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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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2
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Kanjira SC, Adams MJ, Jiang Y, Tian C, Lewis CM, Kuchenbaecker K, McIntosh AM. Polygenic prediction of major depressive disorder and related traits in African ancestries UK Biobank participants. Mol Psychiatry 2024:10.1038/s41380-024-02662-x. [PMID: 39014000 DOI: 10.1038/s41380-024-02662-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Genome-Wide Association Studies (GWAS) over-represent European ancestries, neglecting all other ancestry groups and low-income nations. Consequently, polygenic risk scores (PRS) more accurately predict complex traits in Europeans than African Ancestries groups. Very few studies have looked at the transferability of European-derived PRS for behavioural and mental health phenotypes to Africans. We assessed the comparative accuracy of depression PRS trained on European and African Ancestries GWAS studies to predict major depressive disorder (MDD) and related traits in African ancestry participants from the UK Biobank. UK Biobank participants were selected based on Principal component analysis clustering with an African genetic similarity reference population, MDD was assessed with the Composite International Diagnostic Interview (CIDI). PRS were computed using PRSice2 software using either European or African Ancestries GWAS summary statistics. PRS trained on European ancestry samples (246,363 cases) predicted case control status in Africans of the UK Biobank with similar accuracies (R2 = 2%, β = 0.32, empirical p-value = 0.002) to PRS trained on far much smaller samples of African Ancestries participants from 23andMe, Inc. (5045 cases, R² = 1.8%, β = 0.28, empirical p-value = 0.008). This suggests that prediction of MDD status from Africans to Africans had greater efficiency relative to discovery sample size than prediction of MDD from Europeans to Africans. Prediction of MDD status in African UK Biobank participants using GWAS findings of likely causal risk factors from European ancestries was non-significant. GWAS of MDD in European ancestries are inefficient for improving polygenic prediction in African samples; urgent MDD studies in Africa are needed.
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Affiliation(s)
- S C Kanjira
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
| | - M J Adams
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Y Jiang
- 23andMe Inc, Sunnyvale, CA, USA
| | - C Tian
- 23andMe Inc, Sunnyvale, CA, USA
| | - C M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - K Kuchenbaecker
- UCL Genetics Institute, University College London, London, UK
| | - A M McIntosh
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK.
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3
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Dasgupta S. Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:347-356. [PMID: 38856681 DOI: 10.1089/omi.2024.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.
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Nieto-Caballero VE, Reijneveld JF, Ruvalcaba A, Innocenzi G, Abeydeera N, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Budzik JM, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. PLoS Genet 2024; 20:e1011313. [PMID: 38870230 PMCID: PMC11208071 DOI: 10.1371/journal.pgen.1011313] [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: 09/13/2023] [Revised: 06/26/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos, Mexico
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Josephine F. Reijneveld
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Angel Ruvalcaba
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gabriel Innocenzi
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nalin Abeydeera
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Samira Asgari
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yang Luo
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Aparna Nathan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Segundo R. León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Jonathan M. Budzik
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sara Suliman
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, California, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Initiative Biohub, San Francisco, California, United States of America
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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5
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Millager RA, Feldman JI, Williams ZJ, Shibata K, Martinez-Torres KA, Bryan KM, Pruett DG, Mitchell JT, Markfeld JE, Merritt B, Daniels DE, Jones RM, Woynaroski T. Diversity of Research Participant Gender, Race, and Ethnicity in Communication Sciences and Disorders: A Systematic Review and Quantitative Synthesis of American Speech-Language-Hearing Association Publications in 2020. PERSPECTIVES OF THE ASHA SPECIAL INTEREST GROUPS 2024; 9:836-852. [PMID: 38912383 PMCID: PMC11192539 DOI: 10.1044/2024_persp-23-00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Purpose One manifestation of systemic inequities in communication sciences and disorders (CSD) is the chronic underreporting and underrepresentation of sex, gender, race, and ethnicity in research. The present study characterized recent demographic reporting practices and representation of participants across CSD research. Methods We systematically reviewed and extracted key reporting and participant data from empirical studies conducted in the United States (US) with human participants published in the year 2020 in journals by the American Speech-Language-Hearing Association (ASHA; k = 407 articles comprising a total n = 80,058 research participants, search completed November 2021). Sex, gender, race, and ethnicity were operationalized per National Institutes of Health guidelines (National Institutes of Health, 2015a, 2015b). Results Sex or gender was reported in 85.5% of included studies; race was reported in 33.7%; and ethnicity was reported in 13.8%. Sex and gender were clearly differentiated in 3.4% of relevant studies. Where reported, median proportions for race and ethnicity were significantly different from the US population, with underrepresentation noted for all non-White racial groups and Hispanic participants. Moreover, 64.7% of studies that reported sex or gender and 67.2% of studies that reported race or ethnicity did not consider these respective variables in analyses or discussion. Conclusion At present, research published in ASHA journals frequently fails to report key demographic data summarizing the characteristics of participants. Moreover, apparent gaps in representation of minoritized racial and ethnic groups threaten the external validity of CSD research and broader health care equity endeavors in the US. Although our study is limited to a single year and publisher, our results point to several steps for readers that may bring greater accountability, consistency, and diversity to the discipline.
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Affiliation(s)
- Ryan A. Millager
- Department of Hearing and Speech Sciences, Vanderbilt University
| | - Jacob I. Feldman
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center
- Frist Center for Autism and Innovation, Vanderbilt University
| | - Zachary J. Williams
- Department of Hearing and Speech Sciences, Vanderbilt University
- Frist Center for Autism and Innovation, Vanderbilt University
- Vanderbilt Brain Institute, Vanderbilt University
- Medical Scientist Training Program, Vanderbilt University School of Medicine
| | - Kiiya Shibata
- Department of Hearing and Speech Sciences, Vanderbilt University
| | - Keysha A. Martinez-Torres
- Department of Hearing and Speech Sciences, Vanderbilt University
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center
| | | | - Dillon G. Pruett
- Department of Hearing and Speech Sciences, Vanderbilt University
| | - Jade T. Mitchell
- Department of Hearing and Speech Sciences, Vanderbilt University
| | - Jennifer E. Markfeld
- Department of Hearing and Speech Sciences, Vanderbilt University
- Frist Center for Autism and Innovation, Vanderbilt University
| | - Brandon Merritt
- Department of Speech, Language, and Hearing Sciences, The University of Texas at El Paso
| | - Derek E. Daniels
- Department of Communication Sciences and Disorders, Wayne State University
| | - Robin M. Jones
- Department of Hearing and Speech Sciences, Vanderbilt University
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center
| | - Tiffany Woynaroski
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center
- Frist Center for Autism and Innovation, Vanderbilt University
- Vanderbilt Brain Institute, Vanderbilt University
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center
- Department of Communication Sciences and Disorders, John A. Burns School of Medicine, University of Hawaii at Manoa
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6
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Wang Y, He Y, Shi Y, Qian DC, Gray KJ, Winn R, Martin AR. Aspiring toward equitable benefits from genomic advances to individuals of ancestrally diverse backgrounds. Am J Hum Genet 2024; 111:809-824. [PMID: 38642557 PMCID: PMC11080611 DOI: 10.1016/j.ajhg.2024.04.002] [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: 10/05/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.
