1
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Stark Z, Glazer D, Hofmann O, Rendon A, Marshall CR, Ginsburg GS, Lunt C, Allen N, Effingham M, Hastings Ward J, Hill SL, Ali R, Goodhand P, Page A, Rehm HL, North KN, Scott RH. A call to action to scale up research and clinical genomic data sharing. Nat Rev Genet 2024:10.1038/s41576-024-00776-0. [PMID: 39375561 DOI: 10.1038/s41576-024-00776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2024] [Indexed: 10/09/2024]
Abstract
Genomic data from millions of individuals have been generated worldwide to drive discovery and clinical impact in precision medicine. Lowering the barriers to using these data collectively is needed to equitably realize the benefits of the diversity and scale of population data. We examine the current landscape of global genomic data sharing, including the evolution of data sharing models from data aggregation through to data visiting, and for certain use cases, cross-cohort analysis using federated approaches across multiple environments. We highlight emerging examples of best practice relating to participant, patient and community engagement; evolution of technical standards, tools and infrastructure; and impact of research and health-care policy. We outline 12 actions we can all take together to scale up efforts to enable safe global data sharing and move beyond projects demonstrating feasibility to routinely cross-analysing research and clinical data sets, optimizing benefit.
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Affiliation(s)
- Zornitza Stark
- Australian Genomics, Melbourne, Victoria, Australia.
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- University of Melbourne, Melbourne, Victoria, Australia.
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA.
| | - Oliver Hofmann
- Australian Genomics, Melbourne, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Melbourne, Victoria, Australia
| | | | - Christian R Marshall
- Division of Genome Diagnostics, Pediatric Laboratory Medicine Department, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Geoffrey S Ginsburg
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Chris Lunt
- All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Naomi Allen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- UK Biobank, Stockport, UK
| | | | | | - Sue L Hill
- National Health Service England, London, UK
| | - Raghib Ali
- Our Future Health, Manchester, UK
- Oxford University Hospitals NHS Trust, Oxford, UK
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Angela Page
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Heidi L Rehm
- Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn N North
- Australian Genomics, Melbourne, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
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2
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LeBaron von Baeyer S, Crocker RM, Rakotoarivony R, Ranaivoarisoa JF, Spiral GJ, Pascart T, Wheeler V, Mairai T, Gregersen NO, Castel SE, Yerges-Armstrong LM, Fox K, Wasik KA. Nothing about us without us: Sharing results with communities that provide genomic data. Cell 2024; 187:5483-5489. [PMID: 39303717 DOI: 10.1016/j.cell.2024.08.023] [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: 01/04/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 09/22/2024]
Abstract
Sharing genetic and other study results with the communities who participate in research falls under benefit-sharing and capacity-building initiatives that underpin a more equitable biomedical research relationship. Yet, which results to return and how remain fundamental challenges that persist in the absence of practical guidance and institutional policies. Here, we discuss how the return of results can be implemented across different geographies, study designs, and project budgets.
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Affiliation(s)
| | | | | | | | | | | | - Vehia Wheeler
- Australian National University, Canberra, ACT, Australia; Sustainable Oceania Solutions, Afareaitu, Mo'orea, French Polynesia
| | | | - Noomi O Gregersen
- Faroe Genome Project, Tórshavn, Faroe Islands; University of the Faroe Islands, Tórshavn, Faroe Islands
| | | | | | - Keolu Fox
- Indigenous Futures Institute, University of California, San Diego, La Jolla, CA, USA; J. Craig Venter Research Institute, La Jolla, CA, USA.
| | - Kaja A Wasik
- Variant Bio, Seattle, WA, USA; J. Craig Venter Research Institute, La Jolla, CA, USA.
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3
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Ha EK, Shriner D, Callier SL, Riley L, Adeyemo AA, Rotimi CN, Bentley AR. Native Hawaiian and Pacific Islander populations in genomic research. NPJ Genom Med 2024; 9:45. [PMID: 39349931 PMCID: PMC11442686 DOI: 10.1038/s41525-024-00428-6] [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: 07/31/2023] [Accepted: 09/06/2024] [Indexed: 10/04/2024] Open
Abstract
The role of genomic research and medicine in improving health continues to grow significantly, highlighting the need for increased equitable inclusion of diverse populations in genomics. Native Hawaiian and Pacific Islander (NHPI) communities are often missing from these efforts to ensure that the benefits of genomics are accessible to all individuals. In this article, we analyze the qualities of NHPI populations relevant to their inclusion in genomic research and investigate their current representation using data from the genome-wide association studies (GWAS) catalog. A discussion of the barriers NHPI experience regarding participating in research and recommendations to improve NHPI representation in genomic research are also included.
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Affiliation(s)
- Edra K Ha
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- University of Hawai'i at Mānoa, Honolulu, HI, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shawneequa L Callier
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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4
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de Groot NF. A contextual integrity approach to genomic information: what bioethics can learn from big data ethics. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2024; 27:367-379. [PMID: 38865053 PMCID: PMC11310229 DOI: 10.1007/s11019-024-10211-0] [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: 05/27/2024] [Indexed: 06/13/2024]
Abstract
Genomic data is generated, processed and analysed at an increasingly rapid pace. This data is not limited to the medical context, but plays an important role in other contexts in society, such as commercial DNA testing, the forensic setting, archaeological research, and genetic surveillance. Genomic information also crosses the borders of these domains, e.g. forensic use of medical genetic information, insurance use of medical genomic information, or research use of commercial genomic data. This paper (1) argues that an informed consent approach for genomic information has limitations in many societal contexts, and (2) seeks to broaden the bioethical debate on genomic information by suggesting an approach that is applicable across multiple societal contexts. I argue that the contextual integrity framework, a theory rooted in information technology and big data ethics, is an effective tool to explore ethical challenges that arise from genomic information within a variety of different contexts. Rather than focusing on individual control over information, the contextual integrity approach holds that information should be shared and protected according to the norms that govern certain distinct social contexts. Several advantages of this contextual integrity approach will be discussed. The paper concludes that the contextual integrity framework helps to articulate and address a broad spectrum of ethical, social, and political factors in a variety of different societal contexts, while giving consideration to the interests of individuals, groups, and society at large.
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Affiliation(s)
- Nina F de Groot
- Department of Philosophy, Faculty of Humanities, VU University Amsterdam, Amsterdam, the Netherlands.
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5
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Yracheta J, Morriseau T, Dale K, Gerth A, McGavock J. Scientists and scientific journals should adhere to ethical standards for the use and reporting of data from Indigenous people. Diabetologia 2024:10.1007/s00125-024-06236-y. [PMID: 39103722 DOI: 10.1007/s00125-024-06236-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/20/2024] [Indexed: 08/07/2024]
Abstract
Internationally, governments and scientists are bound by legal and treaty rights when working with Indigenous nations. These rights include the right of Indigenous people to control the conduct of science with Indigenous nations. Unfortunately, in some cases, individual scientists and scientific teams working with biological and genetic data collected from Indigenous people have not respected these international rights. Here, we argue that the scientific community should understand and acknowledge the historical harms experienced by Indigenous people under the veil of scientific progress (truth) and implement existing standards for ethical conduct of research and sovereign control of data collected within Indigenous communities (reconciliation). Specifically, we outline the rationale for why scientists, scientific journals and research integrity and institutional review boards/ethics committees should adopt, and be held accountable for upholding, current international standards of Indigenous data sovereignty and ethical use of Indigenous biological samples.
