1
|
Gibbon VE, Thompson JC, Alves S. Informed proxy consent for ancient DNA research. Commun Biol 2024; 7:815. [PMID: 38965340 PMCID: PMC11224335 DOI: 10.1038/s42003-024-06413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2024] [Indexed: 07/06/2024] Open
Abstract
Embracing the underlying principles and processes of informed proxy consent or relational autonomy consent in human ancient DNA research can transform research.
Collapse
Affiliation(s)
- Victoria E Gibbon
- Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Observatory 7935, Cape Town, South Africa.
| | - Jessica C Thompson
- Department of Anthropology, Yale University, 10 Sachem Street, New Haven, CT, 06511, USA
- Yale Peabody Museum, Yale University, 170 Whitney Avenue, New Haven, CT, 06511, USA
| | - Sianne Alves
- Office for Inclusivity & Change, Office of the Deputy Vice Chancellor for Transformation: University of Cape Town, Ivan Toms Building, 28 Rhodes Avenue Mowbray, Cape Town, South Africa
| |
Collapse
|
2
|
Lewis DA, Mitchell T, Kowal E. Precision medicine in Australia: indigenous health professionals are needed to improve equity for Aboriginal and Torres Strait Islanders. Int J Equity Health 2024; 23:134. [PMID: 38965527 PMCID: PMC11223270 DOI: 10.1186/s12939-024-02202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Dawn Alison Lewis
- University of Adelaide, Adelaide, 5005, Australia
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Burwood Campus, 3125, Melbourne, Australia
| | - Tala Mitchell
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Burwood Campus, 3125, Melbourne, Australia
| | - Emma Kowal
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Burwood Campus, 3125, Melbourne, Australia.
| |
Collapse
|
3
|
Clark Adnyamathanha JR, Buck Kamilaroi J, Richards-Satour Adnyamathanha And Barngarla A, Lyons Jaadwa L, Brown Yuin A. Towards precision cancer medicine for Aboriginal and Torres Strait Islander cancer health equity. Med J Aust 2024; 221:68-73. [PMID: 38946636 DOI: 10.5694/mja2.52346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/09/2024] [Indexed: 07/02/2024]
Abstract
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.
Collapse
Affiliation(s)
| | - Jessica Buck Kamilaroi
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA
- Centre for Child Health Research, University of Western Australia, Perth, WA
| | | | | | - Alex Brown Yuin
- Telethon Kids Institute, Adelaide, SA
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT
| |
Collapse
|
4
|
Barton KS, Porter KM, Mai T, Claw KG, Hiratsuka VY, Carroll SR, Burke W, Garrison NA. Genetic research within Indigenous communities: Engagement opportunities and pathways forward. Genet Med 2024; 26:101158. [PMID: 38699966 DOI: 10.1016/j.gim.2024.101158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Krysta S Barton
- Biostatistics Epidemiology and Analytics for Research (BEAR) Core, Seattle Children's Research Institute, Seattle, WA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics and Palliative Care, Seattle Children's Research Institute, Seattle, WA
| | - Thyvu Mai
- Institute for Public Health Genetics, University of Washington School of Medicine, Seattle, WA
| | - Katrina G Claw
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Vanessa Y Hiratsuka
- Center for Human Development, College of Health, University of Alaska Anchorage, Anchorage, AK; Southcentral Foundation, Anchorage, AK
| | - Stephanie Russo Carroll
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ; Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA; Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA; Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA.
| |
Collapse
|
5
|
Olowoyo JO, Okoya AA, Adesiyan IM, Awe YT, Lion GN, Agboola OO, Oladeji OM. Environmental health science research: opportunities and challenges for some developing countries in Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-25. [PMID: 38909292 DOI: 10.1080/09603123.2024.2370388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
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.
Collapse
Affiliation(s)
- J O Olowoyo
- Department of Health Sciences and The Water School, Florida Gulf Coast University, Fort Myers, FL, USA
- Department of Biology and Environmental Sciences, Sefako Makgatho Health Sciences, South Africa
| | - A A Okoya
- Institute of Ecology and Environmental Studies, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - I M Adesiyan
- Department of Environmental and Occupational Health, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - Y T Awe
- Environmental Management Program, Pan African University of Life and Earth Sciences, University of Ibadan, Oyo State, Nigeria
| | - G N Lion
- Department of Biology and Environmental Sciences, Sefako Makgatho Health Sciences, South Africa
| | - O O Agboola
- Department of Botany, University Lokoja, Kogi State, Nigeria
- Department of Biological Sciences, Federal University of Health Sciences Otukpo, Benue State, Nigeria
| | - O M Oladeji
- Department of Biology and Environmental Sciences, Sefako Makgatho Health Sciences, South Africa
| |
Collapse
|
6
|
Passmore S, Wood ALC, Barbieri C, Shilton D, Daikoku H, Atkinson QD, Savage PE. Global musical diversity is largely independent of linguistic and genetic histories. Nat Commun 2024; 15:3964. [PMID: 38729968 PMCID: PMC11087526 DOI: 10.1038/s41467-024-48113-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Sam Passmore
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
- Evolution of Cultural Diversity Initiative (ECDI), Australian National University, Canberra, Australia.
| | | | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
- Centre for the Interdisciplinary Study of Language Evolution (ISLE), University of Zurich, Zurich, 8050, Switzerland
- Department of Life and Environmental Sciences, University of Cagliari, 09126, Cagliari, Italy
| | - Dor Shilton
- Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel
- Edelstein Centre for the History and Philosophy of Science, Technology, and Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hideo Daikoku
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | | | - Patrick E Savage
- School of Psychology, University of Auckland, Auckland, New Zealand.
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.
| |
Collapse
|
7
|
Berseth V, Taylor J, Hutchen J, Nguyen V, Schott S, Klenk N. Constructing the public in public perceptions research: A case study of forest genomics. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2024; 33:483-503. [PMID: 38095191 PMCID: PMC11056085 DOI: 10.1177/09636625231210453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
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.
Collapse
|
8
|
Jacko G, Thorpe R, Daly J. Equity in blood transfusion precision services. Int J Equity Health 2024; 23:77. [PMID: 38637779 PMCID: PMC11027542 DOI: 10.1186/s12939-024-02170-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Georgina Jacko
- Pathology and Clinical Governance, Australian Red Cross Lifeblood, Brisbane, QLD, Australia.
| | - Rachel Thorpe
- Strategy and Growth, Australian Red Cross Lifeblood, Melbourne, VIC, Australia
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - James Daly
- Pathology and Clinical Governance, Australian Red Cross Lifeblood, Brisbane, QLD, Australia
| |
Collapse
|
9
|
Rajagopalan RM, Cakici J, Bloss CS. A Vision for Empirical ELSI along the R&D Pipeline. AJOB Empir Bioeth 2024; 15:81-86. [PMID: 38214924 DOI: 10.1080/23294515.2023.2297931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Affiliation(s)
- Ramya M Rajagopalan
- Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, La Jolla, USA
- Center for Empathy and Technology, T. Denny Sanford Institute for Empathy and Compassion, UC San Diego, La Jolla, USA
| | - Julie Cakici
- Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, La Jolla, USA
- School of Public Health, San Diego State University, La Jolla, USA
| | - Cinnamon S Bloss
- Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, La Jolla, USA
- Center for Empathy and Technology, T. Denny Sanford Institute for Empathy and Compassion, UC San Diego, La Jolla, USA
| |
Collapse
|
10
|
Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e15. [PMID: 38516374 PMCID: PMC10955370 DOI: 10.1017/ehs.2024.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
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.
