policy. We outline 12 actions we can all take together to scale up efforts to enable safe global data sharing and move beyond projects demonstrating feasibility to routinely cross-analysing research and clinical data sets, optimizing benefit.

Consideration and Disclosure of Group Risks in Genomics and Other Data-Centric Research: Does the Common Rule Need Revision?

Harms and risks to groups and third-parties can be significant in the context of research, particularly in data-centric studies involving genomic, artificial intelligence, and/or machine learning technologies. This article explores whether and how United States federal regulations should be adapted to better align with current ethical thinking and protect group interests. Three aspects of the Common Rule deserve attention and reconsideration with respect to group interests: institutional review board (IRB) assessment of the risks/benefits of research; disclosure requirements in the informed consent process; and criteria for waivers of informed consent. In accordance with respect for persons and communities, investigators and IRBs should systematically consider potential group harm when designing and reviewing protocols, respectively. Research participants should be informed about any potential group harm in the consent process. We call for additional public discussion, empirical research, and normative analysis on these issues to determine the right regulatory and policy path forward.

Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data

The Aotearoa Genomic Data Repository (AGDR) is an initiative to provide a secure within-nation option for the storage, management and sharing of non-human genomic data generated from biological and environmental samples originating in Aotearoa New Zealand. This resource has been developed to follow the principles of Māori Data Sovereignty, and to enable the right of kaitiakitanga (guardianship), so that iwi, hapū and whānau (tribes, kinship groups and families) can effectively exercise their responsibilities as guardians over biological entities that they regard as taonga (precious or treasured). While the repository is designed to facilitate the sharing of data-making it findable by researchers and interoperable with data held in other genomic repositories-the decision-making process regarding who can access the data is entirely in the hands of those holding kaitiakitanga over each data set. No data are made available to the requesting researcher until the request has been approved, and the conditions for access (which can vary by data set) have been agreed to. Here we describe the development of the AGDR, from both a cultural perspective, and a technical one, and outline the processes that underpin its operation.

ProHap enables human proteomic database generation accounting for population diversity

Amid the advances in genomics, the availability of large reference panels of human haplotypes is key to account for human diversity within and across populations. However, mass spectrometry-based proteomics does not benefit from this information. To address this gap, we introduce ProHap, a Python-based tool that constructs protein sequence databases from phased genotypes of reference panels. ProHap enables researchers to account for haplotype diversity in proteomic searches.

Fish germ cell cryobanking and transplanting for conservation

The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.

The Genomics Revolution Drives a New Era in Entomology

Thanks to the fast development of sequencing techniques and bioinformatics tools, sequencing the genome of an insect species for specific research purposes has become an increasingly popular practice. Insect genomes not only provide sets of gene sequences but also represent a change in focus from reductionism to systemic biology in the field of entomology. Using insect genomes, researchers are able to identify and study the functions of all members of a gene family, pathway, or gene network associated with a trait of interest. Comparative genomics studies provide new insights into insect evolution, addressing long-lasting controversies in taxonomy. It is also now feasible to uncover the genetic basis of important traits by identifying variants using genome resequencing data of individual insects, followed by genome-wide association analysis. Here, we review the current progress in insect genome sequencing projects and the application of insect genomes in uncovering the phylogenetic relationships between insects and unraveling the mechanisms of important life-history traits. We also summarize the challenges in genome data sharing and possible solutions. Finally, we provide guidance for fully and deeply mining insect genome data.

Federated Learning: Breaking Down Barriers in Global Genomic Research

Recent advancements in Next-Generation Sequencing (NGS) technologies have revolutionized genomic research, presenting unprecedented opportunities for personalized medicine and population genetics. However, issues such as data silos, privacy concerns, and regulatory challenges hinder large-scale data integration and collaboration. Federated Learning (FL) has emerged as a transformative solution, enabling decentralized data analysis while preserving privacy and complying with regulations such as the General Data Protection Regulation (GDPR). This review explores the potential use of FL in genomics, detailing its methodology, including local model training, secure aggregation, and iterative improvement. Key challenges, such as heterogeneous data integration and cybersecurity risks, are examined alongside regulations like GDPR. In conclusion, successful implementations of FL in global and national initiatives demonstrate its scalability and role in supporting collaborative research. Finally, we discuss future directions, including AI integration and the necessity of education and training, to fully harness the potential of FL in advancing precision medicine and global health initiatives.