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Affiliation(s)
| | - Taylor Morriseau
- First Nations Health and Secretariat of Manitoba, Winnipeg, MB, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Kali Dale
- Native BioData Consortium, Eagle Butte, SD, USA
| | | | - Jonathan McGavock
- Diabetes Research Envisioned and Accomplished in Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
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6
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Mc Cartney AM, Scholz AH, Groussin M, Staunton C. Benefit-Sharing by Design: A Call to Action for Human Genomics Research. Annu Rev Genomics Hum Genet 2024; 25:369-395. [PMID: 38608642 DOI: 10.1146/annurev-genom-021623-104241] [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] [Indexed: 04/14/2024]
Abstract
The ethical standards for the responsible conduct of human research have come a long way; however, concerns surrounding equity remain in human genetics and genomics research. Addressing these concerns will help society realize the full potential of human genomics research. One outstanding concern is the fair and equitable sharing of benefits from research on human participants. Several international bodies have recognized that benefit-sharing can be an effective tool for ethical research conduct, but international laws, including the Convention on Biological Diversity and its Nagoya Protocol on Access and Benefit-Sharing, explicitly exclude human genetic and genomic resources. These agreements face significant challenges that must be considered and anticipated if similar principles are applied in human genomics research. We propose that benefit-sharing from human genomics research can be a bottom-up effort and embedded into the existing research process. We propose the development of a "benefit-sharing by design" framework to address concerns of fairness and equity in the use of human genomic resources and samples and to learn from the aspirations and decade of implementation of the Nagoya Protocol.
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Affiliation(s)
- Ann M Mc Cartney
- Genomics Institute, University of California, Santa Cruz, California, USA;
| | - Amber Hartman Scholz
- Department of Science Policy and Internationalisation, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany;
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany;
| | - Ciara Staunton
- School of Law, University of KwaZulu-Natal, Durban, South Africa
- Institute for Biomedicine, Eurac Research, Bolzano, Italy;
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7
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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.
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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
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8
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Stantis C, Schaefer BJ, Correia MA, Alaica AK, Huffer D, Plomp E, Di Giusto M, Chidimuro B, Rose AK, Nayak A, Kendall EJ. Ethics and applications of isotope analysis in archaeology. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e24992. [PMID: 38949078 DOI: 10.1002/ajpa.24992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 07/02/2024]
Abstract
This synthesis explores specific ethical questions that commonly arise in isotopic analysis. For more than four decades, isotope analysis has been employed in archeological studies to explore past human and animal dietary habits, mobility patterns, and the environment in which a human or animal inhabited during life. These analyses require consideration of ethical issues. While theoretical concepts are discussed, we focus on practical aspects: working with descendant communities and other rights holders, choosing methods, creating and sharing data, and working mindfully within academia. These layers of respect and care should surround our science. This paper is relevant for specialists in isotope analysis as well as those incorporating these methods into larger projects. By covering the whole of the research process, from design to output management, we appeal broadly to archaeology and provide actionable solutions that build on the discussions in the general field.
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Affiliation(s)
- Chris Stantis
- Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah, USA
| | - Benjamin J Schaefer
- Department of Anthropology, Gender and Women's Studies, and Latin American and Latino Studies, University of Illinois at Chicago, Chicago, Illinois, USA
- The Center for the Recovery and Identification of the Missing, University of Illinois at Chicago, Chicago, Illinois, USA
- Division of Anthropology, The Field Museum of Natural History, Chicago, Illinois, USA
| | - Maria Ana Correia
- Interdisciplinary Center for Archaeology and the Evolution of Human Behaviour (ICArEHB), Universidade do Algarve, Algarve, Portugal
- Laboratório de Arqueologia e Antropologia Ambiental e Evolutiva, Universidade de São Paulo, Sao Paulo, Brazil
| | - Aleksa K Alaica
- Department of Anthropology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Damien Huffer
- Department of History, Carleton University, Ottawa, Ontario, Canada
- School of Social Sciences, University of Queensland, Saint Lucia, Queensland, Australia
- The Alliance to Counter Crime Online, Washington, DC, USA
| | - Esther Plomp
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Marina Di Giusto
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, Sao Paulo, Brazil
| | - Blessing Chidimuro
- Department of Geography and Environmental Science, University of Reading, Reading, UK
| | - Alice K Rose
- Department of Archaeology, Durham University, Durham, UK
| | - Ayushi Nayak
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
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9
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Gaydarska H, Takashima K, Shahrier S, Raz A, Minari J. The interplay of ethics and genetic technologies in balancing the social valuation of the human genome in UNESCO declarations. Eur J Hum Genet 2024; 32:725-730. [PMID: 38355962 PMCID: PMC11153547 DOI: 10.1038/s41431-024-01549-3] [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: 07/25/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
This study investigates changes in the social valuation of the human genome over the more than 30 years since the establishment of the Human Genome Project. It offers a descriptive sociological analysis of the three waves of this valuation, mainly by considering three key UNESCO declarations and a relevant report. These waves represent a shifting balance between collectivism and individualism, starting with a broadly constructed valuation of the human genome as common human heritage and moving toward a valuation of dynamic applications within various social and medical contexts (e.g., personalized genomic medicine and genome editing). We seek to broaden the analytical perspective by examining how the declarations' ethical foci are framed within the context of rapidly evolving genetic technologies and their social applications. We conclude by discussing continuity and change in value balancing vis-à-vis changing genomic technologies.
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Affiliation(s)
- Hristina Gaydarska
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kayo Takashima
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shibly Shahrier
- Teesside University International Business School, Teesside University, Tees Valley, UK
| | - Aviad Raz
- Department of Sociology and Anthropology, Ben-Gurion University of the Negev, Beersheba, Israel.
| | - Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
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10
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Bear Don't Walk OJ, Paullada A, Everhart A, Casanova-Perez R, Cohen T, Veinot T. Opportunities for incorporating intersectionality into biomedical informatics. J Biomed Inform 2024; 154:104653. [PMID: 38734158 PMCID: PMC11146624 DOI: 10.1016/j.jbi.2024.104653] [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: 11/18/2023] [Revised: 04/06/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Many approaches in biomedical informatics (BMI) rely on the ability to define, gather, and manipulate biomedical data to support health through a cyclical research-practice lifecycle. Researchers within this field are often fortunate to work closely with healthcare and public health systems to influence data generation and capture and have access to a vast amount of biomedical data. Many informaticists also have the expertise to engage with stakeholders, develop new methods and applications, and influence policy. However, research and policy that explicitly seeks to address the systemic drivers of health would more effectively support health. Intersectionality is a theoretical framework that can facilitate such research. It holds that individual human experiences reflect larger socio-structural level systems of privilege and oppression, and cannot be truly understood if these systems are examined in isolation. Intersectionality explicitly accounts for the interrelated nature of systems of privilege and oppression, providing a lens through which to examine and challenge inequities. In this paper, we propose intersectionality as an intervention into how we conduct BMI research. We begin by discussing intersectionality's history and core principles as they apply to BMI. We then elaborate on the potential for intersectionality to stimulate BMI research. Specifically, we posit that our efforts in BMI to improve health should address intersectionality's five key considerations: (1) systems of privilege and oppression that shape health; (2) the interrelated nature of upstream health drivers; (3) the nuances of health outcomes within groups; (4) the problematic and power-laden nature of categories that we assign to people in research and in society; and (5) research to inform and support social change.
