1
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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
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2
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Gancz AS, Farrer AG, Nixon MP, Wright S, Arriola L, Adler C, Davenport ER, Gully N, Cooper A, Britton K, Dobney K, Silverman JD, Weyrich LS. Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain. Nat Microbiol 2023; 8:2315-2325. [PMID: 38030898 DOI: 10.1038/s41564-023-01527-3] [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: 05/25/2022] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - Andrew G Farrer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Michelle P Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA, USA
| | - Sterling Wright
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - Luis Arriola
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christina Adler
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Emily R Davenport
- Department of Biology, The Pennsylvania State University, State College, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, USA
- Institute for Computational and Data Sciences, The Pennsylvania State University, State College, PA, USA
| | - Neville Gully
- School of Dentistry, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Alan Cooper
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Gulbali Institute, Charles Sturt University, Albury, New South Wales, Australia
| | - Kate Britton
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
- Department of Archaeology, Faculty of Arts and Social Sciences, University of Sydney, Sydney, New South Wales, Australia
- Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK
- Department of Archaeology, Faculty of Environment, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Justin D Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA, USA
- Institute for Computational and Data Sciences, The Pennsylvania State University, State College, PA, USA
- Department of Statistics, The Pennsylvania State University, State College, PA, USA
- Department of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA.
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, USA.
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3
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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.
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4
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Data sovereignty in genomics and medical research. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00578-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Boscarino N, Cartwright RA, Fox K, Tsosie KS. Federated learning and Indigenous genomic data sovereignty. NAT MACH INTELL 2022; 4:909-911. [PMID: 36504698 PMCID: PMC9731328 DOI: 10.1038/s42256-022-00551-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Indigenous peoples are under-represented in genomic datasets, which can lead to limited accuracy and utility of machine learning models in precision health. While open data sharing undermines rights of Indigenous communities to govern data decisions, federated learning may facilitate secure and community-consented data sharing.
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Affiliation(s)
| | - Reed A. Cartwright
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Keolu Fox
- Department of Anthropology and Global Health, University of California, San Diego, La Jolla, CA, USA
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6
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Rodriguez JJRB, Cuales JMD, Herrera MJB, Zubiri LAM, Muallil RM, Ishmael AI, Jimenez EB, Stoneking M, De Ungria MCA. Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago. Front Genet 2022; 13:901515. [DOI: 10.3389/fgene.2022.901515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
The Philippines, with the recent discovery of an archaic hominin in Luzon and an extensive ethnolinguistic diversity of more than 100 Indigenous peoples, is crucial to understanding human evolution and population history in Island Southeast Asia. Advances in DNA sequencing technologies enable the rapid generation of genomic data to robustly address questions about origins, relatedness, and population movements. With the increased genetic sampling in the country, especially by international scientists, it is vital to revisit ethical rules and guidelines relevant to conducting research among Indigenous peoples. Our team led fieldwork expeditions between 2019 and February 2020 in Zamboanga and the Sulu Archipelago, a chain of islands connecting the Mindanao and Borneo landmasses. The trips concluded with a collection of 2,149 DNA samples from 104 field sites. We present our fieldwork experience among the mostly sea-oriented Sama-Bajaw and Tausug-speaking communities and propose recommendations to address the ethical challenges of conducting such research. This work contributes toward building an enabling research environment in the Philippines that respects the rights and autonomy of Indigenous peoples, who are the rightful owners of their DNA and all genetic information contained therein.