Heuristics Identified in Health Data-Sharing Preferences of Patients With Cancer: Qualitative Focus Group Study

BACKGROUND

Evaluating precision oncology outcomes requires access to real-world and clinical trial data. Access is based on consent, and consent is based on patients' informed preferences when deciding to share their data. Decision-making is often modeled using utility theory, but a complex decision context calls for a consideration of how heuristic, intuitive thought processes interact with rational utility maximization. Data-sharing decision-making has been studied using heuristic theory, but almost no heuristic research exists in the health data context. This study explores this evidence gap, applying a qualitative approach to probe for evidence of heuristic mechanisms behind the health data-sharing preferences of those who have experienced cancer. Exploring qualitative decision-making reveals the types of heuristics used and how they are related to the process of decision-making to better understand whether consent mechanisms should consider nonrational processes to better serve patient decision-making.

OBJECTIVE

This study aimed to explore how patients with cancer use heuristics when deciding whether to share their data for research.

METHODS

The researchers conducted a focus group study of Canadians who have experienced cancer. We recruited participants through an online advertisement, screening individuals based on their ability to increase demographic diversity in the sample. We reviewed the literature on data-sharing platforms to develop a semistructured topic guide on concerns about data sharing, incentives to share, and consent and control. Focus group facilitators led the open-ended discussions about data-sharing preferences that revealed underlying heuristics. Two qualitative analysts coded transcripts using a heuristic framework developed from a review of the literature. Transcripts were analyzed for heuristic instances which were grouped according to sociocultural categories. Using thematic analysis, the analysts generated reflexive themes through norming sessions and consultations.

RESULTS

A total of 3 focus groups were held with 19 participants in total. The analysis identified 12 heuristics underlying intentions to share data. From the thematic analysis, we identified how the heuristics of social norms and community building were expressed through altruism; the recognition, reputation, and authority heuristics led to (dis)trust in certain institutions; the need for security prompted the illusion of control and transparency heuristics; and the availability and affect heuristics influenced attitudes around risk and benefit. These thematic relationships all had impacts on the participants' intentions to share their health data.

CONCLUSIONS

The findings provide a novel qualitative understanding of how health data-sharing decisions and preferences may be based on heuristic processing. As patients consider the extent of risks and benefits, heuristic processes influence their assessment of anticipated outcomes, which may not result in rational, truly informed consent. This study shows how considering heuristic processing when designing current consent mechanisms opens up the opportunity for more meaningful and realistic interactions with the complex decision-making context.

A Just Genomics Needs an ELSI of Translation

The rapid advances in genomics over the last decade have come to fruition amid intense public discussions of justice in medicine and health care. While much emphasis has been placed on increasing diversity in genomics research participation, an overly narrow focus on recruitment eschews recognition of the disparities in health care that will ultimately shape access to the benefits of genomic medicine. In this essay, we suggest that achieving a just genomics, both now and in the future, requires an explicit ELSI of translation-normative and pragmatic scholarship that embraces the interconnectedness of research and clinical care and centers the obligations of researchers, institutions, and funders to mitigate inequities throughout the translational pipeline. We propose core principles to guide an ELSI of translation and to ensure that this work balances the value of the generalizable knowledge that genomics research generates and the value of the individuals and communities who make this research possible.

Expanding the Agenda for a More Just Genomics

The integration of genomics into public health and medicine is happening at a faster rate than the accrual of the capabilities necessary to ensure the equitable, global distribution of its clinical benefits. Uneven access to genetic testing and follow-up care, unequal distribution of the resources required to access and participate in research, and underrepresentation of some descent groups in genetic and clinical datasets (and thus uncertain genetic results for some patients) are just some of the reasons to center justice in genomics. A more just genomics is an imperative rooted in the ethical obligations incurred by a publicly funded science that is reliant on human data. These features of genomics indebt the genomics enterprise and compel the expanded scope of responsibility proposed by the authors of this special report. The report begins to define justice in genomics for different stakeholder groups and proposes substantial shifts in power, resource distribution, scientific practice, and governance that could enable genomics to meet its obligations to humanity.