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Affiliation(s)
- Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Yixuan He
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yue Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - David C Qian
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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7
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Cheung MM, Hubert PA, Reed DR, Pouget ER, Jiang X, Hwang LD. Understanding the determinants of sweet taste liking in the African and East Asian ancestry groups in the U.S.-A study protocol. PLoS One 2024; 19:e0300071. [PMID: 38683826 PMCID: PMC11057733 DOI: 10.1371/journal.pone.0300071] [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: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The liking for sweet taste is a powerful driver for consuming added sugars, and therefore, understanding how sweet liking is formed is a critical step in devising strategies to lower added sugars consumption. However, current research on the influence of genetic and environmental factors on sweet liking is mostly based on research conducted with individuals of European ancestry. Whether these results can be generalized to people of other ancestry groups warrants investigation. METHODS We will determine the differences in allele frequencies in sweet-related genetic variants and their effects on sweet liking in 426 adults of either African or East Asian ancestry, who have the highest and lowest average added sugars intake, respectively, among ancestry groups in the U.S. We will collect information on participants' sweet-liking phenotype, added sugars intake (sweetness exposure), anthropometric measures, place-of-birth, and for immigrants, duration of time living in the U.S. and age when immigrated. Ancestry-specific polygenic scores of sweet liking will be computed based on the effect sizes of the sweet-related genetic variants on the sweet-liking phenotype for each ancestry group. The predictive validity of the polygenic scores will be tested using individuals of African and East Asian ancestry from the UK Biobank. We will also compare sweet liking between U.S.-born individuals and immigrants within each ancestry group to test whether differences in environmental sweetness exposure during childhood affect sweet liking in adulthood. DISCUSSION Expanding genetic research on taste to individuals from ancestry groups traditionally underrepresented in such research is consistent with equity goals in sensory and nutrition science. Findings from this study will help in the development of a more personalized nutrition approach for diverse populations. TRIAL REGISTRATION This protocol has been preregistered with the Center for Open Science (https://doi.org/10.17605/OSF.IO/WPR9E).
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Affiliation(s)
- May M. Cheung
- City University of New York, Brooklyn College, Brooklyn, New York, United States of America
| | - Patrice A. Hubert
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, United States of America
| | - Danielle R. Reed
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, United States of America
| | - Enrique R. Pouget
- City University of New York, Brooklyn College, Brooklyn, New York, United States of America
| | - Xinyin Jiang
- City University of New York, Brooklyn College, Brooklyn, New York, United States of America
| | - Liang-Dar Hwang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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8
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Zhang J, Chen W, Chen G, Flannick J, Fikse E, Smerin G, Degner K, Yang Y, Xu C, Li Y, Hanover JA, Simonds WF. Ancestry-specific high-risk gene variant profiling unmasks diabetes-associated genes. Hum Mol Genet 2024; 33:655-666. [PMID: 36255737 PMCID: PMC11000659 DOI: 10.1093/hmg/ddac255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
How ancestry-associated genetic variance affects disparities in the risk of polygenic diseases and influences the identification of disease-associated genes warrants a deeper understanding. We hypothesized that the discovery of genes associated with polygenic diseases may be limited by the overreliance on single-nucleotide polymorphism (SNP)-based genomic investigation, as most significant variants identified in genome-wide SNP association studies map to introns and intergenic regions of the genome. To overcome such potential limitations, we developed a gene-constrained, function-based analytical method centered on high-risk variants (hrV) that encode frameshifts, stopgains or splice site disruption. We analyzed the total number of hrV per gene in populations of different ancestry, representing a total of 185 934 subjects. Using this analysis, we developed a quantitative index of hrV (hrVI) across 20 428 genes within each population. We then applied hrVI analysis to the discovery of genes associated with type 2 diabetes mellitus (T2DM), a polygenic disease with ancestry-related disparity. HrVI profiling and gene-to-gene comparisons of ancestry-specific hrV between the case (20 781 subjects) and control (24 440 subjects) populations in the T2DM national repository identified 57 genes associated with T2DM, 40 of which were discoverable only by ancestry-specific analysis. These results illustrate how a function-based, ancestry-specific analysis of genetic variations can accelerate the identification of genes associated with polygenic diseases. Besides T2DM, such analysis may facilitate our understanding of the genetic basis for other polygenic diseases that are also greatly influenced by environmental and behavioral factors, such as obesity, hypertension and Alzheimer's disease.
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Affiliation(s)
- Jianhua Zhang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Weiping Chen
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, United States
| | - Jason Flannick
- Metabolism Program, Broad Institute, Cambridge, MA 02142, United States
| | - Emma Fikse
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Glenda Smerin
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Katherine Degner
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - Yanqin Yang
- Laboratory of Transplantation Genomics, National Heart Lung and Blood Institute; National Institutes of Health, Bethesda, MD 20892, United States
| | - Catherine Xu
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | | | - Yulong Li
- Milton S. Hershey Medical Center, Division of Endocrinology, Diabetes and Metabolism, Penn State University, Hershey, PA 17033, United States
| | - John A Hanover
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
| | - William F Simonds
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, United States
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Boakye Serebour T, Cribbs AP, Baldwin MJ, Masimirembwa C, Chikwambi Z, Kerasidou A, Snelling SJB. Overcoming barriers to single-cell RNA sequencing adoption in low- and middle-income countries. Eur J Hum Genet 2024:10.1038/s41431-024-01564-4. [PMID: 38565638 DOI: 10.1038/s41431-024-01564-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
The advent of single-cell resolution sequencing and spatial transcriptomics has enabled the delivery of cellular and molecular atlases of tissues and organs, providing new insights into tissue health and disease. However, if the full potential of these technologies is to be equitably realised, ancestrally inclusivity is paramount. Such a goal requires greater inclusion of both researchers and donors in low- and middle-income countries (LMICs). In this perspective, we describe the current landscape of ancestral inclusivity in genomic and single-cell transcriptomic studies. We discuss the collaborative efforts needed to scale the barriers to establishing, expanding, and adopting single-cell sequencing research in LMICs and to enable globally impactful outcomes of these technologies.