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Affiliation(s)
- Oliver J Bear Don't Walk
- Department of Biomedical Informatics and Medical Education, University of Washington, United States.
| | - Amandalynne Paullada
- Department of Biomedical Informatics and Medical Education, University of Washington, United States
| | - Avery Everhart
- Department of Geography, Faculty of Arts, University of British Columbia, Canada
| | - Reggie Casanova-Perez
- Department of Biomedical Informatics and Medical Education, University of Washington, United States
| | - Trevor Cohen
- Department of Biomedical Informatics and Medical Education, University of Washington, United States
| | - Tiffany Veinot
- School of Information and School of Public Health, University of Michigan, United States
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11
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Xiang R, Kelemen M, Xu Y, Harris LW, Parkinson H, Inouye M, Lambert SA. Recent advances in polygenic scores: translation, equitability, methods and FAIR tools. Genome Med 2024; 16:33. [PMID: 38373998 PMCID: PMC10875792 DOI: 10.1186/s13073-024-01304-9] [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: 06/09/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
Polygenic scores (PGS) can be used for risk stratification by quantifying individuals' genetic predisposition to disease, and many potentially clinically useful applications have been proposed. Here, we review the latest potential benefits of PGS in the clinic and challenges to implementation. PGS could augment risk stratification through combined use with traditional risk factors (demographics, disease-specific risk factors, family history, etc.), to support diagnostic pathways, to predict groups with therapeutic benefits, and to increase the efficiency of clinical trials. However, there exist challenges to maximizing the clinical utility of PGS, including FAIR (Findable, Accessible, Interoperable, and Reusable) use and standardized sharing of the genomic data needed to develop and recalculate PGS, the equitable performance of PGS across populations and ancestries, the generation of robust and reproducible PGS calculations, and the responsible communication and interpretation of results. We outline how these challenges may be overcome analytically and with more diverse data as well as highlight sustained community efforts to achieve equitable, impactful, and responsible use of PGS in healthcare.
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Affiliation(s)
- Ruidong Xiang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Martin Kelemen
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Yu Xu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Laura W Harris
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
| | - Samuel A Lambert
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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12
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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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13
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Hsieh E, Morrissey BS, Chiareli IA. The Landscape of Direct-To-Consumer Genetic Testing in Reproductive Health Contexts: An Analytical Framework of Stakeholders and Their Competing Motivations. HEALTH COMMUNICATION 2024:1-14. [PMID: 38317624 DOI: 10.1080/10410236.2024.2312607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
We propose a theoretical framework that identifies (a) the different categories of stakeholders and (b) the normative values that drive their attitudes toward direct-to-consumer genetic testing, with an emphasis on the reproductive health contexts. We conducted a literature search using varied combinations of search terms, including direct-to-consumer genetic testing, decision-making, reproductive health, and policy. Using a grounded theory approach to existing literature and in combination with a narrative review, we present a systematic framework of five categories of stakeholders (i.e., genome-driven stakeholders, industry-driven stakeholders, history-driven stakeholders, value-driven stakeholders, and social justice-driven stakeholders) that shape the public's discourse. Moving beyond the dialectical ethics that have governed the public discourse, we also identify the normative values and interests that motivate different stakeholders' attitudes and decision-making through theoretical sampling under the grounded theory. We investigate the competing and conflicting values within the same category of stakeholders. For example, despite being industry-driven stakeholders, medical professionals' attitudes are driven by concerns about standards of care; in contrast, health insurance companies' concerns are centered on profit. We further explore the tensions between these stakeholders that impact their strategic alliances and pose challenges to the practices of direct-to-consumer genetic testing. Finally, we examine how these stakeholders and their corresponding values may shape future development and policies of direct-to-consumer genetic testing in the context of reproductive health.
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Affiliation(s)
- Elaine Hsieh
- Department of Communication Studies, University of Minnesota-Twin Cities
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14
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Nogueira LM, Yabroff KR. Climate change and cancer: the Environmental Justice perspective. J Natl Cancer Inst 2024; 116:15-25. [PMID: 37813679 DOI: 10.1093/jnci/djad185] [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: 06/01/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 10/11/2023] Open
Abstract
Despite advances in cancer control-prevention, screening, diagnosis, treatment, and survivorship-racial disparities in cancer incidence and survival persist and, in some cases, are widening in the United States. Since 2020, there's been growing recognition of the role of structural racism, including structurally racist policies and practices, as the main factor contributing to historical and contemporary disparities. Structurally racist policies and practices have been present since the genesis of the United States and are also at the root of environmental injustices, which result in disproportionately high exposure to environmental hazards among communities targeted for marginalization, increased cancer risk, disruptions in access to care, and worsening health outcomes. In addition to widening cancer disparities, environmental injustices enable the development of polluting infrastructure, which contribute to detrimental health outcomes in the entire population, and to climate change, the most pressing public health challenge of our time. In this commentary, we describe the connections between climate change and cancer through an Environmental Justice perspective (defined as the fair treatment and meaningful involvement of people of all racialized groups, nationalities, or income, in all aspects, including development, implementation, and enforcement, of policies and practices that affect the environment and public health), highlighting how the expertise developed in communities targeted for marginalization is crucial for addressing health disparities, tackling climate change, and advancing cancer control efforts for the entire population.
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Affiliation(s)
- Leticia M Nogueira
- Surveillance and Health Equity Science, American Cancer Society, Atlanta, GA, USA
| | - K Robin Yabroff
- Surveillance and Health Equity Science, American Cancer Society, Atlanta, GA, USA
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15
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Dinh BL, Tang E, Taparra K, Nakatsuka N, Chen F, Chiang CWK. Recombination map tailored to Native Hawaiians may improve robustness of genomic scans for positive selection. Hum Genet 2024; 143:85-99. [PMID: 38157018 PMCID: PMC10794367 DOI: 10.1007/s00439-023-02625-2] [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: 09/02/2023] [Accepted: 11/25/2023] [Indexed: 01/03/2024]
Abstract
Recombination events establish the patterns of haplotypic structure in a population and estimates of recombination rates are used in several downstream population and statistical genetic analyses. Using suboptimal maps from distantly related populations may reduce the efficacy of genomic analyses, particularly for underrepresented populations such as the Native Hawaiians. To overcome this challenge, we constructed recombination maps using genome-wide array data from two study samples of Native Hawaiians: one reflecting the current admixed state of Native Hawaiians (NH map) and one based on individuals of enriched Polynesian ancestries (PNS map) with the potential to be used for less admixed Polynesian populations such as the Samoans. We found the recombination landscape to be less correlated with those from other continental populations (e.g. Spearman's rho = 0.79 between PNS and CEU (Utah residents with Northern and Western European ancestry) compared to 0.92 between YRI (Yoruba in Ibadan, Nigeria) and CEU at 50 kb resolution), likely driven by the unique demographic history of the Native Hawaiians. PNS also shared the fewest recombination hotspots with other populations (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analyses in the Native Hawaiian population, such as local ancestry inference, imputation, and IBD segment and relatedness detections, would achieve similar efficacy when using the NH map compared to an omnibus map. However, for genome scans of adaptive loci using integrated haplotype scores, we found several loci with apparent genome-wide significant signals (|Z-score|> 4) in Native Hawaiians that would not have been significant when analyzed using NH-specific maps. Population-specific recombination maps may therefore improve the robustness of haplotype-based statistics and help us better characterize the evolutionary history that may underlie Native Hawaiian-specific health conditions that persist today.