Data sharing ethics toolkit: The Human Cell Atlas

Striving to build an exhaustive guidebook of the types and properties of human cells, the Human Cell Atlas' (HCA) success relies on the sampling of diverse populations, developmental stages, and tissue types. Its open science philosophy preconizes the rapid, seamless sharing of data - as openly as possible. In light of the scope and ambition of such an international initiative, the HCA Ethics Working Group (EWG) has been working to build a solid foundation to address the complexities of data collection and sharing as part of Atlas development. Indeed, a particular challenge of the HCA is the diversity of sampling scenarios (e.g., living participants, deceased donors, pediatric populations, culturally diverse backgrounds, tissues from various developmental stages, etc.), and associated ethical and legal norms, which vary across countries contributing to the effort. Hence, to the extent possible, the EWG set out to provide harmonised, international and interoperable policies and tools, to guide its research community. This paper provides a high-level overview of the types of challenges and approaches proposed by the EWG.

The commitment of the human cell atlas to humanity

The Human Cell Atlas (HCA) is a global partnership "to create comprehensive reference maps of all human cells-the fundamental units of life - as a basis for both understanding human health and diagnosing, monitoring, and treating disease." ( https://www.humancellatlas.org/ ) The atlas shall characterize cells from diverse individuals across the globe to better understand human biology. HCA proactively considers the priorities of, and benefits accrued to, contributing communities. Here, we lay out principles and action items that have been adopted to affirm HCA's commitment to equity so that the atlas is beneficial to all of humanity.

Culturally responsive strategies and practical considerations for live tissue studies in Māori participant cohorts

Introduction

Indigenous communities globally are inequitably affected by non-communicable diseases such as cancer and coronary artery disease. Increased focus on personalized medicine approaches for the treatment of these diseases offers opportunities to improve the health of Indigenous people. Conversely, poorly implemented approaches pose increased risk of further exacerbating current inequities in health outcomes for Indigenous peoples. The advancement of modern biology techniques, such as three-dimensional (3D) in vitro models and next generation sequencing (NGS) technologies, have enhanced our understanding of disease mechanisms and individualized treatment responses. However, current representation of Indigenous peoples in these datasets is lacking. It is crucial that there is appropriate and ethical representation of Indigenous peoples in generated datasets to ensure these technologies can be used to maximize the benefit of personalized medicine for Indigenous peoples.

Methods

This project discusses the use of 3D tumor organoids and single cell/nucleus RNA sequencing to study cancer treatment responses and explore immune cell roles in coronary artery disease. Using key pillars from currently available Indigenous bioethics frameworks, strategies were developed for the use of Māori participant samples for live tissue and sequencing studies. These were based on extensive collaborations with local Māori community, scientific leaders, clinical experts, and international collaborators from the Broad Institute of MIT and Harvard. Issues surrounding the use of live tissue, genomic data, sending samples overseas and Indigenous data sovereignty were discussed.

Results

This paper illustrates a real-world example of how collaboration with community and the incorporation of Indigenous worldviews can be applied to molecular biology studies in a practical and culturally responsive manner, ensuring fair and equitable representation of Indigenous peoples in modern scientific data.

Scientists and scientific journals should adhere to ethical standards for the use and reporting of data from Indigenous people

Internationally, governments and scientists are bound by legal and treaty rights when working with Indigenous nations. These rights include the right of Indigenous people to control the conduct of science with Indigenous nations. Unfortunately, in some cases, individual scientists and scientific teams working with biological and genetic data collected from Indigenous people have not respected these international rights. Here, we argue that the scientific community should understand and acknowledge the historical harms experienced by Indigenous people under the veil of scientific progress (truth) and implement existing standards for ethical conduct of research and sovereign control of data collected within Indigenous communities (reconciliation). Specifically, we outline the rationale for why scientists, scientific journals and research integrity and institutional review boards/ethics committees should adopt, and be held accountable for upholding, current international standards of Indigenous data sovereignty and ethical use of Indigenous biological samples.