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Affiliation(s)
- Tracy Boakye Serebour
- The Botnar Institute for Musculoskeletal Science, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Adam P Cribbs
- The Botnar Institute for Musculoskeletal Science, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathew J Baldwin
- The Botnar Institute for Musculoskeletal Science, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Collen Masimirembwa
- The African Institute of Biomedical Science and Technology, Harare, Zimbabwe
| | - Zedias Chikwambi
- The African Institute of Biomedical Science and Technology, Harare, Zimbabwe
| | - Angeliki Kerasidou
- The Ethox Centre and the Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sarah J B Snelling
- The Botnar Institute for Musculoskeletal Science, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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10
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Jaffe K, Greene AK, Chen L, Ryan KA, Krenz C, Roberts JS, Zikmund-Fisher BJ, McGuire AL, Thomas JD, Marsh EE, Spector-Bagdady K. Genetic Researchers' Use of and Interest in Research With Diverse Ancestral Groups. JAMA Netw Open 2024; 7:e246805. [PMID: 38625702 PMCID: PMC11022111 DOI: 10.1001/jamanetworkopen.2024.6805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/18/2024] [Indexed: 04/17/2024] Open
Abstract
Importance Genetic researchers must have access to databases populated with data from diverse ancestral groups to ensure research is generalizable or targeted for historically excluded communities. Objective To determine genetic researchers' interest in doing research with diverse ancestral populations, which database stewards offer adequate samples, and additional facilitators for use of diverse ancestral data. Design, Setting, and Participants This survey study was conducted from June to December 2022 and was part of an exploratory sequential mixed-methods project in which previous qualitative results informed survey design. Eligible participants included genetic researchers who held US academic affiliations and conducted research using human genetic databases. Exposure Internet-administered survey to genetic research professionals. Main Outcomes and Measures The survey assessed respondents' experience and interest in research with diverse ancestral data, perceptions of adequacy of diverse data across database stewards (ie, private, government, or consortia), and identified facilitators for encouraging use of diverse ancestral data. Descriptive statistics, χ2 tests, and z tests were used to describe respondents' perspectives and experiences. Results A total of 294 researchers (171 men [58.5%]; 121 women [41.2%]) were included in the study, resulting in a response rate of 20.4%. Across seniority level, 109 respondents (37.1%) were senior researchers, 85 (28.9%) were mid-level researchers, 71 (24.1%) were junior researchers, and 27 (9.2%) were trainees. Significantly more respondents worked with data from European ancestral populations (261 respondents [88.8%]) compared with any other ancestral population. Respondents who had not done research with Indigenous ancestral groups (210 respondents [71.4%]) were significantly more likely to report interest in doing so than not (121 respondents [41.2%] vs 89 respondents [30.3%]; P < .001). Respondents reported discrepancies in the adequacy of ancestral populations with significantly more reporting European samples as adequate across consortium (203 respondents [90.6%]), government (200 respondents [89.7%]), and private (42 respondents [80.8%]) databases, compared with any other ancestral population. There were no significant differences in reported adequacy of ancestral populations across database stewards. A majority of respondents without access to adequate diverse samples reported that increasing the ancestral diversity of existing databases (201 respondents [68.4%]) and increasing access to databases that are already diverse (166 respondents [56.5%]) would increase the likelihood of them using a more diverse sample. Conclusions and Relevance In this survey study of US genetic researchers, respondents reported existing databases only provide adequate ancestral samples for European populations, despite their interest in other ancestral populations. These findings suggest there are specific gaps in access to and composition of genetic databases, highlighting the urgent need to boost diversity in research samples to improve inclusivity in genetic research practices.
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Affiliation(s)
- Kaitlyn Jaffe
- Department of Health Promotion and Policy, University of Massachusetts, Amherst
| | - Amanda K. Greene
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
| | - Luyun Chen
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor
| | - Kerry A. Ryan
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
| | - Chris Krenz
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
| | - J. Scott Roberts
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor
| | - Brian J. Zikmund-Fisher
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - J. Denard Thomas
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
| | - Erica E. Marsh
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor
| | - Kayte Spector-Bagdady
- Center for Bioethics and Social Sciences in Medicine, University of Michigan Medical School, Ann Arbor
- Department of Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor
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11
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McMahon CE, Foti N, Jeske M, Britton WR, Fullerton SM, Shim JK, Lee SSJ. Interrogating the Value of Return of Results for Diverse Populations: Perspectives from Precision Medicine Researchers. AJOB Empir Bioeth 2024; 15:108-119. [PMID: 37962912 PMCID: PMC11090989 DOI: 10.1080/23294515.2023.2279965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
BACKGROUND Over the last decade, the return of results (ROR) in precision medicine research (PMR) has become increasingly routine. Calls for individual rights to research results have extended the "duty to report" from clinically useful genetic information to traits and ancestry results. ROR has thus been reframed as inherently beneficial to research participants, without a needed focus on who benefits and how. This paper addresses this gap, particularly in the context of PMR aimed at increasing participant diversity, by providing investigator and researcher perspectives on and questions about the assumed value of ROR in PMR. METHODS Semi-structured interviews with a purposive sample of investigators and researchers across federally funded PMR studies in three national consortia, as well as observations of study activities, focused on how PM researchers conceptualize diversity and implement inclusive practices across research stages, including navigating ROR. RESULTS Interviewees (1) validated the value of ROR as a benefit of PMR, while others (2) questioned the benefit of clinically actionable results to individuals in the absence of sufficient resources for translating findings into health care for diverse and disadvantaged populations; (3) expressed uncertainties in applying the presumed value of ROR as a benefit for non-clinical results; and (4) and debated when the promise of the value of ROR may undermine trust in PMR, and divert efforts to return value beyond ROR. CONCLUSIONS Conceptualizations of diversity and inclusion among PM researchers and investigators raise unique ethical questions where unexamined assumptions of the value of ROR inform study recruitment efforts to enroll minoritized and under-represented populations. A lack of consideration for resources and infrastructure necessary to translate ROR into actionable information may hinder trustworthy community-research relationships. Thus, we argue for a more intentional interrogation of ROR practices as an offer of benefit and for whom.
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Affiliation(s)
- Caitlin E. McMahon
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY, United States of America
| | - Nicole Foti
- Department of Social and Behavioral Sciences, University of California, San Francisco, California, United States of America
| | - Melanie Jeske
- Institute on the Formation of Knowledge, University of Chicago, Chicago, Illinois, United States of America
| | - William R. Britton
- Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, United States of America
| | - Stephanie M. Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Janet K. Shim
- Department of Social and Behavioral Sciences, University of California, San Francisco, California, United States of America
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY, United States of America
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12
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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13
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Zhang J, Pandey M, Awe A, Lue N, Kittock C, Fikse E, Degner K, Staples J, Mokhasi N, Chen W, Yang Y, Adikaram P, Jacob N, Greenfest-Allen E, Thomas R, Bomeny L, Zhang Y, Petros TJ, Wang X, Li Y, Simonds WF. The association of GNB5 with Alzheimer disease revealed by genomic analysis restricted to variants impacting gene function. Am J Hum Genet 2024; 111:473-486. [PMID: 38354736 PMCID: PMC10940018 DOI: 10.1016/j.ajhg.2024.01.005] [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: 10/25/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Disease-associated variants identified from genome-wide association studies (GWASs) frequently map to non-coding areas of the genome such as introns and intergenic regions. An exclusive reliance on gene-agnostic methods of genomic investigation could limit the identification of relevant genes associated with polygenic diseases such as Alzheimer disease (AD). To overcome such potential restriction, we developed a gene-constrained analytical method that considers only moderate- and high-risk variants that affect gene coding sequences. We report here the application of this approach to publicly available datasets containing 181,388 individuals without and with AD and the resulting identification of 660 genes potentially linked to the higher AD prevalence among Africans/African Americans. By integration with transcriptome analysis of 23 brain regions from 2,728 AD case-control samples, we concentrated on nine genes that potentially enhance the risk of AD: AACS, GNB5, GNS, HIPK3, MED13, SHC2, SLC22A5, VPS35, and ZNF398. GNB5, the fifth member of the heterotrimeric G protein beta family encoding Gβ5, is primarily expressed in neurons and is essential for normal neuronal development in mouse brain. Homozygous or compound heterozygous loss of function of GNB5 in humans has previously been associated with a syndrome of developmental delay, cognitive impairment, and cardiac arrhythmia. In validation experiments, we confirmed that Gnb5 heterozygosity enhanced the formation of both amyloid plaques and neurofibrillary tangles in the brains of AD model mice. These results suggest that gene-constrained analysis can complement the power of GWASs in the identification of AD-associated genes and may be more broadly applicable to other polygenic diseases.