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Affiliation(s)
- Bryan L Dinh
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Kekoa Taparra
- Department of Radiation Oncology, Stanford University, Palo Alto, CA, USA
| | | | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Charleston W K Chiang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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16
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Zhang TR. Ethics of 'Counting Me In': framing the implications of direct-to-patient genomics research. JOURNAL OF MEDICAL ETHICS 2023; 50:45-49. [PMID: 37130755 DOI: 10.1136/jme-2022-108741] [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: 11/07/2022] [Accepted: 04/03/2023] [Indexed: 05/04/2023]
Abstract
Count Me In (CMI) was launched in 2015 as a patient-driven research initiative aimed at accelerating the study of cancer genomics through direct participant engagement, electronic consent and open-access data sharing. It is an example of a large-scale direct-to-patient (DTP) research project which has since enrolled thousands of individuals. Within the broad scope of 'citizen science', DTP genomics research is defined here as a specific form of 'top-down' research endeavour developed and overseen by institutions within the traditional human subjects research context; in novel ways, it engages and recruits patients with defined diseases, consents them for medical information and biospecimens sharing, and stores and disseminates genomic information. Importantly, these projects simultaneously aim to empower participants in the research process while increasing sample size, particularly in rare disease states. Using CMI as a case study, this paper discusses how DTP genomics research raises new questions in the context of traditional human subjects research ethics, including issues surrounding participant selection, remote consent, privacy and return of results. It aims to demonstrate how current research ethics frameworks may be insufficient in this context, and that institutions, institutional review boards and investigators should be aware of these gaps and their role in ensuring the conduct of ethical, novel forms of research together with participants. Ultimately, a broader question is raised of whether the rhetoric of participatory genomics research advocates for an ethic of personal and social duty for contributing to the advancement of generalisable knowledge about health and disease.
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Affiliation(s)
- Tenny R Zhang
- Department of Urology, NewYork-Presbyterian/Weill Cornell Medicine, New York, NY, USA
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17
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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.
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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
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18
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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.
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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
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19
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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.
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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.
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20
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Brockhoven F, Raphael M, Currier J, Jäderholm C, Mody P, Shannon J, Starling B, Turner-Uaandja H, Pashayan N, Arteaga I. REPRESENT recommendations: improving inclusion and trust in cancer early detection research. Br J Cancer 2023; 129:1195-1208. [PMID: 37689805 PMCID: PMC10575902 DOI: 10.1038/s41416-023-02414-8] [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: 01/20/2023] [Revised: 08/01/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023] Open
Abstract
Detecting cancer early is essential to improving cancer outcomes. Minoritized groups remain underrepresented in early detection cancer research, which means that findings and interventions are not generalisable across the population, thus exacerbating disparities in cancer outcomes. In light of these challenges, this paper sets out twelve recommendations to build relations of trust and include minoritized groups in ED cancer research. The Recommendations were formulated by a range of stakeholders at the 2022 REPRESENT consensus-building workshop and are based on empirical data, including a systematic literature review and two ethnographic case studies in the US and the UK. The recommendations focus on: Long-term relationships that build trust; Sharing available resources; Inclusive and accessible communication; Harnessing community expertise; Unique risks and benefits; Compensation and support; Representative samples; Demographic data; Post-research support; Sharing results; Research training; Diversifying research teams. For each recommendation, the paper outlines the rationale, specifications for how different stakeholders may implement it, and advice for best practices. Instead of isolated recruitment, public involvement and engagement activities, the recommendations here aim to advance mutually beneficial and trusting relationships between researchers and research participants embedded in ED cancer research institutions.
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Grants
- EICEDAAP\100011 Cancer Research UK
- Cancer Research UK (CRUK)
- The International Alliance for Cancer Early Detection, an alliance between Cancer Research UK [EICEDAAP\100011], Canary Center at Stanford University, the University of Cambridge, OHSU Knight Cancer Institute, University College London and the University of Manchester.
- This work was supported by the International Alliance for Cancer Early Detection, an alliance between Cancer Research UK [EICEDAAP\100011], Canary Center at Stanford University, the University of Cambridge, OHSU Knight Cancer Institute, University College London and the University of Manchester.
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Affiliation(s)
| | - Maya Raphael
- Department of Social Anthropology, University of Cambridge, Cambridge, UK
| | - Jessica Currier
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Christina Jäderholm
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, USA
| | - Perveez Mody
- Department of Social Anthropology, University of Cambridge, Cambridge, UK
| | - Jackilen Shannon
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Bella Starling
- Vocal, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Ignacia Arteaga
- Department of Social Anthropology, University of Cambridge, Cambridge, UK.
- Early Cancer Institute, University of Cambridge, Cambridge, UK.
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21
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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.
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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.
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22
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Middleton A, Adams A, Aidid H, Atutornu J, Boraschi D, Borra J, Bircan T, Burch C, Costa A, Dickinson A, Enticknap A, Galloway C, Gale F, Garlick E, Haydon E, Henriques S, Mitchell M, Milne R, Monaghan J, Morley KI, Muella Santos M, Olivares Boldu L, Olumogba F, Orviss K, Parry V, Patch C, Robarts L, Shingles S, Smidt C, Tomlin B, Parkinson S. Public engagement with genomics. Wellcome Open Res 2023; 8:310. [PMID: 37928209 PMCID: PMC10624956 DOI: 10.12688/wellcomeopenres.19473.2] [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] [Accepted: 09/13/2023] [Indexed: 11/07/2023] Open
Abstract
As detailed in its flagship report, Genome UK, the UK government recognises the vital role that broad public engagement across whole populations plays in the field of genomics. However, there is limited evidence about how to do this at scale. Most public audiences do not feel actively connected to science, are oftenunsure of the relevance to their lives and rarely talk to their family and friends about; we term this dis-connection a 'disengaged public audience'. We use a narrative review to explore: (i) UK attitudes towards genetics and genomics and what may influence reluctance to engage with these topics; (ii) innovative public engagement approaches that have been used to bring diverse public audiences into conversations about the technology. Whilst we have found some novel engagement methods that have used participatory arts, film, social media and deliberative methods, there is no clear agreement on best practice. We did not find a consistently used, evidence-based strategy for delivering public engagement about genomics across diverse and broad populations, nor a specific method that is known to encourage engagement from groups that have historically felt (in terms of perception) and been (in reality) excluded from genomic research. We argue there is a need for well-defined, tailor-made engagement strategies that clearly articulate the audience, the purpose and the proposed impact of the engagement intervention. This needs to be coupled with robust evaluation frameworks to build the evidence-base for population-level engagement strategies.