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7
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Montgomery LM, Supernant K. Archaeology in 2021: Repatriation, reclamation, and reckoning with historical trauma. AMERICAN ANTHROPOLOGIST 2022. [DOI: 10.1111/aman.13778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Lindsay M. Montgomery
- Department of Anthropology and Centre for Indigenous Studies University of Toronto Canada
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8
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Wonkam A, Bardien S, Diallo RN, Gaye A, Alimohamed MZ, Kya S, Makani J, Landoure G, Mutesa L, El-Kamah G, Mohamed A, Newport M, Williams SM, Ramsay M, Nembaware V. "Black Lives Matter and Black Research Matters": the African Society of Human Genetics' call to halt racism in science. Mol Biol Cell 2022; 33:vo2. [PMID: 35862495 DOI: 10.1091/mbc.e22-04-0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The African Society of Human Genetics (AfSHG) was formed to provide a forum for human genetics and genomics scientists in Africa to interact, network, and collaborate. This is critical to facilitate development of solutions to the public health burden of many rare and common diseases across the continent. AfSHG fully supports the Black Lives Matter movement, which is dedicated to fighting racism and ensuring that society values the lives and humanity of Black people. The AfSHG would like to add its "voice" to the public outcry against racism sparked by George Floyd's death and to declare its commitment to ensuring that injustice and systematic racism, as well as abuse and exploitation of Africans and their biological material, are no longer tolerated. This is particularly relevant now as African genomic variation is poised to make significant contributions across several disciplines including ancestry, personalized medicine, and novel drug discovery. "Black Lives Matter and Black Research Matters" is AfSHG's call for the global community to support halting, and reversing, the perpetuation of exploitation of African people through neocolonial malpractices in genomic research. We also propose five key ways to curb racism in science, so that we can move forward together, with a common humanity, collectively embracing scientific endeavors.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa.,McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Cape Town 7505, South Africa
| | - Rokhaya Ndiaye Diallo
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odontology, University Cheikh Anta Diop, Dakar P. O. Box 5005, Senegal
| | - Amadou Gaye
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Mohamed Zahir Alimohamed
- Department of Haematology and Blood Transfusion, School of Medicine, MUHAS, Dar es Saalam P. O. Box 65001, Tanzania.,Department of Research and Training, Shree Hindu Mandal Hospital, Dar es Salaam P. O. Box 581, Tanzania
| | - Siana Kya
- Department of Haematology and Blood Transfusion, School of Medicine, MUHAS, Dar es Saalam P. O. Box 65001, Tanzania
| | - Julie Makani
- Department of Haematology and Blood Transfusion, School of Medicine, MUHAS, Dar es Saalam P. O. Box 65001, Tanzania
| | - Guida Landoure
- Hopital du point G, University of Bamako, Bamako P. O. Box 333, Mali
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali P. O. Box 4285, Rwanda
| | - Ghada El-Kamah
- Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Amal Mohamed
- Brighton & Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Sussex, BN1 9RH, UK
| | - Melanie Newport
- Brighton & Sussex Centre for Global Health Research, Brighton and Sussex Medical School, University of Sussex, Sussex, BN1 9RH, UK
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Institute of Computational Biology, Case Western Reserve University, Cleveland, 44106 OH
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Private Bag 3, Wits 2050, South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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9
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Elishaev M, Hodonsky CJ, Ghosh SKB, Finn AV, von Scheidt M, Wang Y. Opportunities and Challenges in Understanding Atherosclerosis by Human Biospecimen Studies. Front Cardiovasc Med 2022; 9:948492. [PMID: 35872917 PMCID: PMC9300954 DOI: 10.3389/fcvm.2022.948492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last few years, new high-throughput biotechnologies and bioinformatic methods are revolutionizing our way of deep profiling tissue specimens at the molecular levels. These recent innovations provide opportunities to advance our understanding of atherosclerosis using human lesions aborted during autopsies and cardiac surgeries. Studies on human lesions have been focusing on understanding the relationship between molecules in the lesions with tissue morphology, genetic risk of atherosclerosis, and future adverse cardiovascular events. This review will highlight ways to utilize human atherosclerotic lesions in translational research by work from large cardiovascular biobanks to tissue registries. We will also discuss the opportunities and challenges of working with human atherosclerotic lesions in the era of next-generation sequencing.
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Affiliation(s)
- Maria Elishaev
- Department of Pathology and Laboratory Medicine, Center for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Chani J. Hodonsky
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | | | - Aloke V. Finn
- Cardiovascular Pathology Institute, Gaithersburg, MD, United States
| | - Moritz von Scheidt
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung, Partner Site Munich Heart Alliance, Munich, Germany
| | - Ying Wang
- Department of Pathology and Laboratory Medicine, Center for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Ying Wang ; orcid.org/0000-0002-1444-5778
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10
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Rahimzadeh V. Regulatory Angels and Technology Demons? Making Sense of Evolving Realities in Health Data Privacy for the Digital Age. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2022; 22:68-70. [PMID: 35737504 PMCID: PMC9748849 DOI: 10.1080/15265161.2022.2075981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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11
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Appelbaum PS, Burke W, Parens E, Zeevi DA, Arbour L, Garrison NA, Bonham VL, Chung WK. Is there a way to reduce the inequity in variant interpretation on the basis of ancestry? Am J Hum Genet 2022; 109:981-988. [PMID: 35659933 PMCID: PMC9247826 DOI: 10.1016/j.ajhg.2022.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The underrepresentation of non-European ancestry groups in current genomic databases complicates interpretation of their genetic test results, yielding a much higher prevalence of variants of uncertain significance (VUSs). Such VUS findings can frustrate the goals of genetic testing, create anxiety in patients, and lead to unnecessary medical interventions. Approaches to addressing underrepresentation of people with genetic ancestries other than European are being undertaken by broad-based recruitment efforts. However, some underrepresented groups have concerns that might preclude participation in such efforts. We describe here two initiatives aimed at meeting the needs of underrepresented ancestry groups in genomic datasets. The two communities, the Sephardi Jewish community in New York and First Peoples of Canada, have very different concerns about contributing to genomic research and datasets. Sephardi concerns focus on the possible negative effects of genetic findings on the marriage prospects of family members. Canadian Indigenous populations seek control over the research uses to which their genetic data would be put. Both cases involve targeted efforts to respond to the groups' concerns; these efforts include governance models aimed at ensuring that the data are used primarily to inform clinical test analyses and at achieving successful engagement and participation of community members. We suggest that these initiatives could provide models for other ancestral groups seeking to improve the accuracy and utility of clinical genetic testing while respecting the underlying preferences and values of community members with regard to the use of their genetic data.