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Affiliation(s)
- Jianhua Zhang
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Mritunjay Pandey
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam Awe
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Lue
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claire Kittock
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emma Fikse
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine Degner
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenna Staples
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neha Mokhasi
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Weiping Chen
- Genomic Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bldg. 8/Rm 1A11, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yanqin Yang
- Laboratory of Transplantation Genomics, National Heart Lung and Blood Institute, Bldg. 10/Rm 7S261, National Institutes of Health, Bethesda, MD 20892, USA
| | - Poorni Adikaram
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nirmal Jacob
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Greenfest-Allen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel Thomas
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Bomeny
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yajun Zhang
- Unit on Cellular and Molecular Neurodevelopment, Bldg. 35/Rm 3B 1002, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy J Petros
- Unit on Cellular and Molecular Neurodevelopment, Bldg. 35/Rm 3B 1002, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaowen Wang
- Partek Incorporated, 12747 Olive Boulevard, St. Louis, MO 63141, USA
| | - Yulong Li
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA
| | - William F Simonds
- Metabolic Diseases Branch, Bldg. 10/Rm 8C-101, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. EVOLUTIONARY HUMAN SCIENCES 2024; 6:e15. [PMID: 38516374 PMCID: PMC10955370 DOI: 10.1017/ehs.2024.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/17/2024] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
Major developments in the field of genetics in the past few decades have revolutionised notions of what it means to be human. Although currently only a few populations around the world practise a hunting and gathering lifestyle, this mode of subsistence has characterised members of our species since its very origins and allowed us to migrate across the planet. Therefore, the geographical distribution of hunter-gatherer populations, dependence on local ecosystems and connections to past populations and neighbouring groups have provided unique insights into our evolutionary origins. However, given the vulnerable status of hunter-gatherers worldwide, the development of the field of anthropological genetics requires that we reevaluate how we conduct research with these communities. Here, we review how the inclusion of hunter-gatherer populations in genetics studies has advanced our understanding of human origins, ancient population migrations and interactions as well as phenotypic adaptations and adaptability to different environments, and the important scientific and medical applications of these advancements. At the same time, we highlight the necessity to address yet unresolved questions and identify areas in which the field may benefit from improvements.
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Affiliation(s)
| | - Inez Derkx
- Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
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15
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Chappell E, Arbour L, Laksman Z. The Inclusion of Underrepresented Populations in Cardiovascular Genetics and Epidemiology. J Cardiovasc Dev Dis 2024; 11:56. [PMID: 38392270 PMCID: PMC10888590 DOI: 10.3390/jcdd11020056] [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: 12/24/2023] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Novel genetic risk markers have helped us to advance the field of cardiovascular epidemiology and refine our current understanding and risk stratification paradigms. The discovery and analysis of variants can help us to tailor prognostication and management. However, populations underrepresented in cardiovascular epidemiology and cardiogenetics research may experience inequities in care if prediction tools are not applicable to them clinically. Therefore, the purpose of this article is to outline the barriers that underrepresented populations can face in participating in genetics research, to describe the current efforts to diversify cardiogenetics research, and to outline strategies that researchers in cardiovascular epidemiology can implement to include underrepresented populations. Mistrust, a lack of diverse research teams, the improper use of sensitive biodata, and the constraints of genetic analyses are all barriers for including diverse populations in genetics studies. The current work is beginning to address the paucity of ethnically diverse genetics research and has already begun to shed light on the potential benefits of including underrepresented and diverse populations. Reducing barriers for individuals, utilizing community-driven research processes, adopting novel recruitment strategies, and pushing for organizational support for diverse genetics research are key steps that clinicians and researchers can take to develop equitable risk stratification tools and improve patient care.
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Affiliation(s)
- Elias Chappell
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Zachary Laksman
- Department of Medicine and the School of Biomedical Engineering, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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16
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Gharani N, Calendo G, Kusic D, Madzo J, Scheinfeldt L. Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens. BMC Genomics 2024; 25:116. [PMID: 38279110 PMCID: PMC10811916 DOI: 10.1186/s12864-024-09994-6] [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: 08/08/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
Here we describe a new public pharmacogenetic (PGx) annotation database of a large (n = 3,202) and diverse biospecimen collection of 1000 Genomes Project cell lines and DNAs. The database is searchable with a user friendly, web-based tool ( www.coriell.org/StarAllele/Search ). This resource leverages existing whole genome sequencing data and PharmVar annotations to characterize *alleles for each biospecimen in the collection. This new tool is designed to facilitate in vitro functional characterization of *allele haplotypes and diplotypes as well as support clinical PGx assay development, validation, and implementation.
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Affiliation(s)
- N Gharani
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
- Gharani Consulting Limited, 272 Regents Park Road, London, N3 3HN, UK
| | - G Calendo
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
| | - D Kusic
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
| | - J Madzo
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA
- Cooper Medical School of Rowan University, 401 South Broadway, Camden, NJ, 08103, USA
| | - L Scheinfeldt
- Coriell Institute for Medical Research, 403 Haddon Ave, Camden, NJ, 08103, USA.
- Cooper Medical School of Rowan University, 401 South Broadway, Camden, NJ, 08103, USA.
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17
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Dokuru DR, Horwitz TB, Freis SM, Stallings MC, Ehringer MA. South Asia: The Missing Diverse in Diversity. Behav Genet 2024; 54:51-62. [PMID: 37917228 PMCID: PMC11129896 DOI: 10.1007/s10519-023-10161-y] [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: 04/23/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
South Asia, making up around 25% of the world's population, encompasses a wide range of individuals with tremendous genetic and environmental diversity. This region, which spans eight countries, is home to over 4500 anthropologically defined groups that speak numerous languages and have an array of religious beliefs and cultures, making it one of the most diverse places in the world. Much of the region's rich genetic diversity and structure is the result of a complex combination of population history, migration patterns, and endogamous practices. Despite the overwhelming size and diversity, South Asians have often been underrepresented in genetic research, making up less than 2% of the participants in genetic studies. This has led to a lack of population specific understanding of genetic disease risks. We aim to raise awareness about underlying genetic diversity in this ancestry group, call attention to the lack of representation of the group, and to highlight strategies for future studies in South Asians.
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Affiliation(s)
- Deepika R Dokuru
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA.