Qualitative genomic research with Indigenous peoples: a scoping review of participatory practice

INTRODUCTION

Indigenous peoples and perspectives are under-represented within genomic research. Qualitative methods can help redress this under-representation by informing the development of inclusive genomic resources aligned with Indigenous rights and interests. The difficult history of genomic research with Indigenous peoples requires that research be conducted responsibly and collaboratively. Research guidelines offer structuring principles, yet little guidance exists on how principles translate into practical, community-led methods. We identified the scope and nature of participatory practice described in published qualitative genomic research studies with Indigenous peoples.

METHODS

We performed a search of PubMed, CINAHL, Embase, Scopus and the Bibliography of Indigenous Peoples in North America. Eligible studies reported qualitative methods investigating genomics-related topics with Indigenous populations in Canada, the USA, Australia or New Zealand. Abstracted participatory practices were defined through a literature review and mapped to a published ethical genomic research framework.

RESULTS

We identified 17 articles. Published articles described a breadth of methods across a diversity of Indigenous peoples and settings. Reported practices frequently promoted Indigenous-partnered research regulation, community engagement and co-creation of research methods. The extent of participatory and community-led practice appeared to decrease as studies progressed.

CONCLUSION

Applying non-prescriptive Indigenous genomic research guidelines to qualitative inquiry can be achieved through varied methodological approaches. Our findings affirm the adaptive nature of this process in real-world settings and identify opportunities for participatory practice and improved reporting across the research lifecycle. These findings and the breadth of characterised applied research practices are instructive for researchers seeking to develop much-needed qualitative genomic research partnerships.

Use of Cognitive Interviews in the Development of a Survey Assessing American Indian and Alaska Native Adult Perspectives on Genetics and Biological Specimens

The cognitive interview process is a method to validate a survey instrument's face validity and enhance confidence in item interpretation, as well as a method to engage communities in the research process. Trained American Indian and Alaska Native (AIAN) interviewers conducted retrospective cognitive interviews at three AIAN communities to assess the item quality of a 131-item survey item that measures AIAN knowledge and attitudes on genetics and biological specimens. A cognitive interview process was used to assess cultural consonance, thought processes used when considering survey instructions, items and responses, and language preference of survey items in the development of a survey to assess public knowledge and attitudes on genetics. Content analysis was used to analyze interview data. Survey instructions, items and scales generated no cognitive difficulties. The participants noted being unfamiliar with terminology used to describe genetic and biological specimens. In several cases, the participants' written response in the survey and verbal response in the interview did not align. A resultant 52-item survey for use in AIAN communities was finalized. Cognitive interviewing is resource-intensive; however, ignoring community engagement during survey development results in inappropriate interpretations about culturally diverse populations such as AIAN peoples.

Public Involvement and Engagement in Big Data Research: Scoping Review

BACKGROUND

The success of big data initiatives depends on public support. Public involvement and engagement could be a way of establishing public support for big data research.

OBJECTIVE

This review aims to synthesize the evidence on public involvement and engagement in big data research.

METHODS

This scoping review mapped the current evidence on public involvement and engagement activities in big data research. We searched 5 electronic databases, followed by additional manual searches of Google Scholar and gray literature. In total, 2 public contributors were involved at all stages of the review.

RESULTS

A total of 53 papers were included in the scoping review. The review showed the ways in which the public could be involved and engaged in big data research. The papers discussed a broad range of involvement activities, who could be involved or engaged, and the importance of the context in which public involvement and engagement occur. The findings show how public involvement, engagement, and consultation could be delivered in big data research. Furthermore, the review provides examples of potential outcomes that were produced by involving and engaging the public in big data research.

CONCLUSIONS

This review provides an overview of the current evidence on public involvement and engagement in big data research. While the evidence is mostly derived from discussion papers, it is still valuable in illustrating how public involvement and engagement in big data research can be implemented and what outcomes they may yield. Further research and evaluation of public involvement and engagement in big data research are needed to better understand how to effectively involve and engage the public in big data research.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-https://doi.org/10.1136/bmjopen-2021-050167.