Collapse
Affiliation(s)
| | - Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
11
|
LeBaron von Baeyer S, Crocker R, Rakotoarivony R, Ranaivoarisoa JF, Spiral GJ, Castel S, Farnum A, Vance H, Collins N, Fox K, Wasik K. Why community consultation matters in genomic research benefit-sharing models. Genome Res 2024; 34:1-6. [PMID: 38296591 PMCID: PMC10904008 DOI: 10.1101/gr.278308.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Affiliation(s)
| | - Rebecca Crocker
- Cancer Center, University of Arizona, Tucson, Arizona 85721, USA
| | - Rindra Rakotoarivony
- Department of Anthropobiology and Sustainable Development, University of Antananarivo, Antananarivo 101, Madagascar
| | - Jean Freddy Ranaivoarisoa
- Department of Anthropobiology and Sustainable Development, University of Antananarivo, Antananarivo 101, Madagascar
| | - Germain Jules Spiral
- Department of Anthropobiology and Sustainable Development, University of Antananarivo, Antananarivo 101, Madagascar
| | | | | | | | - Noah Collins
- Department of Anthropology, Princeton University, Princeton, New Jersey 08540, USA
| | - Keolu Fox
- Indigenous Futures Institute, University of California, San Diego, La Jolla, California 92093, USA;
- J. Craig Venter Research Institute, La Jolla, California 92037, USA
| | - Kaja Wasik
- Variant Bio, Seattle, Washington 98109, USA;
- J. Craig Venter Research Institute, La Jolla, California 92037, USA
| |
Collapse
|
12
|
Baynam G, Julkowska D, Bowdin S, Hermes A, McMaster CR, Prichep E, Richer É, van der Westhuizen FH, Repetto GM, Malherbe H, Reichardt JKV, Arbour L, Hudson M, du Plessis K, Haendel M, Wilcox P, Lynch SA, Rind S, Easteal S, Estivill X, Caron N, Chongo M, Thomas Y, Letinturier MCV, Vorster BC. Advancing diagnosis and research for rare genetic diseases in Indigenous peoples. Nat Genet 2024; 56:189-193. [PMID: 38332370 PMCID: PMC11229440 DOI: 10.1038/s41588-023-01642-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Affiliation(s)
- Gareth Baynam
- Rare Care Centre and Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.
- Faculty of Health and Medicine, Division of Pediatrics, University of Western Australia, Perth, Western Australia, Australia.
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia.
- Faculty of Medicine, University of Notre Dame, Fremantle, Western Australia, Australia.
- Faculty of Science and Engineering, Spatial Sciences, Curtin University, Perth, Western Australia, Australia.
- Faculty of Medicine, Notre Dame University, Perth, Western Australia, Australia.
- School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia.
| | - Daria Julkowska
- IRDiRC Scientific Secretariat, French National Institute of Health and Medical Research (Inserm), Paris, France
| | - Sarah Bowdin
- Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge, UK
| | - Azure Hermes
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christopher R McMaster
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute of Genetics, Canadian Institutes of Health Research, Halifax, Nova Scotia, Canada
| | - Elissa Prichep
- Platform on Shaping the Future of Health and Healthcare, World Economic Forum, New York, NY, USA
| | - Étienne Richer
- Institute of Genetics, Canadian Institutes of Health Research, Halifax, Nova Scotia, Canada
| | | | - Gabriela M Repetto
- Facultad de Medicina, Center for Genetics and Genomics, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Helen Malherbe
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Rare Diseases South Africa, Johannesburg, South Africa
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland, Australia
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Victoria, British Columbia, Canada
| | - Maui Hudson
- Faculty of Maori and Indigenous Studies, University of Waikato, Hamilton, New Zealand
| | | | - Melissa Haendel
- Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Sally Ann Lynch
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Ireland
- Academic Centre on Rare Diseases, University College Dublin, Dublin, Ireland
| | - Shamir Rind
- Western Australian Register of Developmental Anomalies, Perth, Western Australia, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xavier Estivill
- Quantitative Genomics Medicine Laboratories (qgenomics), Esplugues de Llobregat, Barcelona, Spain
| | - Nadine Caron
- UBC Centre for Excellence in Indigenous Health, Vancouver, British Columbia, Canada
- UBC Northern Medical Program and Department of Surgery, Prince George, British Columbia, Canada
| | - Meck Chongo
- UBC Centre for Excellence in Indigenous Health, Vancouver, British Columbia, Canada
| | - Yarlalu Thomas
- Western Australian Register of Developmental Anomalies, Perth, Western Australia, Australia
| | | | | |
Collapse
|
13
|
Schubach M, Maass T, Nazaretyan L, Röner S, Kircher M. CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions. Nucleic Acids Res 2024; 52:D1143-D1154. [PMID: 38183205 PMCID: PMC10767851 DOI: 10.1093/nar/gkad989] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 01/07/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Max Schubach
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Thorben Maass
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| | - Lusiné Nazaretyan
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sebastian Röner
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Kircher
- Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany
| |
Collapse
|
14
|
Kępińska AP, Johnson JS, Huckins LM. Open Science Practices in Psychiatric Genetics: A Primer. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:110-119. [PMID: 38298792 PMCID: PMC10829621 DOI: 10.1016/j.bpsgos.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 02/02/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Adrianna P. Kępińska
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Jessica S. Johnson
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Psychiatry Department, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Laura M. Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Psychiatry, Yale University, New Haven, Connecticut
| |
Collapse
|
15
|
Lo YC, Chan TF, Jeon S, Maskarinec G, Taparra K, Nakatsuka N, Yu M, Chen CY, Lin YF, Wilkens LR, Le Marchand L, Haiman CA, Chiang CWK. The accuracy of polygenic score models for anthropometric traits and Type II Diabetes in the Native Hawaiian Population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.25.23300499. [PMID: 38234828 PMCID: PMC10793530 DOI: 10.1101/2023.12.25.23300499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
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.
Collapse
Affiliation(s)
- Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gertraud Maskarinec
- Epidemiology Program, University of Hawai'i Cancer Center, University of Hawai'i, Manoa, Honolulu, HI, USA
| | - Kekoa Taparra
- Standard Health Care, Department of Radiation Oncology, Palo Alto, CA, USA
| | | | - Mingrui Yu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
- Biogen, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
- Department of Public Health & Medical Humanities, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawai'i Cancer Center, University of Hawai'i, Manoa, Honolulu, HI, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawai'i Cancer Center, University of Hawai'i, Manoa, Honolulu, HI, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Epidemiology Program, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Epidemiology Program, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
16
|
Valiani AA, Anderson D, Gonzales A, Gray M, Hardcastle L, Turin TC. Precision health equity for racialized communities. Int J Equity Health 2023; 22:259. [PMID: 38087341 PMCID: PMC10714611 DOI: 10.1186/s12939-023-02049-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Arafaat A Valiani
- The Department of History and Global Health Program, University of Oregon, 1288 University of Oregon, Eugene, OR, 97403, USA.