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA.
| | - Tanya B Horwitz
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Samantha M Freis
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, 1480 30 St, Boulder, CO, 80303, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
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18
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Trevino AD, Jamil B, Su J, Aliev F, Elam KK, Lemery-Chalfant K. Alcohol Use Disorder Polygenic Risk Scores and Trajectories of Early Adolescent Externalizing Behaviors: Examining the Role of Parenting and Family Conflict in the Racially/Ethnically Diverse ABCD Sample. Behav Genet 2024; 54:101-118. [PMID: 37792148 DOI: 10.1007/s10519-023-10155-w] [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: 04/11/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
This study examined the independent and interactive effects of alcohol use disorder genome-wide polygenic scores (AUD-PGS) and parenting and family conflict on early adolescent externalizing behaviors. Data were drawn from White (N = 6181, 46.9% female), Black/African American (N = 1784, 50.1% female), and Hispanic/Latinx (N = 2410, 48.0% female) youth from the adolescent brain cognitive development Study (ABCD). Parents reported on youth externalizing behaviors at baseline (T1, age 9/10), 1-year (T2, age 10/11) and 2-year (T3, age 11/12) assessments. Youth reported on parenting and family environment at T1 and provided saliva or blood samples for genotyping. Results from latent growth models indicated that in general externalizing behaviors decreased from T1 to T3. Across all groups, higher family conflict was associated with more externalizing behaviors at T1, and we did not find significant associations between parental monitoring and early adolescent externalizing behaviors. Parental acceptance was associated with lower externalizing behaviors among White and Hispanic youth, but not among Black youth. Results indicated no significant main effect of AUD-PGS nor interaction effect between AUD-PGS and family variables on early adolescent externalizing behaviors. Post hoc exploratory analysis uncovered an interaction between AUD-PGS and parental acceptance such that AUD-PGS was positively associated with externalizing rule-breaking behaviors among Hispanic youth, but only when parental acceptance was very low. Findings highlight the important role of family conflict and parental acceptance in externalizing behaviors among early adolescents, and emphasize the need to examine other developmental pathways underlying genetic risk for AUD across diverse populations.
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Affiliation(s)
- Angel D Trevino
- Department of Psychology, Arizona State University, Phoenix, AZ, USA.
| | - Belal Jamil
- Department of Psychology, Arizona State University, Phoenix, AZ, USA
| | - Jinni Su
- Department of Psychology, Arizona State University, Phoenix, AZ, USA
| | - Fazil Aliev
- Department of Psychiatry, Rutgers University, New Brunswick, NJ, USA
| | - Kit K Elam
- Department of Applied Health Science, Indiana University, Bloomington, IN, USA
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Kanjira SC, Adams MJ, Yunxuan J, Chao T, Lewis CM, Kuchenbaecker K, McIntosh AM. Polygenic prediction of major depressive disorder and related traits in African ancestries UK Biobank participants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.24.23300412. [PMID: 38234770 PMCID: PMC10793522 DOI: 10.1101/2023.12.24.23300412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Introduction Genome-Wide Association Studies (GWAS) over-represent European ancestries compared to the global population, neglecting all other ancestry groups and low-income nations. Consequently, polygenic risk scores (PRS) more accurately predict complex traits in Europeans than African Ancestries groups. Very few studies have looked at the transferability of European-derived PRS for behavioural and mental health phenotypes to non-Europeans. We assessed the comparative accuracy of PRS for Major Depressive Disorder (MDD) trained on European and African Ancestries GWAS studies to predict MDD and related traits in African Ancestries participants from the UK Biobank. Methods UK Biobank participants were selected based on Principal component analysis (PCA) clustering with an African genetic similarity reference population and MDD was assessed with the Composite International Diagnostic Interview (CIDI). Polygenic Risk Scores (PRS) were computed using PRSice2 using either European or African Ancestries GWAS summary statistics. Results PRS trained on European ancestry samples (246,363 cases) predicted case control status in Africans of the UK Biobank with similar accuracies (190 cases, R2=2%) to PRS trained on far much smaller samples of African Ancestries participants from 23andMe, Inc. (5045 cases, R2=1.8%). This suggests that prediction of MDD status from Africans to Africans had greater efficiency per unit increase in the discovery sample size than prediction of MDD from Europeans to Africans. Prediction of MDD status in African UK Biobank participants using GWAS findings of causal risk factors from European ancestries was non-significant. Conclusion GWAS studies of MDD in European ancestries are an inefficient means of improving polygenic prediction accuracy in African samples.
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Affiliation(s)
- S C Kanjira
- Centre for Clinical Brain Sciences, University of Edinburgh, UK
- Malawi Epidemiology and Intervention Research Unit, Lilongwe, Malawi
| | - M J Adams
- Centre for Clinical Brain Sciences, University of Edinburgh, UK
| | | | | | | | | | - A M McIntosh
- Centre for Clinical Brain Sciences, University of Edinburgh, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, UK
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20
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Thami PK, Choga WT, Dandara C, O’Brien SJ, Essex M, Gaseitsiwe S, Chimusa ER. Whole genome sequencing reveals population diversity and variation in HIV-1 specific host genes. Front Genet 2023; 14:1290624. [PMID: 38179408 PMCID: PMC10765519 DOI: 10.3389/fgene.2023.1290624] [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: 09/07/2023] [Accepted: 11/20/2023] [Indexed: 01/06/2024] Open
Abstract
HIV infection continues to be a major global public health issue. The population heterogeneity in susceptibility or resistance to HIV-1 and progression upon infection is attributable to, among other factors, host genetic variation. Therefore, identifying population-specific variation and genetic modifiers of HIV infectivity can catapult the invention of effective strategies against HIV-1 in African populations. Here, we investigated whole genome sequences of 390 unrelated HIV-positive and -negative individuals from Botswana. We report 27.7 million single nucleotide variations (SNVs) in the complete genomes of Botswana nationals, of which 2.8 million were missing in public databases. Our population structure analysis revealed a largely homogenous structure in the Botswana population. Admixture analysis showed elevated components shared between the Botswana population and the Niger-Congo (65.9%), Khoe-San (32.9%), and Europeans (1.1%) ancestries in the population of Botswana. Statistical significance of the mutational burden of deleterious and loss-of-function variants per gene against a null model was estimated. The most deleterious variants were enriched in five genes: ACTRT2 (the Actin Related Protein T2), HOXD12 (homeobox D12), ABCB5 (ATP binding cassette subfamily B member 5), ATP8B4 (ATPase phospholipid transporting 8B4) and ABCC12 (ATP Binding Cassette Subfamily C Member 12). These genes are enriched in the glycolysis and gluconeogenesis (p < 2.84e-6) pathways and therefore, may contribute to the emerging field of immunometabolism in which therapy against HIV-1 infection is being evaluated. Published transcriptomic evidence supports the role of the glycolysis/gluconeogenesis pathways in the regulation of susceptibility to HIV, and that cumulative effects of genetic modifiers in glycolysis/gluconeogenesis pathways may potentially have effects on the expression and clinical variability of HIV-1. Identified genes and pathways provide novel avenues for other interventions, with the potential for informing the design of new therapeutics.