Benefit-Sharing by Design: A Call to Action for Human Genomics Research

The ethical standards for the responsible conduct of human research have come a long way; however, concerns surrounding equity remain in human genetics and genomics research. Addressing these concerns will help society realize the full potential of human genomics research. One outstanding concern is the fair and equitable sharing of benefits from research on human participants. Several international bodies have recognized that benefit-sharing can be an effective tool for ethical research conduct, but international laws, including the Convention on Biological Diversity and its Nagoya Protocol on Access and Benefit-Sharing, explicitly exclude human genetic and genomic resources. These agreements face significant challenges that must be considered and anticipated if similar principles are applied in human genomics research. We propose that benefit-sharing from human genomics research can be a bottom-up effort and embedded into the existing research process. We propose the development of a "benefit-sharing by design" framework to address concerns of fairness and equity in the use of human genomic resources and samples and to learn from the aspirations and decade of implementation of the Nagoya Protocol.

Informed proxy consent for ancient DNA research

Embracing the underlying principles and processes of informed proxy consent or relational autonomy consent in human ancient DNA research can transform research.

Precision medicine in Australia: indigenous health professionals are needed to improve equity for Aboriginal and Torres Strait Islanders

Precision medicine, also known as "personalised medicine", seeks to identify strategies in the prevention and treatment of disease informed by a patient's genomic information. This allows a targeted approach to disease identification with the intention of reducing the burden of illness. Currently, both the emerging field of precision medicine and the established field of clinical genetics are highly reliant on genomic databases which are fraught with inbuilt biases, particularly from sample populations. The inequities of most concern here are those affecting Aboriginal and Torres Strait Islander (or Zenadth Kes) peoples of Australia (hereafter, respectfully, Indigenous Australians). It is with this perspective that the Summer internship forINdigenous peoples inGenomics Australia endeavours to support the development of culturally appropriate genomic research with Indigenous Australians. We argue here that Indigenous researchers are best placed to create the informed, culturally safe environment necessary for Indigenous Australians to participate in genomic research.

Towards precision cancer medicine for Aboriginal and Torres Strait Islander cancer health equity

Delivering cancer control at scale for Aboriginal and Torres Strait Islander communities is a national priority that requires Aboriginal and Torres Strait Islander leadership and codesign, as well as significant involvement of the Aboriginal community-controlled health sector. The unique genomic variation observed among Aboriginal and Torres Strait Islander peoples may have implications for standard and precision medicine. Yet, Aboriginal and Torres Strait Islander peoples are absent from, or under-represented within, human reference genome resources, genomic studies, cancer studies, cancer cell lines, patient-derived xenografts and cancer clinical trials. Genomics-guided precision cancer medicine offers an opportunity to reduce cancer health disparities experienced by Aboriginal and Torres Strait Islander peoples through personalising prevention, diagnosis, treatment and long term management. Here, we describe what is required to ensure that Aboriginal and Torres Strait Islander peoples can receive the benefits of precision cancer medicine. Equity of access to care, an Aboriginal and Torres Strait Islander cancer workforce, and appropriate genome reference resources are important for safe and effective cancer medicine. Building Indigenous data sovereignty principles and Aboriginal and Torres Strait Islander governance into research is required to protect Aboriginal and Torres Strait Islander rights and collective interests. Aboriginal and Torres Strait Islander community engagement should be undertaken to develop an understanding of the unique cultural and ethical considerations for precision cancer research. Local and national genomic health research guidelines are needed to define a consensus best practice in genomics research with Aboriginal and Torres Strait Islander peoples.

Genetic research within Indigenous communities: Engagement opportunities and pathways forward

PURPOSE

Against a historical backdrop of researchers who violated trust through lack of benefit sharing, transparency, and engagement, efforts are underway to develop better approaches for genetic and genomic research with Indigenous communities. To increase engagement, there is a need to understand factors that affect researcher and community collaborations. This study aimed to understand the barriers, challenges, and facilitators of Indigenous Peoples in the United States participating in genetic research.

METHODS

We conducted 42 semistructured interviews with Tribal leaders, clinicians, researchers, policy makers, and Tribal research review board members across the United States to explore perceived risks, benefits, barriers, and facilitators of genetic research participation.