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3D10, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
| | - David Anderson
- The Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, HMRB 231, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| | - Angela Gonzales
- School of Social Transformation, College of Liberal Arts and Sciences, Arizona State University, PO Box 876403, Tempe, AZ, 85287-6403, USA
| | - Mandi Gray
- The Department of Sociology, Otonabee College 221.1, Trent University, 1600 West Bank Drive, Peterborough, ON, K9J 7B8, Canada
| | - Lorian Hardcastle
- Faculty of Law, University of Calgary, Murray Fraser Hall 3345, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Tanvir C Turin
- The Department of Family Medicine, Cumming School of Medicine, University of Calgary, HSC G012, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada
| |
Collapse
|
17
|
Chapman CR, Quinn GP, Natri HM, Berrios C, Dwyer P, Owens K, Heraty S, Caplan AL. Consideration and Disclosure of Group Risks in Genomics and Other Data-Centric Research: Does the Common Rule Need Revision? THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023:1-14. [PMID: 38010648 PMCID: PMC11167719 DOI: 10.1080/15265161.2023.2276161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
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.
Collapse
Affiliation(s)
| | | | | | - Courtney Berrios
- Children's Mercy Kansas City
- University of Missouri-Kansas City School of Medicine
| | | | | | | | | |
Collapse
|
18
|
Garrison NA, Carroll SR. Genetic research with Indigenous Peoples: perspectives on governance and oversight in the US. Front Res Metr Anal 2023; 8:1286948. [PMID: 38078202 PMCID: PMC10702594 DOI: 10.3389/frma.2023.1286948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/30/2023] [Indexed: 02/12/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Nanibaa' A. Garrison
- Traditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Traditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Traditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stephanie Russo Carroll
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
19
|
Garba I, Sterling R, Plevel R, Carson W, Cordova-Marks FM, Cummins J, Curley C, David-Chavez D, Fernandez A, Hiraldo D, Hiratsuka V, Hudson M, Jäger MB, Jennings LL, Martinez A, Yracheta J, Garrison NA, Carroll SR. Indigenous Peoples and research: self-determination in research governance. Front Res Metr Anal 2023; 8:1272318. [PMID: 38033627 PMCID: PMC10685893 DOI: 10.3389/frma.2023.1272318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/26/2023] [Indexed: 12/02/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Ibrahim Garba
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Rogena Sterling
- Living on the lands of Waikato-Tainui, Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Rebecca Plevel
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
- Lands of the Congaree, Catawba, Muscogee, and Eastern Cherokee, Law Library, School of Law, University of South Carolina, Columbia, SC, United States
| | - William Carson
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | - Felina M. Cordova-Marks
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | - Jewel Cummins
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
- Lands of the O'odham and Yaqui peoples, American Indian Studies-Graduate Interdisciplinary Program, College of Social and Behavioral Sciences, University of Arizona, Tucson, AZ, United States
| | - Caleigh Curley
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | - Dominique David-Chavez
- Nunt'zi (Ute), Hinono'eino' (Arapaho), and Tsitsistas (Cheyenne) homelands, Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO, United States
| | - Adam Fernandez
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Danielle Hiraldo
- Ancestral homeland of Eastern Siouan-speaking Indigenous peoples (Yesàh, “The People”), American Indian Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Vanessa Hiratsuka
- Dena'ina Ełnena, Center for Human Development, College of Health, University of Alaska Anchorage, Anchorage, AK, United States
| | - Maui Hudson
- Living on the lands of Waikato-Tainui, Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Mary Beth Jäger
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Lydia L. Jennings
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Andrew Martinez
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Joseph Yracheta
- Lands of the Oceti Sakowin (Seven council fires of the Lakota/Nakoda/Dakota), Native BioData Consortium, Eagle Butte, SD, United States
- Ancestral homelands of the Paskestikweya (Piscataway) band of Chaptico, the Moyaone, Nanjemoy, and the Potapoco, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Nanibaa' A. Garrison
- Traditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Institute for Society and Genetics, College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
- Traditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Traditional, ancestral and unceded territory of the Gabrielino/Tongva peoples, Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stephanie Russo Carroll
- Lands of the O'odham and Yaqui peoples, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Lands of the O'odham and Yaqui peoples, Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
20
|
Skantharajah N, Baichoo S, Boughtwood TF, Casas-Silva E, Chandrasekharan S, Dave SM, Fakhro KA, Falcon de Vargas AB, Gayle SS, Gupta VK, Hendricks-Sturrup R, Hobb AE, Li S, Llamas B, Lopez-Correa C, Machirori M, Melendez-Zajgla J, Millner MA, Page AJ, Paglione LD, Raven-Adams MC, Smith L, Thomas EM, Kumuthini J, Corpas M. Equity, diversity, and inclusion at the Global Alliance for Genomics and Health. CELL GENOMICS 2023; 3:100386. [PMID: 37868041 PMCID: PMC10589617 DOI: 10.1016/j.xgen.2023.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
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.
Collapse
Affiliation(s)
- Neerjah Skantharajah
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | | | | | - Sanjay M. Dave
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Khalid A. Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Aida B. Falcon de Vargas
- Hospital Vargas de Caracas, Vargas Medical School, Universidad Central de Venezuela, Caracas, Venezuela
- Hospital de Clínicas Caracas, Caracas, Venezuela
| | | | - Vivek K. Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | | - Stephanie Li
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
| | | | - Mavis Machirori
- Ada Lovelace Institute, London, UK
- PEALS, Newcastle University, Newcastle Upon Tyne, UK
| | | | - Mareike A. Millner
- Maastricht University, Health Law and Governance Group, Maastricht, the Netherlands
| | - Angela J.H. Page
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Laura D. Paglione
- Spherical Cow Group, New York, NY, USA
- Laura Paglione LLC, New York, NY, USA
| | - Maili C. Raven-Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | - Lindsay Smith
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Ericka M. Thomas
- The All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Judit Kumuthini
- South African National Bioinformatics Institute, University of Western Cape, Cape Town, South Africa
| | - Manuel Corpas
- School of Life Sciences, University of Westminster, London, UK
| |
Collapse
|
21
|
Handsley-Davis M, Anderson MZ, Bader AC, Ehau-Taumaunu H, Fox K, Kowal E, Weyrich LS. Microbiome ownership for Indigenous peoples. Nat Microbiol 2023; 8:1777-1786. [PMID: 37770744 DOI: 10.1038/s41564-023-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
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.