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Affiliation(s)
- Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, and New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA 98195, USA
| | - Erik Parens
- The Hastings Center, Garrison, NY 10524, USA
| | - David A Zeevi
- Dor Yeshorim, The Committee for the Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada; BC Children's Hospital Research Institute, Victoria, BC V8P 5C2, Canada
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095; Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, Los Angeles, CA 9009, USA5
| | - Vence L Bonham
- Social and Behavioral Research Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
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12
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Fleskes RE, Bader AC, Tsosie KS, Wagner JK, Claw KG, Garrison NA. Ethical Guidance in Human Paleogenomics: New and Ongoing Perspectives. Annu Rev Genomics Hum Genet 2022; 23:627-652. [PMID: 35537469 DOI: 10.1146/annurev-genom-120621-090239] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past two decades, the study of ancient genomes from Ancestral humans, or human paleogenomic research, has expanded rapidly in both scale and scope. Ethical discourse has subsequently emerged to address issues of social responsibility and scientific robusticity in conducting research. Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among existing guidelines, while addressing core issues such as consent, destructive research methods, and data access and management. Currently, there is a dissonance between guidelines that focus on scientific outcomes and those that hold scientists accountable to stakeholder communities, such as descendants. Thus, we provide additional tools to navigate the complexities of ancient DNA research while centering engagement with stakeholder communities in the scientific process. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Raquel E Fleskes
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA;
| | - Alyssa C Bader
- Department of Anthropology, University of Colorado Boulder, Boulder, Colorado, USA; .,Sealaska Heritage Institute, Juneau, Alaska, USA
| | - Krystal S Tsosie
- Native BioData Consortium, Eagle Butte, South Dakota, USA; .,College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer K Wagner
- School of Engineering Design, Technology, and Professional Programs; Institute for Computational and Data Sciences; and Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Katrina G Claw
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Nanibaa' A Garrison
- Institute for Society and Genetics, Institute for Precision Health, and Division of General Internal Medicine and Health Services Research, University of California, Los Angeles, California, USA;
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13
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Abdill RJ, Adamowicz EM, Blekhman R. Public human microbiome data are dominated by highly developed countries. PLoS Biol 2022; 20:e3001536. [PMID: 35167588 PMCID: PMC8846514 DOI: 10.1371/journal.pbio.3001536] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/11/2022] [Indexed: 02/07/2023] Open
Abstract
The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack a full understanding of the global distribution of sampling in research studies. This information is crucial to better understand global patterns of microbiome-associated diseases and to extend the health benefits of this research to all populations. Here, we analyze the country of origin of all 444,829 human microbiome samples that are available from the world’s 3 largest genomic data repositories, including the Sequence Read Archive (SRA). The samples are from 2,592 studies of 19 body sites, including 220,017 samples of the gut microbiome. We show that more than 71% of samples with a known origin come from Europe, the United States, and Canada, including 46.8% from the US alone, despite the country representing only 4.3% of the global population. We also find that central and southern Asia is the most underrepresented region: Countries such as India, Pakistan, and Bangladesh account for more than a quarter of the world population but make up only 1.8% of human microbiome samples. These results demonstrate a critical need to ensure more global representation of participants in microbiome studies. The importance of sampling from globally representative populations has been well established in human genomics, but what about the microbiome? This study shows that metadata from almost half a million samples reveals worldwide human microbiome research is skewed heavily in favor of Europe and North America and excludes large but less developed nations in Asia and Africa.
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Affiliation(s)
- Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Elizabeth M. Adamowicz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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14
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Ethics of DNA research on human remains: five globally applicable guidelines. Nature 2021; 599:41-46. [PMID: 34671160 PMCID: PMC7612683 DOI: 10.1038/s41586-021-04008-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/08/2021] [Indexed: 11/08/2022]
Abstract
We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.
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