RESULTS

Participants, identifying as Indigenous (88%) or non-Indigenous allies (12%), described their concerns, hesitancy, and fears about genetic research, as well as the roles of trust, transparency, and respect for culture in facilitating partnerships. Previous harms-such as sample and data misuse, stigmatization, or misrepresentation by researchers-revealed strategies for building trust to create more equitable and reciprocal research partnerships.

CONCLUSION

Participants in this study offered strategies for increasing genetic research engagement. The pathway forward should foster transparent research policies and practices to facilitate informed research that supports the needs and priorities of participants, communities, and researchers.

Environmental health science research: opportunities and challenges for some developing countries in Africa

Due to ongoing developmental projects, there is a need for regular monitoring of the impact of pollutants on the environment. This review documented the challenges and opportunities in the field of environmental health sciences in some African countries. A systematic review was used to investigate opportunities and challenges in the field of environmental health science in Africa by examining published work with a specific focus on Africa. The reports showed that funding and infrastructure as the major problems. The study also highlighted recruiting study participants, retention, and compensation as a bane in the field in Africa. The absence of modern equipment also hinders research. The review, however, noted research collaboration from the region including studies on emerging pollutants such as pharmaceuticals, per and polyfluoroalkyl substances (PFAS), and microplastic (MPs) as great opportunities. The study concluded that collaboration with other continents, exchange programs and improved governmental interventions may help.

Global musical diversity is largely independent of linguistic and genetic histories

Music is a universal yet diverse cultural trait transmitted between generations. The extent to which global musical diversity traces cultural and demographic history, however, is unresolved. Using a global musical dataset of 5242 songs from 719 societies, we identify five axes of musical diversity and show that music contains geographical and historical structures analogous to linguistic and genetic diversity. After creating a matched dataset of musical, genetic, and linguistic data spanning 121 societies containing 981 songs, 1296 individual genetic profiles, and 121 languages, we show that global musical similarities are only weakly and inconsistently related to linguistic or genetic histories, with some regional exceptions such as within Southeast Asia and sub-Saharan Africa. Our results suggest that global musical traditions are largely distinct from some non-musical aspects of human history.

Constructing the public in public perceptions research: A case study of forest genomics

Contemporary scientific and technological endeavours face public and political pressure to adopt open, transparent and democratically accountable practices of public engagement. Prior research has identified different ways that experts 'imagine publics' - as uninformed, as disengaged, as a risk to science, and as co-producers of knowledge - but there has yet to be a systematic exploration of how these views emerge, interact and evolve. This article introduces a typology of imagined publics to analyse how publics are constructed in the field of forest genomics. We find that deficit views of publics have not been replaced by co-production. Instead, deficit and co-productive approaches to publics co-exist and overlap, informing both how publics are characterized and how public perceptions are studied. We outline an agenda for deepening and expanding research on public perceptions of novel technologies. Specifically, we call for more diverse and complex methodological approaches that account for relational dynamics over time.

Equity in blood transfusion precision services

BACKGROUND

Blood collection agencies are integrating precision medicine techniques to improve and individualise blood donor and recipient outcomes. These organisations have a role to play in ensuring equitable application of precision medicine technologies for both donors and transfusion recipients. BODY: Precision medicine techniques, including molecular genetic testing and next generation sequencing, have been integrated in transfusion services to improve blood typing and matching with the aim to reduce a variety of known transfusion complications. Internationally, priorities in transfusion research have aimed to optimise services through the use of precision medicine technologies and consider alternative uses of genomic information to personalise transfusion experiences for both recipients and donors. This has included focusing on the use of genomics when matching blood products for transfusion recipients, to personalise a blood donor's donation type or frequency, and longitudinal donor research utilising blood donor biobanks.

CONCLUSION

Equity in precision services and research must be of highest importance for blood collection agencies to maintain public trust, especially when these organisations rely on volunteer donors to provide transfusion services. The investment in implementing equitable precision medicine services, including development of blood donor biobanks, has the potential to optimise and personalise services for both blood donors and transfusion recipients.