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Affiliation(s)
- Prisca K. Thami
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wonderful T. Choga
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- UCT/SAMRC Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council, Cape Town, South Africa
| | - Stephen J. O’Brien
- Laboratory of Genomics Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
- Guy Harvey Oceanographic Center Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Myron Essex
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health AIDS Initiative, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health AIDS Initiative, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Emile R. Chimusa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
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21
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Ruderman A. Population diversity and equity in the genomic era: going global to return to the local. J Community Genet 2023; 14:519-525. [PMID: 37670200 PMCID: PMC10725358 DOI: 10.1007/s12687-023-00669-5] [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: 06/21/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Advances in precision medicine depend on the quantity and quality of available genomic information. Various articles alert about the current disparities between the world's regions regarding the amount of genomic information available and the negative impact this will have on global health. The objective of this paper is to review these articles to describe what aspects they emphasize and highlight some issues that remain to be analyzed from the perspective of a "peripheral" country. Most of these articles come from central countries, where the need for more diversity in genomics is already detected. Several authors analyze lack of human diversity with focus on national, while others analyze the problem from a global perspective. Depending on the country of origin of the research, the claim for greater diversity has different meanings. Broadly, high-income countries advocate for better coverage looking within the boundaries of their own countries. In other regions of the world, where this field of research has not yet been massively developed, the same need for greater inclusiveness of origins in population genomics studies is not detected. An under-analyzed aspect is the unequal starting point between regions regarding the economic resources available for the development of this field of medicine, and for science and health in general. Although this macroeconomic and social aspect is usually absent in scientific analyses, without it solved, it will be impossible to guarantee that all world populations are equally represented in the panels or genomic databases that serve as input for precision medicine development.
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Affiliation(s)
- Anahí Ruderman
- Patagonian Institute of Social and Human Science. CONICET. Bv. Almirante Brown 2915, Puerto Madryn, Argentina.
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22
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Cheung MM, Hubert PA, Reed DR, Pouget ER, Jiang X, Hwang LD. Understanding the Determinants of Sweet Liking in the African and East Asian Ancestry Groups in the U.S. - A Study Protocol. RESEARCH SQUARE 2023:rs.3.rs-3644422. [PMID: 38076869 PMCID: PMC10705709 DOI: 10.21203/rs.3.rs-3644422/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Background The liking for sweet taste is a powerful driver for consuming added sugars, and therefore, understanding how sweet liking is formed is a critical step in devising strategies to lower added sugars consumption. However, current research on the influence of genetic and environmental factors on sweet liking is mostly based on research conducted with individuals of European ancestry. Whether these results can be generalized to people of other ancestry groups warrants investigation. Methods We will determine the differences in allele frequencies in sweet-related genetic variants and their effects on sweet liking in 426 adults of either African or East Asian ancestry, who have the highest and lowest average added sugars intake, respectively, among ancestry groups in the U.S. We will collect information on participants' sweet-liking phenotype, added sugars intake (sweetness exposure), anthropometric measures, place-of-birth, and for immigrants, duration of time living in the U.S. and age when immigrated. Ancestry-specific polygenic scores of sweet liking will be computed based on the effect sizes of the sweet-related genetic variants on the sweet-liking phenotype for each ancestry group. The predictive validity of the polygenic scores will be tested using individuals of African and East Asian ancestry from the UK Biobank. We will also compare sweet liking between U.S.-born individuals and immigrants within each ancestry group to test whether differences in environmental sweetness exposure during childhood affect sweet liking in adulthood. Discussion Expanding genetic research on taste to individuals from ancestry groups traditionally underrepresented in such research is consistent with equity goals in sensory and nutrition science. Findings from this study will help in the development of a more personalized nutrition approach for diverse populations. Trial registration This protocol has been preregistered with the Center for Open Science (https://doi.org/10.17605/OSF.IO/WPR9E) and is approved by the City University of New York Human Research Protection Program (IRB#: 2023-0064-Brooklyn).
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23
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Bukowski A, Hoyo C, Vielot NA, Graff M, Kosorok MR, Brewster WR, Maguire RL, Murphy SK, Nedjai B, Ladoukakis E, North KE, Smith JS. Epigenome-wide methylation and progression to high-grade cervical intraepithelial neoplasia (CIN2+): a prospective cohort study in the United States. BMC Cancer 2023; 23:1072. [PMID: 37932662 PMCID: PMC10629205 DOI: 10.1186/s12885-023-11518-6] [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: 05/04/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Methylation levels may be associated with and serve as markers to predict risk of progression of precancerous cervical lesions. We conducted an epigenome-wide association study (EWAS) of CpG methylation and progression to high-grade cervical intraepithelial neoplasia (CIN2 +) following an abnormal screening test. METHODS A prospective US cohort of 289 colposcopy patients with normal or CIN1 enrollment histology was assessed. Baseline cervical sample DNA was analyzed using Illumina HumanMethylation 450K (n = 76) or EPIC 850K (n = 213) arrays. Participants returned at provider-recommended intervals and were followed up to 5 years via medical records. We assessed continuous CpG M values for 9 cervical cancer-associated genes and time-to-progression to CIN2+. We estimated CpG-specific time-to-event ratios (TTER) and hazard ratios using adjusted, interval-censored Weibull accelerated failure time models. We also conducted an exploratory EWAS to identify novel CpGs with false discovery rate (FDR) < 0.05. RESULTS At enrollment, median age was 29.2 years; 64.0% were high-risk HPV-positive, and 54.3% were non-white. During follow-up (median 24.4 months), 15 participants progressed to CIN2+. Greater methylation levels were associated with a shorter time-to-CIN2+ for CADM1 cg03505501 (TTER = 0.28; 95%CI 0.12, 0.63; FDR = 0.03) and RARB Cluster 1 (TTER = 0.46; 95% CI 0.29, 0.71; FDR = 0.01). There was evidence of similar trends for DAPK1 cg14286732, PAX1 cg07213060, and PAX1 Cluster 1. The EWAS detected 336 novel progression-associated CpGs, including those located in CpG islands associated with genes FGF22, TOX, COL18A1, GPM6A, XAB2, TIMP2, GSPT1, NR4A2, and APBB1IP. CONCLUSIONS Using prospective time-to-event data, we detected associations between CADM1-, DAPK1-, PAX1-, and RARB-related CpGs and cervical disease progression, and we identified novel progression-associated CpGs. IMPACT Methylation levels at novel CpG sites may help identify individuals with ≤CIN1 histology at higher risk of progression to CIN2+ and inform risk-based cervical cancer screening guidelines.
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Affiliation(s)
- Alexandra Bukowski
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA.
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
| | - Michael R Kosorok
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Wendy R Brewster
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rachel L Maguire
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, 27701, USA
| | - Belinda Nedjai
- Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University London, London, UK
| | - Efthymios Ladoukakis
- Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University London, London, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
| | - Jennifer S Smith
- Department of Epidemiology, University of North Carolina at Chapel Hill, 60 Bondurant Hall, Chapel Hill, NC, 27599, USA
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA
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24
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DeGorter MK, Goddard PC, Karakoc E, Kundu S, Yan SM, Nachun D, Abell N, Aguirre M, Carstensen T, Chen Z, Durrant M, Dwaracherla VR, Feng K, Gloudemans MJ, Hunter N, Moorthy MPS, Pomilla C, Rodrigues KB, Smith CJ, Smith KS, Ungar RA, Balliu B, Fellay J, Flicek P, McLaren PJ, Henn B, McCoy RC, Sugden L, Kundaje A, Sandhu MS, Gurdasani D, Montgomery SB. Transcriptomics and chromatin accessibility in multiple African population samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.04.564839. [PMID: 37986808 PMCID: PMC10659267 DOI: 10.1101/2023.11.04.564839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.