Collapse
Affiliation(s)
- Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada
| | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, USA
| | - Keolu Fox
- Department of Anthropology, Global Health Program, and Indigenous Futures Institute, University of California, San Diego, CA, USA
| | - Emma Kowal
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Melbourne, Victoria, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, USA.
| |
Collapse
|
22
|
Bader AC, Van Zuylen EM, Handsley-Davis M, Alegado RA, Benezra A, Pollet RM, Ehau-Taumaunu H, Weyrich LS, Anderson MZ. A relational framework for microbiome research with Indigenous communities. Nat Microbiol 2023; 8:1768-1776. [PMID: 37770743 DOI: 10.1038/s41564-023-01471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/26/2023] [Indexed: 09/30/2023]
Abstract
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.
Collapse
Affiliation(s)
- Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada.
| | - Essie M Van Zuylen
- Department of Microbiology and Immunology, University of Otago, Dunedin North, Dunedin, New Zealand
- School of Product Design, University of Canterbury, Christchurch, New Zealand
| | - Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
| | - Rosanna A Alegado
- Department of Oceanography, University of Hawai'i Mānoa, Honolulu, HI, USA
| | - Amber Benezra
- Department of Science and Technology Studies, Stevens Institute of Technology, Hoboken, NJ, USA
| | | | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, USA
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
23
|
Tamburrini C, Dahinten SL, Saihueque RRR, Ávila-Arcos MC, Parolin ML. Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:161-176. [PMID: 37525572 DOI: 10.1002/ajpa.24821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 06/12/2023] [Accepted: 07/09/2023] [Indexed: 08/02/2023]
Abstract
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.
Collapse
Affiliation(s)
- Camila Tamburrini
- Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina
| | - Silvia Lucrecia Dahinten
- Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina
| | - Rubén Ricardo Romero Saihueque
- Dirección de Asuntos Indígenas, Subsecretaría de Derechos Humanos, Ministerio de Gobierno y Justicia del Chubut, Rawson, Chubut, Argentina
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, Universidad Nacional Autónoma de Mexico (UNAM), Santiago de Querétaro, Mexico
| | - María Laura Parolin
- Instituto de Diversidad y Evolución Austral (IDEAus, CCT CONICET-CENPAT), Puerto Madryn, Chubut, Argentina
| |
Collapse
|
24
|
Te Aika B, Liggins L, Rye C, Perkins EO, Huh J, Brauning R, Godfery T, Black MA. Aotearoa genomic data repository: An āhuru mōwai for taonga species sequencing data. Mol Ecol Resour 2023. [PMID: 37712601 DOI: 10.1111/1755-0998.13866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/04/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
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.
Collapse
Affiliation(s)
- Ben Te Aika
- Research and Enterprise Office, University of Otago, Dunedin, New Zealand
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
- Genomics Aotearoa, New Zealand
| | - Claire Rye
- New Zealand eScience Infrastructure, University of Auckland, Auckland, New Zealand
| | - E Owen Perkins
- New Zealand eScience Infrastructure, University of Auckland, Auckland, New Zealand
| | - Jun Huh
- New Zealand eScience Infrastructure, University of Auckland, Auckland, New Zealand
| | - Rudiger Brauning
- Genomics Aotearoa, New Zealand
- Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, Otago, New Zealand
| | - Tracey Godfery
- Genomics Aotearoa, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Genomics Aotearoa, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| |
Collapse
|
25
|
Wylie MJ, Kitson J, Russell K, Yoshizaki G, Yazawa R, Steeves TE, Wellenreuther M. Fish germ cell cryobanking and transplanting for conservation. Mol Ecol Resour 2023. [PMID: 37712134 DOI: 10.1111/1755-0998.13868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
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.
Collapse
Affiliation(s)
- Matthew J Wylie
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd, Invercargill, New Zealand
| | - Khyla Russell
- Kāti Huirapa Rūnaka ki Puketeraki, Karitane, New Zealand
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ryosuke Yazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
26
|
Harney É, Sirak K, Sedig J, Micheletti S, Curry R, Ancona Esselmann S, Reich D. Ethical considerations when co-analyzing ancient DNA and data from private genetic databases. Am J Hum Genet 2023; 110:1447-1453. [PMID: 37541241 PMCID: PMC10502734 DOI: 10.1016/j.ajhg.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 08/06/2023] Open
Abstract
Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.
Collapse
Affiliation(s)
- Éadaoin Harney
- 23andMe, Inc., Sunnyvale, CA 94043, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Roslyn Curry
- 23andMe, Inc., Sunnyvale, CA 94043, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
27
|
Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, Kamau J, Kraft TS, Lim YAL, Martins DJ, Mogoi D, Pajukanta P, Perry GH, Pontzer H, Trumble BC, Urlacher SS, Venkataraman VV, Wallace IJ, Gurven M, Lieberman DE, Ayroles JF. Applying an evolutionary mismatch framework to understand disease susceptibility. PLoS Biol 2023; 21:e3002311. [PMID: 37695771 PMCID: PMC10513379 DOI: 10.1371/journal.pbio.3002311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/21/2023] [Indexed: 09/13/2023] Open
Abstract
Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.
Collapse
Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew G. Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America
| | - Andrew W. Dahl
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Orrin Devinsky
- Department of Neurology, NYU Langone Comprehensive Epilepsy Center, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Angela R. Garcia
- Department of Anthropology, Stanford University, Stanford, California, United States of America
| | - Christopher D. Golden
- Department of Nutrition, Harvard T H Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph Kamau
- One Health Centre, Institute of Primate Research, Karen, Nairobi, Kenya
| | - Thomas S. Kraft
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Yvonne A. L. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Dino J. Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, New York, United States of America
| | - Donald Mogoi
- Department of Medical Services and Public Health, Ministry of Health Laikipia County, Nanyuki, Kenya
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, United States of America
| | - George H. Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Herman Pontzer
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Benjamin C. Trumble
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Samuel S. Urlacher
- Department of Anthropology, Baylor University, Waco, Texas, United States of America
| | - Vivek V. Venkataraman
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Ian J. Wallace
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Michael Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Daniel E. Lieberman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Julien F. Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
28
|
Soares GH, Hedges J, Sethi S, Poirier B, Jamieson L. From biocolonialism to emancipation: considerations on ethical and culturally respectful omics research with indigenous Australians. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2023; 26:487-496. [PMID: 37171744 PMCID: PMC10425494 DOI: 10.1007/s11019-023-10151-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
As part of a (bio)colonial project, the biological information of Indigenous Peoples has historically been under scientific scrutiny, with very limited benefits for communities and donors. Negative past experiences have contributed to further exclude Indigenous communities from novel developments in the field of omics research. Over the past decade, new guidelines, reflections, and projects of genetic research with Indigenous Peoples have flourished in Australia, providing opportunities to move the field into a place of respect and ethical relationships. This review explores the ethical and cultural implications of the use of biological samples from Indigenous communities in biomedical research. A structured framework outlining emerging topics of interest for the development of respectful omics research partnerships with Indigenous Australians is presented. This paper highlights aspects related to Indigenous governance, community and individual consent, respectful handling of biological samples, data management, and communication in order to protect Indigenous interests and rights and to promote communities' autonomy.
