Benefit sharing: Why inclusive provenance metadata matter

Navigating COP16's digital sequence information outcomes: What researchers need to do in practice

The UN Convention on Biological Diversity adopted new rules for sharing benefits from publicly available genetic sequence data, also known as digital sequence information (DSI). In this Opinion, the authors describe the key elements researchers need to be aware of, address real-life questions, and explain the practical implications of these rules for research and development.

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.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

Investigating the Roles and Responsibilities of Institutional Signing Officials After Data Sharing Policy Reform for Federally Funded Research in the United States: National Survey

BACKGROUND

New federal policies along with rapid growth in data generation, storage, and analysis tools are together driving scientific data sharing in the United States. At the same, triangulating human research data from diverse sources can also create situations where data are used for future research in ways that individuals and communities may consider objectionable. Institutional gatekeepers, namely, signing officials (SOs), are therefore at the helm of compliant management and sharing of human data for research. Of those with data governance responsibilities, SOs most often serve as signatories for investigators who deposit, access, and share research data between institutions. Although SOs play important leadership roles in compliant data sharing, we know surprisingly little about their scope of work, roles, and oversight responsibilities.

OBJECTIVE

The purpose of this study was to describe existing institutional policies and practices of US SOs who manage human genomic data access, as well as how these may change in the wake of new Data Management and Sharing requirements for National Institutes of Health-funded research in the United States.

METHODS

We administered an anonymous survey to institutional SOs recruited from biomedical research institutions across the United States. Survey items probed where data generated from extramurally funded research are deposited, how researchers outside the institution access these data, and what happens to these data after extramural funding ends.

RESULTS

In total, 56 institutional SOs participated in the survey. We found that SOs frequently approve duplicate data deposits and impose stricter access controls when data use limitations are unclear or unspecified. In addition, 21% (n=12) of SOs knew where data from federally funded projects are deposited after project funding sunsets. As a consequence, most investigators deposit their scientific data into "a National Institutes of Health-funded repository" to meet the Data Management and Sharing requirements but also within the "institution's own repository" or a third-party repository.

CONCLUSIONS

Our findings inform 5 policy recommendations and best practices for US SOs to improve coordination and develop comprehensive and consistent data governance policies that balance the need for scientific progress with effective human data protections.

Indigenous Peoples' Rights in Data: a contribution toward Indigenous Research Sovereignty

Indigenous Peoples' right to sovereignty forms the foundation for advocacy and actions toward greater Indigenous self-determination and control across a range of domains that impact Indigenous Peoples' communities and cultures. Declarations for sovereignty are rising throughout Indigenous communities and across diverse fields, including Network Sovereignty, Food Sovereignty, Energy Sovereignty, and Data Sovereignty. Indigenous Research Sovereignty draws in the sovereignty discourse of these initiatives to consider their applications to the broader research ecosystem. Our exploration of Indigenous Research Sovereignty, or Indigenous self-determination in the context of research activities, has been focused on the relationship between Indigenous Data Sovereignty and efforts to describe Indigenous Peoples' Rights in data.

Indigenous peoples and local communities as partners in the sequencing of global eukaryotic biodiversity

The aim to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity is the shared mission of many ongoing large-scale biodiversity genomics initiatives. Reference genomes of global flora and fauna have the potential to inform a broad range of major issues facing both biodiversity and humanity, such as the impact of climate change, the conservation of endangered species and ecosystems, public health crises, and the preservation and enhancement of ecosystem services. Biodiversity is dramatically declining: 28% of species being assessed by the IUCN are threatened with extinction, and recent reports suggest that a transformative change is needed to conserve and protect what remains. To provide a collective and global genomic response to the biodiversity crisis, many biodiversity genomics initiatives have come together, creating a network of networks under the Earth BioGenome Project. This network seeks to expedite the creation of an openly available, "public good" encyclopedia of high-quality eukaryotic reference genomes, in the hope that by advancing our basic understanding of nature, it can lead to the transformational scientific developments needed to conserve and protect global biodiversity. Key to completing this ambitious encyclopedia of reference genomes, is the ability to responsibly, ethically, legally, and equitably access and use samples from all of the eukaryotic species across the planet, including those that are under the custodianship of Indigenous Peoples and Local Communities. Here, the biodiversity genomics community is subject to the provisions codified in international, national, and local legislations and customary community norms, principles, and protocols. We propose a framework to support biodiversity genomic researchers, projects, and initiatives in building trustworthy and sustainable partnerships with communities, providing minimum recommendations on how to access, utilize, preserve, handle, share, analyze, and communicate samples, genomics data, and associated Traditional Knowledge obtained from, and in partnership with, Indigenous Peoples and Local Communities across the data-lifecycle.

Extending the CARE Principles from tribal research policies to benefit sharing in genomic research

Indigenous Peoples have historically been targets of extractive research that has led to little to no benefit. In genomics, such research not only exposes communities to harms and risks of misuse, but also deprives such communities of potential benefits. Tribes in the US have been exercising their sovereignty to limit this extractive practice by adopting laws and policies to govern research on their territories and with their citizens. Federally and state recognized tribes are in the strongest position to assert research oversight. Other tribes lack the same authority, given that federal and state governments do not recognize their rights to regulate research, resulting in varying levels of oversight by tribes. These governance measures establish collective protections absent from the US federal government's research oversight infrastructure, while setting expectations regarding benefits to tribes as political collectives. Using a legal epidemiology approach, the paper discusses findings from a review of Tribal research legislation, policy, and administrative materials from 26 tribes in the US. The discussion specifies issues viewed by tribes as facilitators and barriers to securing benefits from research for their nations and members/citizens, and describes preemptive and mitigating strategies pursued by tribes in response. These strategies are set within the framing of the CARE Principles for Indigenous Data Governance (Collective Benefit, Authority to Control, Responsibility, Ethics), a set of standards developed to ensure that decisions made about data pertaining to Indigenous communities at the individual and tribal levels are responsive to their values and collective interests. Our findings illustrate gaps to address for benefit sharing and a need to strengthen Responsibility and Ethics in tribal research governance.