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Affiliation(s)
- Anna Middleton
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | | | - Hugbaad Aidid
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | - Jerome Atutornu
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
- School of Health and Sport Sciences, University of Suffolk, Ipswich, England, UK
| | - Daniela Boraschi
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | | | - Tuba Bircan
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | - Claudette Burch
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | | | | | | | - Catherine Galloway
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | | | - Emma Garlick
- Wellcome Connecting Science, Hinxton, England, UK
| | - Em Haydon
- Wellcome Connecting Science, Hinxton, England, UK
| | - Sasha Henriques
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
- Clinical Genetics Department, Guy's and St Thomas' Hospital, London, England, UK
| | - Marion Mitchell
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | - Richard Milne
- Wellcome Connecting Science, Hinxton, England, UK
- Kavli Centre for Ethics, Science and the Public, University of Cambridge, Cambridge, England, UK
| | | | - Katherine I Morley
- RAND Europe, Cambridge, England, UK
- Melbourne School of Population Health, The University of Melbourne, Melbourne, Victoria, Australia
| | | | | | | | | | - Vivienne Parry
- Genomics England, Queen Mary University of London, London, England, UK
| | | | | | - Sam Shingles
- Wellcome Connecting Science, Hinxton, England, UK
| | - Cindy Smidt
- Wellcome Connecting Science, Hinxton, England, UK
| | - Ben Tomlin
- Wellcome Connecting Science, Hinxton, England, UK
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23
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Dinh BL, Tang E, Taparra K, Nakatsuka N, Chen F, Chiang CWK. Recombination map tailored to Native Hawaiians improves robustness of genomic scans for positive selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548735. [PMID: 37503129 PMCID: PMC10370006 DOI: 10.1101/2023.07.12.548735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Recombination events establish the patterns of haplotypic structure in a population and estimates of recombination rates are used in several downstream population and statistical genetic analyses. Using suboptimal maps from distantly related populations may reduce the efficacy of genomic analyses, particularly for underrepresented populations such as the Native Hawaiians. To overcome this challenge, we constructed recombination maps using genome-wide array data from two study samples of Native Hawaiians: one reflecting the current admixed state of Native Hawaiians (NH map), and one based on individuals of enriched Polynesian ancestries (PNS map) with the potential to be used for less admixed Polynesian populations such as the Samoans. We found the recombination landscape to be less correlated with those from other continental populations (e.g. Spearman's rho = 0.79 between PNS and CEU (Utah residents with Northern and Western European ancestry) compared to 0.92 between YRI (Yoruba in Ibadan, Nigeria) and CEU at 50 kb resolution), likely driven by the unique demographic history of the Native Hawaiians. PNS also shared the fewest recombination hotspots with other populations (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analyses in the Native Hawaiian population, such as local ancestry inference, imputation, and IBD segment and relatedness detections, would achieve similar efficacy when using the NH map compared to an omnibus map. However, for genome scans of adaptive loci using integrated haplotype scores, we found several loci with apparent genome-wide significant signals (|Z-score| > 4) in Native Hawaiians that would not have been significant when analyzed using NH-specific maps. Population-specific recombination maps may therefore improve the robustness of haplotype-based statistics and help us better characterize the evolutionary history that may underlie Native Hawaiian-specific health conditions that persist today.
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Affiliation(s)
- Bryan L Dinh
- Department of Quantitative and Computational Biology, University of Southern California
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California
| | - Kekoa Taparra
- Department of Radiation Oncology, Stanford University, Palo Alto, California
| | | | - Fei Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - Charleston W K Chiang
- Department of Quantitative and Computational Biology, University of Southern California
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
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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: 5] [Impact Index Per Article: 5.0] [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.
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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
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25
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Collins B, Jones N. Digital Simulacra: Circumventing Diversity and Inclusion. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:76-78. [PMID: 37647473 DOI: 10.1080/15265161.2023.2237430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
| | - Nora Jones
- Lewis Katz School of Medicine at Temple University
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26
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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.
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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.
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27
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Doerr M, Yu JH. Translational Research and Communities. Ethics Hum Res 2023; 45:34-38. [PMID: 37777978 DOI: 10.1002/eahr.500181] [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] [Indexed: 10/03/2023]
Abstract
Impactful translational research requires new approaches to computational analysis and bioethics, both of which have been advanced by adoption of community-engagement strategies. Community knowledge and experience will hone data collection, research, and insights and accelerate the impact of derived translational applications to improve individual health, medical decision-making, and public health policy. In the context of translational research with big health data, meaningful community-researcher engagement will require developing and deploying coengagement tools across the research life cycle and developing approaches for novel coproduction.
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Affiliation(s)
- Megan Doerr
- Director of Applied ELSI Research at Sage Bionetworks
| | - Joon-Ho Yu
- Research assistant professor of pediatrics and an associate director of the Institute for Public Health Genetics at the University of Washington
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28
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Logue MW, Dasgupta S, Farrer LA. Genetics of Alzheimer's Disease in the African American Population. J Clin Med 2023; 12:5189. [PMID: 37629231 PMCID: PMC10455208 DOI: 10.3390/jcm12165189] [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: 06/26/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Black/African American (AA) individuals have a higher risk of Alzheimer's disease (AD) than White non-Hispanic persons of European ancestry (EUR) for reasons that may include economic disparities, cardiovascular health, quality of education, and biases in the methods used to diagnose AD. AD is also heritable, and some of the differences in risk may be due to genetics. Many AD-associated variants have been identified by candidate gene studies, genome-wide association studies (GWAS), and genome-sequencing studies. However, most of these studies have been performed using EUR cohorts. In this paper, we review the genetics of AD and AD-related traits in AA individuals. Importantly, studies of genetic risk factors in AA cohorts can elucidate the molecular mechanisms underlying AD risk in AA and other populations. In fact, such studies are essential to enable reliable precision medicine approaches in persons with considerable African ancestry. Furthermore, genetic studies of AA cohorts allow exploration of the ways the impact of genes can vary by ancestry, culture, and economic and environmental disparities. They have yielded important gains in our knowledge of AD genetics, and increasing AA individual representation within genetic studies should remain a priority for inclusive genetic study design.
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Affiliation(s)
- Mark W. Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA 02130, USA;
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Shoumita Dasgupta
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Medical Sciences and Education, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA;
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
- Alzheimer’s Disease Research Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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29
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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: 5] [Impact Index Per Article: 5.0] [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).