Hunter-gatherer genetics research: Importance and avenues

Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.

CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions

Machine Learning-based scoring and classification of genetic variants aids the assessment of clinical findings and is employed to prioritize variants in diverse genetic studies and analyses. Combined Annotation-Dependent Depletion (CADD) is one of the first methods for the genome-wide prioritization of variants across different molecular functions and has been continuously developed and improved since its original publication. Here, we present our most recent release, CADD v1.7. We explored and integrated new annotation features, among them state-of-the-art protein language model scores (Meta ESM-1v), regulatory variant effect predictions (from sequence-based convolutional neural networks) and sequence conservation scores (Zoonomia). We evaluated the new version on data sets derived from ClinVar, ExAC/gnomAD and 1000 Genomes variants. For coding effects, we tested CADD on 31 Deep Mutational Scanning (DMS) data sets from ProteinGym and, for regulatory effect prediction, we used saturation mutagenesis reporter assay data of promoter and enhancer sequences. The inclusion of new features further improved the overall performance of CADD. As with previous releases, all data sets, genome-wide CADD v1.7 scores, scripts for on-site scoring and an easy-to-use webserver are readily provided via https://cadd.bihealth.org/ or https://cadd.gs.washington.edu/ to the community.

Open Science Practices in Psychiatric Genetics: A Primer

Open science ensures that research is transparently reported and freely accessible for all to assess and collaboratively build on. Psychiatric genetics has led among the health sciences in implementing some open science practices in common study designs, such as replication as part of genome-wide association studies. However, thorough open science implementation guidelines are limited and largely not specific to data, privacy, and research conduct challenges in psychiatric genetics. Here, we present a primer of open science practices, including selection of a research topic with patients/nonacademic collaborators, equitable authorship and citation practices, design of replicable, reproducible studies, preregistrations, open data, and privacy issues. We provide tips for informative figures and inclusive, precise reporting. We discuss considerations in working with nonacademic collaborators and distributing research through preprints, blogs, social media, and accessible lecture materials. Finally, we provide extra resources to support every step of the research process.

The accuracy of polygenic score models for anthropometric traits and Type II Diabetes in the Native Hawaiian Population

Polygenic scores (PGS) are promising in stratifying individuals based on the genetic susceptibility to complex diseases or traits. However, the accuracy of PGS models, typically trained in European- or East Asian-ancestry populations, tend to perform poorly in other ethnic minority populations, and their accuracies have not been evaluated for Native Hawaiians. Using body mass index, height, and type-2 diabetes as examples of highly polygenic traits, we evaluated the prediction accuracies of PGS models in a large Native Hawaiian sample from the Multiethnic Cohort with up to 5,300 individuals. We evaluated both publicly available PGS models or genome-wide PGS models trained in this study using the largest available GWAS. We found evidence of lowered prediction accuracies for the PGS models in some cases, particularly for height. We also found that using the Native Hawaiian samples as an optimization cohort during training did not consistently improve PGS performance. Moreover, even the best performing PGS models among Native Hawaiians would have lowered prediction accuracy among the subset of individuals most enriched with Polynesian ancestry. Our findings indicate that factors such as admixture histories, sample size and diversity in GWAS can influence PGS performance for complex traits among Native Hawaiian samples. This study provides an initial survey of PGS performance among Native Hawaiians and exposes the current gaps and challenges associated with improving polygenic prediction models for underrepresented minority populations.

Precision health equity for racialized communities

In the last three decades, a cohort of genomicists have intentionally sought to include more racially diverse people in their research in human genomics and precision medicine. How such efforts to be inclusive in human genomic research and precision medicine are modeled and enacted, specifically if the terms of inclusion are equitable for these communities remains to be explored. In this commentary, we review the historical context in which issues of racial inclusion arose with early genome and genetics projects. We then discuss attempts to include racialized peoples in more recent human genomics research. In conclusion, we raise critical issues to consider in the future of equitable human genomics and precision medicine research involving racialized communities, particularly as it concerns working towards what we call Precision Health Equity (PHE). Specifically, we examine issues of genetic data governance and the terms of participation in inclusive human genomics and precision health research. We do so by drawing on insights and protocols developed by researchers investigating Indigenous Data Sovereignty and propose exploring their application and adaptation to precision health research involving racialized communities.