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Affiliation(s)
| | - Page C Goddard
- Department of Genetics, Stanford University, Stanford, CA
| | - Emre Karakoc
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Soumya Kundu
- Department of Computer Science, Stanford University, Stanford CA
| | | | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA
| | - Nathan Abell
- Department of Genetics, Stanford University, Stanford, CA
| | - Matthew Aguirre
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | - Tommy Carstensen
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Ziwei Chen
- Department of Computer Science, Stanford University, Stanford CA
| | | | | | - Karen Feng
- Department of Biomedical Data Science, Stanford University, Stanford, CA
| | | | - Naiomi Hunter
- Department of Genetics, Stanford University, Stanford, CA
| | | | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Kevin S Smith
- Department of Pathology, Stanford University, Stanford, CA
| | - Rachel A Ungar
- Department of Genetics, Stanford University, Stanford, CA
| | - Brunilda Balliu
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA and Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland and Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Paul Flicek
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Canada and Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Brenna Henn
- Department of Anthropology, University of California Davis, Davis CA and Genome Center, University of California Davis, Davis CA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore
| | - Lauren Sugden
- Department of Mathematics and Computer Science, Dusquesne University, Pittsburgh, PA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA
- Department of Computer Science, Stanford University, Stanford CA
| | | | - Deepti Gurdasani
- William Harvey Research Institute, Queen Mary University of London, London, UK; Kirby Institute, University of New South Wales, Australia; School of Medicine, University of Western Australia, Australia
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25
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Arnatkeviciute A, Lemire M, Morrison C, Mooney M, Ryabinin P, Roslin NM, Nikolas M, Coxon J, Tiego J, Hawi Z, Fornito A, Henrik W, Martinot JL, Martinot MLP, Artiges E, Garavan H, Nigg J, Friedman NP, Burton C, Schachar R, Crosbie J, Bellgrove MA. Trans-ancestry meta-analysis of genome wide association studies of inhibitory control. Mol Psychiatry 2023; 28:4175-4184. [PMID: 37500827 PMCID: PMC10827666 DOI: 10.1038/s41380-023-02187-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/01/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
Deficits in effective executive function, including inhibitory control are associated with risk for a number of psychiatric disorders and significantly impact everyday functioning. These complex traits have been proposed to serve as endophenotypes, however, their genetic architecture is not yet well understood. To identify the common genetic variation associated with inhibitory control in the general population we performed the first trans-ancestry genome wide association study (GWAS) combining data across 8 sites and four ancestries (N = 14,877) using cognitive traits derived from the stop-signal task, namely - go reaction time (GoRT), go reaction time variability (GoRT SD) and stop signal reaction time (SSRT). Although we did not identify genome wide significant associations for any of the three traits, GoRT SD and SSRT demonstrated significant and similar SNP heritability of 8.2%, indicative of an influence of genetic factors. Power analyses demonstrated that the number of common causal variants contributing to the heritability of these phenotypes is relatively high and larger sample sizes are necessary to robustly identify associations. In Europeans, the polygenic risk for ADHD was significantly associated with GoRT SD and the polygenic risk for schizophrenia was associated with GoRT, while in East Asians polygenic risk for schizophrenia was associated with SSRT. These results support the potential of executive function measures as endophenotypes of neuropsychiatric disorders. Together these findings provide the first evidence indicating the influence of common genetic variation in the genetic architecture of inhibitory control quantified using objective behavioural traits derived from the stop-signal task.
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Affiliation(s)
- Aurina Arnatkeviciute
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Mathieu Lemire
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claire Morrison
- Department of Psychology and Neuroscience, University of Colorado-Boulder, Boulder, CO, USA
- Institute for Behavioural Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Michael Mooney
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Peter Ryabinin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Nicole M Roslin
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Molly Nikolas
- Department of Psychological and Brain Sciences, University of Iowa, Iowa City, IA, 52242, USA
| | - James Coxon
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Jeggan Tiego
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Ziarih Hawi
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Alex Fornito
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia
| | - Walter Henrik
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu, Berlin, Germany
| | - Jean-Luc Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM U1299 "Developmental trajectories & psychiatry" Université Paris-Saclay, Ecole Normale supérieure Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
| | - Marie-Laure Paillère Martinot
- Institut National de la Santé et de la Recherche Médicale, INSERM U1299 "Developmental trajectories & psychiatry" Université Paris-Saclay, Ecole Normale supérieure Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
- AP-HP, Sorbonne Université, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital, Paris, France
| | - Eric Artiges
- Institut National de la Santé et de la Recherche Médicale, INSERM U1299 "Developmental trajectories & psychiatry" Université Paris-Saclay, Ecole Normale supérieure Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
- Etablissement Public de Santé (EPS) Barthélemy Durand, 91700, Sainte-Geneviève-des-Bois, France
| | - Hugh Garavan
- Departments of Psychiatry and Psychology, University of Vermont, 05405, Burlington, VT, USA
| | - Joel Nigg
- Division of Psychology, Department of Psychiatry, Oregon Health & Science University, Portland, OR, USA
| | - Naomi P Friedman
- Department of Psychology and Neuroscience, University of Colorado-Boulder, Boulder, CO, USA
- Institute for Behavioural Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Christie Burton
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Russell Schachar
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Crosbie
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mark A Bellgrove
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Melbourne, VIC, Australia.
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26
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Doumatey AP, Bentley AR, Akinyemi R, Olanrewaju TO, Adeyemo A, Rotimi C. Genes, environment, and African ancestry in cardiometabolic disorders. Trends Endocrinol Metab 2023; 34:601-621. [PMID: 37598069 PMCID: PMC10548552 DOI: 10.1016/j.tem.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/21/2023]
Abstract
The past two decades have been characterized by a substantial global increase in cardiometabolic diseases, but the prevalence and incidence of these diseases and related traits differ across populations. African ancestry populations are among the most affected yet least included in research. Populations of African descent manifest significant genetic and environmental diversity and this under-representation is a missed opportunity for discovery and could exacerbate existing health disparities and curtail equitable implementation of precision medicine. Here, we discuss cardiometabolic diseases and traits in the context of African descent populations, including both genetic and environmental contributors and emphasizing novel discoveries. We also review new initiatives to include more individuals of African descent in genomics to address current gaps in the field.