Collapse
Affiliation(s)
- Gustavo H Soares
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Hedges
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Sneha Sethi
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Brianna Poirier
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Lisa Jamieson
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
29
|
Joshi AD, Rahnavard A, Kachroo P, Mendez KM, Lawrence W, Julián-Serrano S, Hua X, Fuller H, Sinnott-Armstrong N, Tabung FK, Shutta KH, Raffield LM, Darst BF. An epidemiological introduction to human metabolomic investigations. Trends Endocrinol Metab 2023; 34:505-525. [PMID: 37468430 PMCID: PMC10527234 DOI: 10.1016/j.tem.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
Metabolomics holds great promise for uncovering insights around biological processes impacting disease in human epidemiological studies. Metabolites can be measured across biological samples, including plasma, serum, saliva, urine, stool, and whole organs and tissues, offering a means to characterize metabolic processes relevant to disease etiology and traits of interest. Metabolomic epidemiology studies face unique challenges, such as identifying metabolites from targeted and untargeted assays, defining standards for quality control, harmonizing results across platforms that often capture different metabolites, and developing statistical methods for high-dimensional and correlated metabolomic data. In this review, we introduce metabolomic epidemiology to the broader scientific community, discuss opportunities and challenges presented by these studies, and highlight emerging innovations that hold promise to uncover new biological insights.
Collapse
Affiliation(s)
- Amit D Joshi
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin M Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wayne Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sachelly Julián-Serrano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Public Health, University of Massachusetts Lowell, Lowell, MA, USA
| | - Xinwei Hua
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Harriett Fuller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nasa Sinnott-Armstrong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Fred K Tabung
- The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH, USA
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Burcu F Darst
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| |
Collapse
|
30
|
Casaletto J, Bernier A, McDougall R, Cline MS. Federated Analysis for Privacy-Preserving Data Sharing: A Technical and Legal Primer. Annu Rev Genomics Hum Genet 2023; 24:347-368. [PMID: 37253596 PMCID: PMC10846631 DOI: 10.1146/annurev-genom-110122-084756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Continued advances in precision medicine rely on the widespread sharing of data that relate human genetic variation to disease. However, data sharing is severely limited by legal, regulatory, and ethical restrictions that safeguard patient privacy. Federated analysis addresses this problem by transferring the code to the data-providing the technical and legal capability to analyze the data within their secure home environment rather than transferring the data to another institution for analysis. This allows researchers to gain new insights from data that cannot be moved, while respecting patient privacy and the data stewards' legal obligations. Because federated analysis is a technical solution to the legal challenges inherent in data sharing, the technology and policy implications must be evaluated together. Here, we summarize the technical approaches to federated analysis and provide a legal analysis of their policy implications.
Collapse
Affiliation(s)
- James Casaletto
- Genomics Institute, University of California, Santa Cruz, California, USA; ,
| | - Alexander Bernier
- Centre of Genomics and Policy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; ,
| | - Robyn McDougall
- Centre of Genomics and Policy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada; ,
| | - Melissa S Cline
- Genomics Institute, University of California, Santa Cruz, California, USA; ,
| |
Collapse
|
31
|
Subica AM. CRISPR in Public Health: The Health Equity Implications and Role of Community in Gene-Editing Research and Applications. Am J Public Health 2023; 113:874-882. [PMID: 37200601 PMCID: PMC10323846 DOI: 10.2105/ajph.2023.307315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/20/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) is a Nobel Prize-winning technology that holds significant promise for revolutionizing the prevention and treatment of human disease through gene editing. However, CRISPR's public health implications remain relatively uncertain and underdiscussed because (1) targeting genetic factors alone will have limited influence on population health, and (2) minority populations (racial/ethnic, sexual and gender)-who bear the nation's greatest health burdens-historically suffer unequal benefits from emerging health care innovations and tools. This article introduces CRISPR and its potential public health benefits (e.g., improving virus surveillance, curing genetic diseases that pose public health problems such as sickle cell anemia) while outlining several major ethical and practical threats to health equity. This includes minorities' grave underrepresentation in genomics research, which may lead to less effective and accepted CRISPR tools and therapies for these groups, and their anticipated unequal access to these tools and therapies in health care. Informed by the principles of fairness, justice, and equitable access, ensuring gene editing promotes rather than diminishes health equity will require the meaningful centering and engagement of minority patients and populations in gene-editing research using community-based participatory research approaches. (Am J Public Health. 2023;113(8):874-882. https://doi.org/10.2105/AJPH.2023.307315).
Collapse
Affiliation(s)
- Andrew M Subica
- Andrew M. Subica is with the Department of Social Medicine, Population, and Public Health, University of California, Riverside School of Medicine
| |
Collapse
|
32
|
Crandall ED, Toczydlowski RH, Liggins L, Holmes AE, Ghoojaei M, Gaither MR, Wham BE, Pritt AL, Noble C, Anderson TJ, Barton RL, Berg JT, Beskid SG, Delgado A, Farrell E, Himmelsbach N, Queeno SR, Trinh T, Weyand C, Bentley A, Deck J, Riginos C, Bradburd GS, Toonen RJ. Importance of timely metadata curation to the global surveillance of genetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14061. [PMID: 36704891 PMCID: PMC10751740 DOI: 10.1111/cobi.14061] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 05/18/2023]
Abstract
Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.
Collapse
Affiliation(s)
- Eric D Crandall
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rachel H Toczydlowski
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Libby Liggins
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Ann E Holmes
- Department of Animal Science, University of California, Davis, Davis, California, USA
| | - Maryam Ghoojaei
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Briana E Wham
- Department of Research Informatics and Publishing, The Pennsylvania State University Libraries, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrea L Pritt
- Madlyn L. Hanes Library, The Pennsylvania State University Libraries, Pennsylvania State University, Middletown, Pennsylvania, USA
| | - Cory Noble
- School of Natural Sciences, Massey University, Auckland, New Zealand
| | - Tanner J Anderson
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Randi L Barton
- Department of Marine Science, California State University Monterey Bay, Seaside, California, USA
- Moss Landing Marine Laboratories, Moss Landing, California, USA
| | - Justin T Berg
- UOG Marine Laboratory, University of Guam, Mangilao, Guam
| | - Sofia G Beskid
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Alonso Delgado
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Emily Farrell
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Nan Himmelsbach
- Department of Natural Science, Hawai'i Pacific University, Honolulu, Hawaii, USA
| | - Samantha R Queeno
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Thienthanh Trinh
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Courtney Weyand
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Andrew Bentley
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, USA
| | - John Deck
- Berkeley Natural History Museums, University of California, Berkeley, Berkeley, California, USA
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Gideon S Bradburd
- Ecology, Evolution, and Behavior Program, Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, Hawaii, USA
| |
Collapse
|
33
|
Arango-Isaza E, Capodiferro MR, Aninao MJ, Babiker H, Aeschbacher S, Achilli A, Posth C, Campbell R, Martínez FI, Heggarty P, Sadowsky S, Shimizu KK, Barbieri C. The genetic history of the Southern Andes from present-day Mapuche ancestry. Curr Biol 2023:S0960-9822(23)00607-3. [PMID: 37279753 DOI: 10.1016/j.cub.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/08/2023]
Abstract
The southernmost regions of South America harbor some of the earliest evidence of human presence in the Americas. However, connections with the rest of the continent and the contextualization of present-day indigenous ancestries remain poorly resolved. In this study, we analyze the genetic ancestry of one of the largest indigenous groups in South America: the Mapuche. We generate genome-wide data from 64 participants from three Mapuche populations in Southern Chile: Pehuenche, Lafkenche, and Huilliche. Broadly, we describe three main ancestry blocks with a common origin, which characterize the Southern Cone, the Central Andes, and Amazonia. Within the Southern Cone, ancestors of the Mapuche lineages differentiated from those of the Far South during the Middle Holocene and did not experience further migration waves from the north. We find that the deep genetic split between the Central and Southern Andes is followed by instances of gene flow, which may have accompanied the southward spread of cultural traits from the Central Andes, including crops and loanwords from Quechua into Mapudungun (the language of the Mapuche). Finally, we report close genetic relatedness between the three populations analyzed, with the Huilliche characterized additionally by intense recent exchanges with the Far South. Our findings add new perspectives on the genetic (pre)history of South America, from the first settlement through to the present-day indigenous presence. Follow-up fieldwork took these results back to the indigenous communities to contextualize the genetic narrative alongside indigenous knowledge and perspectives.