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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
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30
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Dolan DD, Cho MK, Lee SSJ. Innovating for a Just and Equitable Future in Genomic and Precision Medicine Research. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:1-4. [PMID: 37353052 PMCID: PMC10339710 DOI: 10.1080/15265161.2023.2215201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Affiliation(s)
- Deanne Dunbar Dolan
- Center for ELSI Resources and Analysis (CERA), Stanford University School of Medicine, Stanford, CA, USA
| | - Mildred K. Cho
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities & Ethics, Columbia University, New York, NY, USA
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31
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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.
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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.
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32
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Ackerman SL, Brown JEH, Zamora A, Outram S. "I Have Fought for so Many Things": Disadvantaged families' Efforts to Obtain Community-Based Services for Their Child after Genomic Sequencing. AJOB Empir Bioeth 2023; 14:208-217. [PMID: 37162201 PMCID: PMC10615790 DOI: 10.1080/23294515.2023.2209747] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
BACKGROUND Families whose child has unexplained intellectual or developmental differences often hope that a genetic diagnosis will lower barriers to community-based therapeutic and support services. However, there is little known about efforts to mobilize genetic information outside the clinic or how socioeconomic disadvantage shapes and constrains outcomes. METHODS We conducted an ethnographic study with predominantly socioeconomically disadvantaged families enrolled in a multi-year genomics research study, including clinic observations and in-depth interviews in English and Spanish at multiple time points. Coding and thematic development were used to collaboratively interpret fieldnotes and transcripts. RESULTS Thirty-two families participated. Themes included familial expectations that a genetic diagnosis could be translated into information, understanding, and assistance to improve the quality of a child's day-to-day life. After sequencing, however, genetic information was not readily converted into improved access to services beyond the clinic, with families often struggling to use a genetic diagnosis to advocate for their child. CONCLUSION Families' ability to use a genetic diagnosis as an effective advocacy tool beyond the clinic was limited by the knowledge and resources available to them, and by the eligibility criteria used by therapeutic service providers' - which focused on clinical diagnosis and functional criteria more than etiologic information. All families undertaking genomic testing, particularly those who are disadvantaged, need additional support to understand the limits and potential benefits of genetic information beyond the clinic.
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Affiliation(s)
- Sara L Ackerman
- Program in Bioethics, University of California San Francisco, San Francisco, California, USA
- Department of Social & Behavioral Sciences, University of California San Francisco, San Francisco, California, USA
- Institute for Health & Aging, University of California San Francisco, San Francisco, California, USA
| | - Julia E H Brown
- Program in Bioethics, University of California San Francisco, San Francisco, California, USA
- Institute for Health & Aging, University of California San Francisco, San Francisco, California, USA
| | - Astrid Zamora
- Program in Bioethics, University of California San Francisco, San Francisco, California, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Simon Outram
- Program in Bioethics, University of California San Francisco, San Francisco, California, USA
- Department of Social & Behavioral Sciences, University of California San Francisco, San Francisco, California, USA
- Institute for Health & Aging, University of California San Francisco, San Francisco, California, USA
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33
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Liverpool L. First human 'pangenome' aims to catalogue genetic diversity. Nature 2023; 617:444-445. [PMID: 37165229 DOI: 10.1038/d41586-023-01576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
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34
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Wu CI. The genetics of race differentiation-should it be studied? Natl Sci Rev 2023; 10:nwad068. [PMID: 37034147 PMCID: PMC10076182 DOI: 10.1093/nsr/nwad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Affiliation(s)
- Chung-I Wu
- Chung-I Wu School of Life Sciences, Sun Yat-sen University, China Associate Editor-in-Chief for Life Sciences at NSR
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35
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Reardon J, Lee SSJ, Goering S, Fullerton SM, Cho MK, Panofsky A, Hammonds EM. Trustworthiness matters: Building equitable and ethical science. Cell 2023; 186:894-898. [PMID: 36724788 PMCID: PMC10580253 DOI: 10.1016/j.cell.2023.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 02/03/2023]
Abstract
Trustworthy science requires research practices that center issues of ethics, equity, and inclusion. We announce the Leadership in the Equitable and Ethical Design (LEED) of Science, Technology, Mathematics, and Medicine (STEM) initiative to create best practices for integrating ethical expertise and fostering equitable collaboration.
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Affiliation(s)
- Jenny Reardon
- Department of Sociology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY 10032, USA
| | - Sara Goering
- Department of Philosophy, University of Washington, Seattle, WA 98195, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA 94305, USA
| | - Aaron Panofsky
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Evelynn M Hammonds
- Department of the History of Science, Harvard University, Cambridge, MA 02138, USA; Department of Comparative Women's Studies, Spelman College, Atlanta, GA 30314, USA
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36
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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.
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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
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37
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Van Horne YO, Alcala CS, Peltier RE, Quintana PJE, Seto E, Gonzales M, Johnston JE, Montoya LD, Quirós-Alcalá L, Beamer PI. An applied environmental justice framework for exposure science. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2023; 33:1-11. [PMID: 35260805 PMCID: PMC8902490 DOI: 10.1038/s41370-022-00422-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/28/2023]
Abstract
On the 30th anniversary of the Principles of Environmental Justice established at the First National People of Color Environmental Leadership Summit in 1991 (Principles of Environmental Justice), we continue to call for these principles to be more widely adopted. We propose an environmental justice framework for exposure science to be implemented by all researchers. This framework should be the standard and not an afterthought or trend dismissed by those who believe that science should not be politicized. Most notably, this framework should be centered on the community it seeks to serve. Researchers should meet with community members and stakeholders to learn more about the community, involve them in the research process, collectively determine the environmental exposure issues of highest concern for the community, and develop sustainable interventions and implementation strategies to address them. Incorporating community "funds of knowledge" will also inform the study design by incorporating the knowledge about the issue that community members have based on their lived experiences. Institutional and funding agency funds should also be directed to supporting community needs both during the "active" research phase and at the conclusion of the research, such as mechanisms for dissemination, capacity building, and engagement with policymakers. This multidirectional framework for exposure science will increase the sustainability of the research and its impact for long-term success.
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Affiliation(s)
- Yoshira Ornelas Van Horne
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 2001 N. Soto Street, Los Angeles, CA, 90032, USA.
| | - Cecilia S Alcala
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, 17 East 102 Street, New York, NY, 10029, USA
| | - Richard E Peltier
- School of Public Health & Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Room 175, Amherst, MA, 01003, USA
| | - Penelope J E Quintana
- School of Public Health, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Edmund Seto
- Department of Environmental & Occupational Health Sciences, School of Public Health, University of Washington, Roosevelt One Building, 4225 Roosevelt Way NE, Suite 100, Seattle, WA, 98195, USA
| | - Melissa Gonzales
- Department of Internal Medicine, University of New Mexico School of Medicine, MSC10 5550 Epidemiology, Albuquerque, NM, 87111, USA
| | - Jill E Johnston
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 2001 N. Soto Street, Los Angeles, CA, 90032, USA
| | | | - Lesliam Quirós-Alcalá
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, 615N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Paloma I Beamer
- Department of Community, Environment and Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295N. Martin Ave., Tucson, AZ, 85724, USA
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38
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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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39
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Epstein HAB. All of Us: A National Effort to Improve Health. JOURNAL OF CONSUMER HEALTH ON THE INTERNET 2022. [DOI: 10.1080/15398285.2022.2138058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Abstract
Genomics data are important for advancing biomedical research, improving clinical care, and informing other disciplines such as forensics and genealogy. However, privacy concerns arise when genomic data are shared. In particular, the identifying nature of genetic information, its direct relationship to health status, and the potential financial harm and stigmatization posed to individuals and their blood relatives call for a survey of the privacy issues related to sharing genetic and related data and potential solutions to overcome these issues. In this work, we provide an overview of the importance of genomic privacy, the information gleaned from genomics data, the sources of potential private information leakages in genomics, and ways to preserve privacy while utilizing the genetic information in research. We discuss the relationship between trust in the scientific community and protecting privacy, illuminating a future roadmap for data sharing and study participation.