Bridging the gap: returning genetic results to indigenous communities in Latin America

In response to inequality in access to genomics research, efforts are underway to include underrepresented minorities, but explicit (and enforcing) guidelines are mostly targeted toward the Global North. In this work, we elaborate on the need to return scientific results to indigenous communities, reporting the actions we have taken in a recent genomic study with Mapuche communities in Chile. Our approach acknowledged the social dynamics perpetuating colonial hierarchies. We framed genetic results to empower indigenous knowledge and communities' history and identities. A fundamental step in our strategy has been sharing the results with the communities before publishing the scientific paper, which allowed us to incorporate community perspectives. We faced the challenge of translating genetic concepts like admixture, emphasizing the distinction between identity and biology. To reach a broad and diverse audience, we disseminated the study results to single community members, cultural representatives, and high schools, highlighting the importance of the history of the region before the European contact. To facilitate results dissemination, we prepared didactic material and a report in Spanish written in non-specialized language, targeting a wider Latin American readership. This work illustrates the benefits of discussing scientific findings with indigenous communities, demonstrating that a collaborative and culturally sensitive approach fosters knowledge sharing and community empowerment and challenges power dynamics in genetic research. Bridging the gap between academia and indigenous communities promotes equity and inclusion in scientific endeavors.

Genetic research with Indigenous Peoples: perspectives on governance and oversight in the US

Introduction

Indigenous Peoples are increasingly exerting governance and oversight over genomic research with citizens of their nations, raising questions about how best to enforce research regulation between American Indian, Alaska Native, and Native Hawaiian peoples and researchers.

Methods

Using a community-engaged research approach, we conducted 42 semi-structured interviews with Tribal leaders, clinicians, researchers, policy makers, and Tribal research review board members about their perspectives on ethical issues related to genetics research with Indigenous Peoples in the US.

Results

We report findings related to (1) considerations for Indigenous governance, (2) institutional relationships upholding sovereignty, (3) expectations for research approvals, and (4) agreements enacting Indigenous governance. Participants described concerns about different ways of exerting oversight, relationships and agreements between Indigenous Peoples and researchers, and gaps that need to be addressed to strengthen existing governance of genomic data.

Discussion

The results will ultimately guide policy-making and development of new strategies for Indigenous Peoples to enforce oversight in research to promote ethically and culturally appropriate research.

Indigenous Peoples and research: self-determination in research governance

Indigenous Peoples are reimagining their relationship with research and researchers through greater self-determination and involvement in research governance. The emerging discourse around Indigenous Data Sovereignty has provoked discussions about decolonizing data practices and highlighted the importance of Indigenous Data Governance to support Indigenous decision-making and control of data. Given that much data are generated from research, Indigenous research governance and Indigenous Data Governance overlap. In this paper, we broaden the concept of Indigenous Data Sovereignty by using the CARE Principles for Indigenous Data Governance to discuss how research legislation and policy adopted by Indigenous Peoples in the US set expectations around recognizing sovereign relationships, acknowledging rights and interests in data, and enabling Indigenous Peoples' participation in research governance.

Equity, diversity, and inclusion at the Global Alliance for Genomics and Health

A lack of diversity in genomics for health continues to hinder equitable leadership and access to precision medicine approaches for underrepresented populations. To avoid perpetuating biases within the genomics workforce and genomic data collection practices, equity, diversity, and inclusion (EDI) must be addressed. This paper documents the journey taken by the Global Alliance for Genomics and Health (a genomics-based standard-setting and policy-framing organization) to create a more equitable, diverse, and inclusive environment for its standards and members. Initial steps include the creation of two groups: the Equity, Diversity, and Inclusion Advisory Group and the Regulatory and Ethics Diversity Group. Following a framework that we call "Reflected in our Teams, Reflected in our Standards," both groups address EDI at different stages in their policy development process.

Microbiome ownership for Indigenous peoples

Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.

A relational framework for microbiome research with Indigenous communities

Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.

Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia

Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.