Collapse
Affiliation(s)
- Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland.
| | - Marco Rosario Capodiferro
- Trinity College Dublin, Dublin 2, Ireland; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | | | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Cosimo Posth
- Institute for Archaeological Sciences, Archaeo, and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Roberto Campbell
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile
| | - Felipe I Martínez
- Escuela de Antropología, Pontificia Universidad Católica de Chile, Santiago 6904411, Chile; Center for Intercultural and Indigenous Research, Santiago 7820436, Chile
| | - Paul Heggarty
- "Waves" ERC Group, Department of Human Behavior, Evolution and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Scott Sadowsky
- Department of Linguistics and Literature, Universidad de Cartagena, Cartagena 130001, Colombia
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland; Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
| |
Collapse
|
34
|
Whitmore L, McCauley M, Farrell JA, Stammnitz MR, Koda SA, Mashkour N, Summers V, Osborne T, Whilde J, Duffy DJ. Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA. Nat Ecol Evol 2023; 7:873-888. [PMID: 37188965 PMCID: PMC10250199 DOI: 10.1038/s41559-023-02056-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/29/2023] [Indexed: 05/17/2023]
Abstract
The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from 'wildlife' environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.
Collapse
Affiliation(s)
- Liam Whitmore
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
- Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | - Mark McCauley
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Jessica A Farrell
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Maximilian R Stammnitz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Samantha A Koda
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Narges Mashkour
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Victoria Summers
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Todd Osborne
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - Jenny Whilde
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA
| | - David J Duffy
- Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA.
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
35
|
Lyle K, Weller S, Horton R, Lucassen A. Immortal data: a qualitative exploration of patients' understandings of genomic data. Eur J Hum Genet 2023; 31:681-686. [PMID: 37002328 PMCID: PMC10250296 DOI: 10.1038/s41431-023-01325-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 04/03/2023] Open
Abstract
As ambitions to 'mainstream' genetic and genomic medicine in the UK advance, patients are increasingly exposed to information about genomic data. Unlike the results of many other medical investigations which are linked to the time of sample collection, genomic testing provides immortal data that do not change across time, and may have relevance for relatives and generations far beyond the patient's own lifespan. This immortality raises new ethical challenges for healthcare professionals, patients and families alike, such as ensuring consent for possible future interpretations; determining when genomic data are best sought (at birth, on illness etc) and reinterpreted; and balancing the confidentiality of patients and duties of care towards others. This paper reports on qualitative work exploring the perspectives of patients and relatives participating in genomic testing, and suggests that their engagements with this immortality are shaped by: the contrast between the simplicity of sample provision and information gathered; understandings of heritability; and notions of genomic data as a collective resource. We discuss the implications this holds for practice and argue that the immortality of genomic data must take a more prominent position in patient and healthcare professional interactions.
Collapse
Affiliation(s)
- Kate Lyle
- Clinical Ethics, Law and Society (CELS), Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Clinical Ethics, Law and Society (CELS), Primary Care Population Sciences and Medical Education, University of Southampton Faculty of Medicine, Southampton, UK.
| | - Susie Weller
- Clinical Ethics, Law and Society (CELS), Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Clinical Ethics, Law and Society (CELS), Primary Care Population Sciences and Medical Education, University of Southampton Faculty of Medicine, Southampton, UK
- Centre for Personalised Medicine, University of Oxford, Oxford, UK
| | - Rachel Horton
- Clinical Ethics, Law and Society (CELS), Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Clinical Ethics, Law and Society (CELS), Primary Care Population Sciences and Medical Education, University of Southampton Faculty of Medicine, Southampton, UK
- Centre for Personalised Medicine, University of Oxford, Oxford, UK
| | - Anneke Lucassen
- Clinical Ethics, Law and Society (CELS), Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Clinical Ethics, Law and Society (CELS), Primary Care Population Sciences and Medical Education, University of Southampton Faculty of Medicine, Southampton, UK
- Centre for Personalised Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
36
|
McWhirter R, Hermes A, Huebner S, Brown A. Community Engagement and the Protection-Inclusion Dilemma. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:100-102. [PMID: 37220360 DOI: 10.1080/15265161.2023.2201202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
|
37
|
Dubowsky JG, Estevez JJ, Craig JE, Appukuttan B, Carr JM. Disease profiles in the Indigenous Australian population are suggestive of a common complement control haplotype. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105453. [PMID: 37245779 DOI: 10.1016/j.meegid.2023.105453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Aboriginal and Torres Strait Islander People (respectfully referred to as Indigenous Australians herein) are disparately burdened by many infectious and chronic diseases relative to Australians with European genetic ancestry. Some of these diseases are described in other populations to be influenced by the inherited profile of complement genes. These include complement factor B, H, I and complement factor H-related (CFHR) genes that can contribute to a polygenic complotype. Here the focus is on the combined deletion of CFHR1 and 3 to form a common haplotype (CFHR3-1Δ). The prevalence of CFHR3-1Δ is high in people with Nigerian and African American genetic ancestry and correlates to a higher frequency and severity of systemic lupus erythematosus (SLE) but a lower prevalence of age-related macular degeneration (AMD) and IgA-nephropathy (IgAN). This pattern of disease is similarly observed among Indigenous Australian communities. Additionally, the CFHR3-1Δ complotype is also associated with increased susceptibility to infection with pathogens, such as Neisseria meningitidis and Streptococcus pyogenes, which also have high incidences in Indigenous Australian communities. The prevalence of these diseases, while likely influenced by social, political, environmental and biological factors, including variants in other components of the complement system, may also be suggestive of the CFHR3-1Δ haplotype in Indigenous Australians. These data highlight a need to define the Indigenous Australian complotypes, which may lead to the discovery of new risk factors for common diseases and progress towards precision medicines for treating complement-associated diseases in Indigenous and non-Indigenous populations. Herein, the disease profiles suggestive of a common complement CFHR3-1Δ control haplotype are examined.