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Affiliation(s)
- Gamze Gürsoy
- Department of Biomedical Informatics, Columbia University, New York, NY, USA; .,New York Genome Center, New York, NY, USA
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41
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Yu JJ, Non AL, Heinrich EC, Gu W, Alcock J, Moya EA, Lawrence ES, Tift MS, O'Brien KA, Storz JF, Signore AV, Khudyakov JI, Milsom WK, Wilson SM, Beall CM, Villafuerte FC, Stobdan T, Julian CG, Moore LG, Fuster MM, Stokes JA, Milner R, West JB, Zhang J, Shyy JY, Childebayeva A, Vázquez-Medina JP, Pham LV, Mesarwi OA, Hall JE, Cheviron ZA, Sieker J, Blood AB, Yuan JX, Scott GR, Rana BK, Ponganis PJ, Malhotra A, Powell FL, Simonson TS. Time Domains of Hypoxia Responses and -Omics Insights. Front Physiol 2022; 13:885295. [PMID: 36035495 PMCID: PMC9400701 DOI: 10.3389/fphys.2022.885295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The ability to respond rapidly to changes in oxygen tension is critical for many forms of life. Challenges to oxygen homeostasis, specifically in the contexts of evolutionary biology and biomedicine, provide important insights into mechanisms of hypoxia adaptation and tolerance. Here we synthesize findings across varying time domains of hypoxia in terms of oxygen delivery, ranging from early animal to modern human evolution and examine the potential impacts of environmental and clinical challenges through emerging multi-omics approaches. We discuss how diverse animal species have adapted to hypoxic environments, how humans vary in their responses to hypoxia (i.e., in the context of high-altitude exposure, cardiopulmonary disease, and sleep apnea), and how findings from each of these fields inform the other and lead to promising new directions in basic and clinical hypoxia research.
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Affiliation(s)
- James J. Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Amy L. Non
- Department of Anthropology, Division of Social Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Erica C. Heinrich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA, United States
| | - Wanjun Gu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Herbert Wertheim School of Public Health and Longevity Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, MX, United States
| | - Esteban A. Moya
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Elijah S. Lawrence
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Michael S. Tift
- Department of Biology and Marine Biology, College of Arts and Sciences, University of North Carolina Wilmington, Wilmington, NC, United States
| | - Katie A. O'Brien
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Physiology, Development and Neuroscience, Faculty of Biology, School of Biological Sciences, University of Cambridge, Cambridge, ENG, United Kingdom
| | - Jay F. Storz
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Anthony V. Signore
- School of Biological Sciences, College of Arts and Sciences, University of Nebraska-Lincoln, Lincoln, IL, United States
| | - Jane I. Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, United States
| | | | - Sean M. Wilson
- Lawrence D. Longo, MD Center for Perinatal Biology, Loma Linda, CA, United States
| | | | | | | | - Colleen G. Julian
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lorna G. Moore
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Aurora, CO, United States
| | - Mark M. Fuster
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jennifer A. Stokes
- Department of Kinesiology, Southwestern University, Georgetown, TX, United States
| | - Richard Milner
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - John B. West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Jiao Zhang
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - John Y. Shyy
- Department of Medicine, UC San Diego School of Medicine, San Diego, CA, United States
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - José Pablo Vázquez-Medina
- Department of Integrative Biology, College of Letters and Science, University of California, Berkeley, Berkeley, CA, United States
| | - Luu V. Pham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Omar A. Mesarwi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - James E. Hall
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Zachary A. Cheviron
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT, United States
| | - Jeremy Sieker
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Arlin B. Blood
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Jason X. Yuan
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Graham R. Scott
- Department of Pediatrics Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, CA, United States
| | - Brinda K. Rana
- Moores Cancer Center, UC San Diego, La Jolla, CA, United States
- Department of Psychiatry, UC San Diego, La Jolla, CA, United States
| | - Paul J. Ponganis
- Center for Marine Biotechnology and Biomedicine, La Jolla, CA, United States
| | - Atul Malhotra
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Frank L. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, United States
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42
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Establishing a blockchain-enabled Indigenous data sovereignty framework for genomic data. Cell 2022; 185:2626-2631. [PMID: 35868267 DOI: 10.1016/j.cell.2022.06.030] [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: 04/18/2022] [Revised: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 11/20/2022]
Abstract
Technological advances have enabled the rapid generation of health and genomic data, though rarely do these technologies account for the values and priorities of marginalized communities. In this commentary, we conceptualize a blockchain genomics data framework built out of the concept of Indigenous Data Sovereignty.
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43
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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] [Key Words] [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
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44
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Raz A, Timmermans S, Eyal G, Brothers K, Minari J. Challenges for precision public health communication in the era of genomic medicine. Genet Med 2022; 24:1814-1820. [PMID: 35657379 DOI: 10.1016/j.gim.2022.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Although still in the early stages of development, the advent of fast, high-output, and cost-effective next-generation DNA sequencing technology is moving precision medicine into public health. Before this shift toward next-generation sequencing in public health settings, individual patients met geneticists after showing symptoms and through limited family screening. In the new era of precision public health, everyone is a possible participant in genetic sequencing, simply by being born (newborn screening), by donating blood (biobanking), or through population screening. These initiatives are increasingly offered to individuals throughout their life and more individuals are encountering opportunities to use DNA sequencing. This article raises awareness of these growing areas and calls for different models of public engagement and communication about genomics, including screening asymptomatic populations, obtaining consent for unspecified and unforeseen future uses of genomic data, and managing variants of uncertain significance. Given that such communication challenges loom large, established norms of practice in genomic medicine and research should be reconsidered.