Collapse
Affiliation(s)
- Joshua G Dubowsky
- Microbiology and Infectious Diseases, College of Medicine and Public Health, and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Jose J Estevez
- Wardliparingga Aboriginal Health Equity Theme, South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia; Flinders Centre for Ophthalmology, Eye and Vision Research, Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia; Caring Futures Institute, College of Nursing and Health Sciences, Optometry and Vision Science, Flinders University, Adelaide, Australia
| | - Jamie E Craig
- Flinders Centre for Ophthalmology, Eye and Vision Research, Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Binoy Appukuttan
- Molecular Medical Science, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Jillian M Carr
- Microbiology and Infectious Diseases, College of Medicine and Public Health, and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia.
| |
Collapse
|
38
|
Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.
Collapse
Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| |
Collapse
|
39
|
Hudson M, Carroll SR, Anderson J, Blackwater D, Cordova-Marks FM, Cummins J, David-Chavez D, Fernandez A, Garba I, Hiraldo D, Jäger MB, Jennings LL, Martinez A, Sterling R, Walker JD, Rowe RK. Indigenous Peoples' Rights in Data: a contribution toward Indigenous Research Sovereignty. Front Res Metr Anal 2023; 8:1173805. [PMID: 37215248 PMCID: PMC10192690 DOI: 10.3389/frma.2023.1173805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Stephanie Russo Carroll
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Jane Anderson
- Anthropology and Program in Museum Studies, New York University, New York, NY, United States
| | | | - Felina M. Cordova-Marks
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | - Jewel Cummins
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Dominique David-Chavez
- Forest and Rangeland Stewardship Department, Colorado State University, Fort Collins, CO, United States
| | - Adam Fernandez
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Ibrahim Garba
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Danielle Hiraldo
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
- American Indian Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Mary Beth Jäger
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Lydia L. Jennings
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Andrew Martinez
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Rogena Sterling
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | | | - Robyn K. Rowe
- School of Computing, Queen's University, Kingston, ON, Canada
| |
Collapse
|
40
|
Mathews DJH, Ferryman K, Faden R. Designing Health Care Artificial Intelligence That Comports With the Values of Patients-Children Are People Whose Voices Must Be Heard. JAMA Netw Open 2023; 6:e2310605. [PMID: 37126351 DOI: 10.1001/jamanetworkopen.2023.10605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Affiliation(s)
- Debra J H Mathews
- Berman Institute of Bioethics, Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Kadija Ferryman
- Berman Institute of Bioethics, Department of Health Policy and Management Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Ruth Faden
- Berman Institute of Bioethics, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
41
|
Bader AC, Carbaugh AE, Davis JL, Krupa KL, Malhi RS. Biological samples taken from Native American Ancestors are human remains under NAGPRA. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37052272 DOI: 10.1002/ajpa.24726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/28/2023] [Accepted: 03/05/2023] [Indexed: 04/14/2023]
Abstract
In the United States, the Native American Graves Protection and Repatriation Act (NAGPRA) provides a specific framework for the disposition of Native American Ancestral remains within its purview. However, samples such as a bone fragment, tooth, or other biological tissue taken from the remains of these Ancestors have been treated by institutions and researchers as independent of the individual from whom they were removed and used in destructive research such as paleogenomic and other archaeometric analyses without consultation, consent, and collaboration from Native American communities; are not cared for in keeping with the current best practices for Indigenous Ancestors; and are not likely to be repatriated to their communities. Here, we demonstrate that any biological samples removed from Ancestors who are covered under NAGPRA must also be handled according to the stipulations defined for "human remains" within the legislation. As such, we are not proposing a change to existing legislation, but rather best practices, specific to the context of the United States and NAGPRA, relating to the use of and care for biological samples taken from Native American Ancestors.
Collapse
Affiliation(s)
- Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada
- Department of Culture and History, Sealaska Heritage Institute, Juneau, Alaska, USA
| | - Aimée E Carbaugh
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jenny L Davis
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- American Indian Studies Program, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Krystiana L Krupa
- Office of the Vice Chancellor for Research and Innovation, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- American Indian Studies Program, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
42
|
Warren V, Critchley C, McWhirter R, Walshe J, Nicol D. Context matters in genomic data sharing: a qualitative investigation into responses from the Australian public. BMC Med Genomics 2023; 15:275. [PMID: 37005651 PMCID: PMC10068139 DOI: 10.1186/s12920-023-01452-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/01/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND Understanding public attitudes to genomic data sharing is widely seen as key in shaping effective governance. However, empirical research in this area often fails to capture the contextual nuances of diverse sharing practices and regulatory concerns encountered in real-world genomic data sharing. This study aimed to investigate factors affecting public attitudes to data sharing through responses to diverse genomic data sharing scenarios. METHODS A set of seven empirically validated genomic data sharing scenarios reflecting a range of current practices in Australia was used in an open-ended survey of a diverse sample of the Australian public (n = 243). Qualitative responses were obtained for each of the scenarios. Respondents were each allocated one scenario and asked five questions on: whether (and why/not) they would share data; what sharing would depend on; benefits and risks of sharing; risks they were willing to accept if sharing was certain to result in benefits; and what could increase their comfort about sharing and any potential risk. A thematic analysis was used to examine responses, coded and validated by two blinded coders. RESULTS Participants indicated an overall high willingness to share genomic information, although this willingness varied considerably between different scenarios. A strong perception of benefits was reported as the foremost explanation for willingness to share across all scenarios. The high degree of convergence in the perception of benefits and the types of benefits identified by participants across all the scenarios suggests that the differentiation in intention to share may lie in perceptions of risk, which showed distinct patterns within and between the different scenarios. Some concerns were shared strongly across all scenarios, particularly benefit sharing, future use, and privacy. CONCLUSIONS Qualitative responses provide insight into popular assumptions regarding existing protections, conceptions of privacy, and which trade-offs are generally acceptable. Our results indicate that public attitudes and concerns are heterogeneous and influenced by the context in which sharing takes place. The convergence of key themes such as benefits and future uses point to core concerns that must be centred in regulatory responses to genomic data sharing.
Collapse
Affiliation(s)
- Vanessa Warren
- School of Law, University of Tasmania, Sandy Bay, TAS, Australia.
| | - Christine Critchley
- School of Law, University of Tasmania, Sandy Bay, TAS, Australia
- School of Health Science, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Rebekah McWhirter
- School of Law, University of Tasmania, Sandy Bay, TAS, Australia
- School of Medicine, Deakin University, Waurn Ponds, VIC, Australia
| | - Jarrod Walshe
- School of Health Science, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Dianne Nicol
- School of Law, University of Tasmania, Sandy Bay, TAS, Australia
| |
Collapse
|
43
|
Abstract
Integration of the world's natural history collections can provide a resource for decision-makers.
Collapse
Affiliation(s)
- Kirk R Johnson
- National Museum of Natural History (NMNH), Smithsonian Institution, Washington, DC, USA
| | - Ian F P Owens
- Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA
| | | |
Collapse
|
44
|
Broderick D, Marsh R, Waite D, Pillarisetti N, Chang AB, Taylor MW. Realising respiratory microbiomic meta-analyses: time for a standardised framework. MICROBIOME 2023; 11:57. [PMID: 36945040 PMCID: PMC10031919 DOI: 10.1186/s40168-023-01499-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
In microbiome fields of study, meta-analyses have proven to be a valuable tool for identifying the technical drivers of variation among studies and results of investigations in several diseases, such as those of the gut and sinuses. Meta-analyses also represent a powerful and efficient approach to leverage existing scientific data to both reaffirm existing findings and generate new hypotheses within the field. However, there are currently limited data in other fields, such as the paediatric respiratory tract, where extension of original data becomes even more critical due to samples often being difficult to obtain and process for a range of both technical and ethical reasons. Performing such analyses in an evolving field comes with challenges related to data accessibility and heterogeneity. This is particularly the case in paediatric respiratory microbiomics - a field in which best microbiome-related practices are not yet firmly established, clinical heterogeneity abounds and ethical challenges can complicate sharing of patient data. Having recently conducted a large-scale, individual participant data meta-analysis of the paediatric respiratory microbiota (n = 2624 children from 20 studies), we discuss here some of the unique barriers facing these studies and open and invite a dialogue towards future opportunities. Video Abstract.
Collapse
Affiliation(s)
- David Broderick
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Robyn Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - David Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| |
Collapse
|
45
|
Cortez AD, Lippert D, Davis JL, Nicholas G, Malhi RS, Weyrich LS, Claw KG, Bader AC, Colwell C. Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 36799477 DOI: 10.1002/ajpa.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES The field of paleogenomics has rapidly grown, influencing a range of scientific fields and drawing notice from the public. In the United States, this work is especially salient for Native Americans, who are frequently the subject of ancient DNA analyses, but are less frequently included as researchers, collaborators, or advisors. This article seeks to deepen our understanding of the current state of paleogenomics so that the field can center Indigenous peoples and their experiences, knowledges, and stakes in the research process. MATERIALS AND METHODS We conducted 31 semi-structured interviews with researchers from three paleogenomics labs located in North America and Europe. We used a responsive interviewing technique where the interview resembled a conversation around a set of questions that could change depending upon the interviewee's answers and experiences. We then employed a theme-based analysis of the interviews. RESULTS Through this analysis, we are able to identify practices in the field related to training, the structuring of labs and projects, consent, data control, Ancestor care, and funding that influence various forms of engagement with Indigenous peoples, and which foster or delimit ethical commitments to descendant communities. DISCUSSION This research not only elucidates contemporary practices in paleogenomics labs but also identifies specific areas of potential intervention to help researchers work toward ethical and collaborative paleogenomic research with Indigenous peoples. Using these results, researchers and community advocates can work toward reorienting the field of paleogenomics toward ethical research with Indigenous peoples.
Collapse
Affiliation(s)
| | - Dorothy Lippert
- Repatriation Office, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jenny L Davis
- American Indian Studies, Department of Anthropology, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| | - George Nicholas
- Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Ripan S Malhi
- Department of Anthropology, Carl R Woese Institute for Genomic Biology, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Katrina G Claw
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Canada
| | | |
Collapse
|
46
|
De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
Collapse
Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
| |
Collapse
|
47
|
Abstract
The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article "Ethics of DNA research on human remains: five globally applicable guidelines" published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of "scientific" and "community" concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines' authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on "ethical" grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research.
Collapse
|
48
|
How does the genomic naive public perceive whole genomic testing for health purposes? A scoping review. Eur J Hum Genet 2023; 31:35-47. [PMID: 36257982 PMCID: PMC9822972 DOI: 10.1038/s41431-022-01208-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 09/25/2022] [Accepted: 09/29/2022] [Indexed: 02/07/2023] Open
Abstract
The benefits of genomic testing are primarily reported in rare disease, cancer diagnosis and disease management. However, as research into its application in common, more complex conditions grows, as well as the increased prevalence of carrier screening programs, the genomic naive public is more likely to be offered testing in future. To promote social acceptability and ethical application of this technology, it is essential that public perceptions of genomics are considered. Previous studies, however, have primarily focussed on the views of those with genetic conditions or those undergoing genetic testing. The aim of this scoping review is to investigate the genomic naive public's perceptions of clinical genomics and clinical genomic testing. Embase, MEDLINE and PubMed databases were searched, with a total of 3460 articles identified. Data analysis was organised according to the nonadoption, abandonment, scale-up, spread, and sustainability (NASSS) framework. Sixteen full-text articles were included in the final analysis. Most of the studies used questionnaires to determine attitudes of the public toward clinical genomics (n = 12). Public perceptions were found to underpin technology (Domain 2), value proposition (Domain 3), the adopter system (Domain 4) and the wider context (Domain 6) of the NASSS framework, highlighting its importance when considering implementation of an innovative technology such as genomic testing. Our study shows public perceptions are diverse, and highlights the need for more studies on the views of underrepresented groups and the impact of cultural contexts on perceptions.
Collapse
|
49
|
Carroll SR, Plevel R, Jennings LL, Garba I, Sterling R, Cordova-Marks FM, Hiratsuka V, Hudson M, Garrison NA. Extending the CARE Principles from tribal research policies to benefit sharing in genomic research. Front Genet 2022; 13:1052620. [PMID: 36437947 PMCID: PMC9691892 DOI: 10.3389/fgene.2022.1052620] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 10/19/2022] [Indexed: 08/11/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Stephanie Russo Carroll
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Rebecca Plevel
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
- Law Library, School of Law, University of South Carolina, Columbia, SC, United States
| | - Lydia L. Jennings
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Ibrahim Garba
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
- Native Nations Institute, Udall Center for Studies in Public Policy, University of Arizona, Tucson, AZ, United States
| | - Rogena Sterling
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Felina M. Cordova-Marks
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, United States
| | - Vanessa Hiratsuka
- Center for Human Development, College of Health, University of Alaska Anchorage, Anchorage, AK, United States
| | - Maui Hudson
- Te Kotahi Research Institute, University of Waikato, Hamilton, New Zealand
| | - Nanibaa’ A. Garrison
- Institute for Society and Genetics, College of Letters and Sciences, University of California, Los Angeles, Los Angeles, CA, United States
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Division of General Internal Medicine & Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
50
|
The gene variant that helped put Latinxs in the 1000 genomes project. Nat Rev Genet 2022; 23:712-713. [PMID: 36198907 DOI: 10.1038/s41576-022-00538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|