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Affiliation(s)
- Aviad Raz
- Department of Sociology & Anthropology, Ben-Gurion University of the Nagev, Beersheba, Israel.
| | | | - Gil Eyal
- Precision Medicine & Society Program, Department of Sociology, Columbia University, New York, NY
| | - Kyle Brothers
- Department of Pediatrics, School of Medicine, University of Louisville, Louisville, KY
| | - Jusaku Minari
- Uehiro Research Division for iPS Cell Ethics, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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45
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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: 16] [Impact Index Per Article: 8.0] [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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46
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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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47
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Muenzen KD, Amendola LM, Kauffman TL, Mittendorf KF, Bensen JT, Chen F, Green R, Powell BC, Kvale M, Angelo F, Farnan L, Fullerton SM, Robinson JO, Li T, Murali P, Lawlor JM, Ou J, Hindorff LA, Jarvik GP, Crosslin DR. Lessons learned and recommendations for data coordination in collaborative research: The CSER consortium experience. HGG ADVANCES 2022; 3:100120. [PMID: 35707062 PMCID: PMC9190054 DOI: 10.1016/j.xhgg.2022.100120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Integrating data across heterogeneous research environments is a key challenge in multi-site, collaborative research projects. While it is important to allow for natural variation in data collection protocols across research sites, it is also important to achieve interoperability between datasets in order to reap the full benefits of collaborative work. However, there are few standards to guide the data coordination process from project conception to completion. In this paper, we describe the experiences of the Clinical Sequence Evidence-Generating Research (CSER) consortium Data Coordinating Center (DCC), which coordinated harmonized survey and genomic sequencing data from seven clinical research sites from 2020 to 2022. Using input from multiple consortium working groups and from CSER leadership, we first identify 14 lessons learned from CSER in the categories of communication, harmonization, informatics, compliance, and analytics. We then distill these lessons learned into 11 recommendations for future research consortia in the areas of planning, communication, informatics, and analytics. We recommend that planning and budgeting for data coordination activities occur as early as possible during consortium conceptualization and development to minimize downstream complications. We also find that clear, reciprocal, and continuous communication between consortium stakeholders and the DCC is equally important to maintaining a secure and centralized informatics ecosystem for pooling data. Finally, we discuss the importance of actively interrogating current approaches to data governance, particularly for research studies that straddle the research-clinical divide.
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48
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McCradden MD, Anderson JA, A Stephenson E, Drysdale E, Erdman L, Goldenberg A, Zlotnik Shaul R. A Research Ethics Framework for the Clinical Translation of Healthcare Machine Learning. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2022; 22:8-22. [PMID: 35048782 DOI: 10.1080/15265161.2021.2013977] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The application of artificial intelligence and machine learning (ML) technologies in healthcare have immense potential to improve the care of patients. While there are some emerging practices surrounding responsible ML as well as regulatory frameworks, the traditional role of research ethics oversight has been relatively unexplored regarding its relevance for clinical ML. In this paper, we provide a comprehensive research ethics framework that can apply to the systematic inquiry of ML research across its development cycle. The pathway consists of three stages: (1) exploratory, hypothesis-generating data access; (2) silent period evaluation; (3) prospective clinical evaluation. We connect each stage to its literature and ethical justification and suggest adaptations to traditional paradigms to suit ML while maintaining ethical rigor and the protection of individuals. This pathway can accommodate a multitude of research designs from observational to controlled trials, and the stages can apply individually to a variety of ML applications.
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Affiliation(s)
- Melissa D McCradden
- Department of Bioethics, The Hospital for Sick Children
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning
- Division of Clinical & Public Health, Dalla Lana School of Public Health
| | - James A Anderson
- Department of Bioethics, The Hospital for Sick Children
- Institute for Health Management Policy, & Evaluation, University of Toronto
| | - Elizabeth A Stephenson
- Labatt Family Heart Centre, The Hospital for Sick Children
- Department of Pediatrics, The Hospital for Sick Children
| | - Erik Drysdale
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning
| | - Lauren Erdman
- Genetics and Genome Biology, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning
- Vector Institute
- Department of Computer Science, University of Toronto
| | - Anna Goldenberg
- Department of Bioethics, The Hospital for Sick Children
- Vector Institute
- Department of Computer Science, University of Toronto
- CIFAR
| | - Randi Zlotnik Shaul
- Department of Bioethics, The Hospital for Sick Children
- Department of Pediatrics, The Hospital for Sick Children
- Child Health Evaluative Sciences, The Hospital for Sick Children
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49
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Rebbeck TR, Bridges JFP, Mack JW, Gray SW, Trent JM, George S, Crossnohere NL, Paskett ED, Painter CA, Wagle N, Kano M, Nez Henderson P, Henderson JA, Mishra SI, Willman CL, Sussman AL. A Framework for Promoting Diversity, Equity, and Inclusion in Genetics and Genomics Research. JAMA HEALTH FORUM 2022; 3:e220603. [PMID: 35755401 PMCID: PMC9223088 DOI: 10.1001/jamahealthforum.2022.0603] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023] Open
Abstract
IMPORTANCE Research into the genetic and genomic ("genomics") foundations of disease is central to our understanding of disease prevention, early detection, diagnostic accuracy, and therapeutic intervention. Inequitable participation in genomics research by historically excluded populations limits the ability to translate genomic knowledge to achieve health equity and ensure that findings are generalizable to diverse populations. OBSERVATIONS We propose a novel framework for promoting diversity, equity, and inclusion in genomics research. Building on principles of community-based participatory research and collective impact frameworks, the framework can guide our understanding of the social, cultural, health system, policy, community, and individual contexts in which engagement and genomics research are being done. Our framework highlights the involvement of a multistakeholder team, including the participants and communities to be engaged, to ensure robust methods for recruitment, retention, return of genomic results, quality of engagement, follow-up, and monitoring of participants. CONCLUSIONS AND RELEVANCE The proposed engagement framework will guide investigators in optimizing equitable representation in research and enhancing the rigor of genomics investigation.
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Affiliation(s)
- Timothy R Rebbeck
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - John F P Bridges
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Jennifer W Mack
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Stacy W Gray
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Jeffrey M Trent
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Suzanne George
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Norah L Crossnohere
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Electra D Paskett
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Corrie A Painter
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Nikhil Wagle
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Miria Kano
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Patricia Nez Henderson
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Jeffrey A Henderson
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Shiraz I Mishra
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Cheryl L Willman
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
| | - Andrew L Sussman
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts (Rebbeck); Dana-Farber Cancer Institute, Boston, Massachusetts (Rebbeck, Mack, George, Wagle); The Ohio State University, Columbus, Ohio (Bridges, Crossnohere, Paskett); City of Hope, Duarte, California (Gray); The Translational Genomics Research Institute, Phoenix, Arizona (Trent); Broad Institute to Broad Institute of MIT and Harvard and Count Me In, Cambridge, Massachusetts (Painter, Wagle); University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque (Kano, Mishra, Willman, Sussman); Black Hills Center for American Indian Health, Rapid City, South Dakota (Nez Henderson, Henderson); Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota (Willman)
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Functional genomics data: privacy risk assessment and technological mitigation. Nat Rev Genet 2022; 23:245-258. [PMID: 34759381 DOI: 10.1038/s41576-021-00428-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
The generation of functional genomics data by next-generation sequencing has increased greatly in the past decade. Broad sharing of these data is essential for research advancement but poses notable privacy challenges, some of which are analogous to those that occur when sharing genetic variant data. However, there are also unique privacy challenges that arise from cryptic information leakage during the processing and summarization of functional genomics data from raw reads to derived quantities, such as gene expression values. Here, we review these challenges and present potential solutions for mitigating privacy risks while allowing broad data dissemination and analysis.
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