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Affiliation(s)
- Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rufus Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training and Centre for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria; Department of Neurology, University College Hospital, Ibadan, Nigeria
| | - Timothy O Olanrewaju
- Division of Nephrology, Department of Medicine, University of Ilorin & University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Trujillo S, Wetmore JB, Camarillo IA, Misiewicz S, May H, Choi H, Siegel K, Chung WK, Phelan JC, Yang LH, Leu CS, Bergner AL, Ottman R. Knowledge and beliefs about epilepsy genetics among Hispanic and non-Hispanic patients. Epilepsia 2023; 64:2443-2453. [PMID: 37353999 PMCID: PMC10529985 DOI: 10.1111/epi.17701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/02/2023] [Accepted: 06/22/2023] [Indexed: 06/25/2023]
Abstract
OBJECTIVE Hispanics continue to face challenges when trying to access health care, including epilepsy care and genetic-related health care services. This study examined epilepsy genetic knowledge and beliefs in this historically underserved population. METHODS Questionnaires were completed by 641 adults with epilepsy without identified cause, of whom 122 self-identified as Hispanic or Latino and 519 as non-Hispanic. Participants were asked about their views on the contribution of genetics to the cause of their epilepsy ("genetic attribution"), optimism for advancements in epilepsy genetic research ("genetic optimism"), basic genetic knowledge, and epilepsy-specific genetic knowledge. Generalized linear models were used to compare the two groups in the means of quantitative measures and percents answered correctly for individual genetic knowledge items. Analyses were adjusted for age, sex, education, religion, family history of epilepsy, and time since last seizure. RESULTS Hispanics did not differ from non-Hispanics in genetic attribution, genetic optimism, or number of six basic genetic knowledge items answered correctly. The number of nine epilepsy-specific genetic knowledge items answered correctly was significantly lower for Hispanics than non-Hispanics (adjusted mean = 6.0 vs. 6.7, p < .001). After adjustment for education and other potential mediators, the proportion answered correctly was significantly lower for Hispanics than non-Hispanics for only two items related to family history and penetrance of epilepsy-related genes. Only 54% of Hispanics and 61% of non-Hispanics answered correctly that "If a person has epilepsy, his or her relatives have an increased chance of getting epilepsy." SIGNIFICANCE Despite large differences in sociodemographic variables including education, most attitudes and beliefs about genetics were similar in Hispanics and non-Hispanics. Epilepsy-specific genetic knowledge was lower among Hispanics than non-Hispanics, and this difference was mostly mediated by differences in demographic variables. Genetic counseling should address key concepts related to epilepsy genetics to ensure they are well understood by both Hispanic and non-Hispanic patients.
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Affiliation(s)
- Shannon Trujillo
- Rutgers-Robert Wood Johnson Medical School, Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, New Brunswick, NJ, USA
| | - John B. Wetmore
- Gertrude H. Sergievsky Center, Columbia University Irving Medical Center, New York, NY
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Itzel A. Camarillo
- Gertrude H. Sergievsky Center, Columbia University Irving Medical Center, New York, NY
| | - Sylwia Misiewicz
- Gertrude H. Sergievsky Center, Columbia University Irving Medical Center, New York, NY
| | - Halie May
- Departments of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Hyunmi Choi
- Departments of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Karolynn Siegel
- Department of Sociomedical Sciences, Columbia University Mailman School of Public Health, New York, NY, USA , Departments of Medicine
| | - Wendy K. Chung
- Departments of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Departments of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jo C. Phelan
- Department of Sociomedical Sciences, Columbia University Mailman School of Public Health, New York, NY, USA , Departments of Medicine
| | - Lawrence H. Yang
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- School of Global Public Health, New York University, New York, NY
| | - Cheng-Shiun Leu
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Amanda L. Bergner
- Departments of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Genetic Counseling Graduate Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ruth Ottman
- Gertrude H. Sergievsky Center, Columbia University Irving Medical Center, New York, NY
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
- Departments of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
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Molina-Aguilar C, Robles-Espinoza CD. Tackling the lack of diversity in cancer research. Dis Model Mech 2023; 16:dmm050275. [PMID: 37681401 PMCID: PMC10499025 DOI: 10.1242/dmm.050275] [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] [Indexed: 09/09/2023] Open
Abstract
Despite the clear benefit of studying biological samples from diverse genetic backgrounds and geographical locations, our current knowledge of disease is mostly derived from the study of European-descent individuals. In the cancer field, this is reflected in the poor representation of African and Amerindian/Latino samples in most large public data repositories. This lack of diversity is due to several reasons, but here we focus on (1) the lack of support for studies on non-European populations that are performed in low- and middle-income countries (LMICs), and (2) unequal partnerships between scientists in LMICs and those in high-income countries. We argue that expanding access to research funding, increasing the participation of underrepresented scientists in editorial boards and international conferences, facilitating the publication of studies conducted in these countries, and properly acknowledging LMIC researchers' contributions in publications and grant applications will promote equity for scientists working in LMICs. We envisage that this will translate to more impactful research in these countries, which will include more samples from diverse populations. For the cancer field, this will broaden our understanding of pathomechanisms and may help to improve the treatment of patients from all backgrounds.
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Affiliation(s)
- Christian Molina-Aguilar
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro 76230, Mexico
| | - C. Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro 76230, Mexico
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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Bountress KE, Bustamante D, de Viteri SSS, Chatzinakos C, Sheerin C, Daskalakis NP, Edenberg HJ, Peterson RE, Webb BT, Meyers J, Amstadter A. Differences in genetic correlations between posttraumatic stress disorder and alcohol-related problems phenotypes compared to alcohol consumption-related phenotypes. Psychol Med 2023; 53:5767-5777. [PMID: 36177877 PMCID: PMC10060434 DOI: 10.1017/s0033291722002999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Posttraumatic Stress Disorder (PTSD) tends to co-occur with greater alcohol consumption as well as alcohol use disorder (AUD). However, it is unknown whether the same etiologic factors that underlie PTSD-alcohol-related problems comorbidity also contribute to PTSD- alcohol consumption. METHODS We used summary statistics from large-scale genome-wide association studies (GWAS) of European-ancestry (EA) and African-ancestry (AA) participants to estimate genetic correlations between PTSD and a range of alcohol consumption-related and alcohol-related problems phenotypes. RESULTS In EAs, there were positive genetic correlations between PTSD phenotypes and alcohol-related problems phenotypes (e.g. Alcohol Use Disorders Identification Test (AUDIT) problem score) (rGs: 0.132-0.533, all FDR adjusted p < 0.05). However, the genetic correlations between PTSD phenotypes and alcohol consumption -related phenotypes (e.g. drinks per week) were negatively associated or non-significant (rGs: -0.417 to -0.042, FDR adjusted p: <0.05-NS). For AAs, the direction of correlations was sometimes consistent and sometimes inconsistent with that in EAs, and the ranges were larger (rGs for alcohol-related problems: -0.275 to 0.266, FDR adjusted p: NS, alcohol consumption-related: 0.145-0.699, FDR adjusted p: NS). CONCLUSIONS These findings illustrate that the genetic associations between consumption and problem alcohol phenotypes and PTSD differ in both strength and direction. Thus, the genetic factors that may lead someone to develop PTSD and high levels of alcohol consumption are not the same as those that lead someone to develop PTSD and alcohol-related problems. Discussion around needing improved methods to better estimate heritabilities and genetic correlations in diverse and admixed ancestry samples is provided.
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Affiliation(s)
| | | | | | - Chris Chatzinakos
- VIPBG. VCU, Richmond, VA, USA
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | | | | | | | | | | | - Bradley T. Webb
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
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Harney É, Micheletti S, Bruwelheide KS, Freyman WA, Bryc K, Akbari A, Jewett E, Comer E, Louis Gates H, Heywood L, Thornton J, Curry R, Ancona Esselmann S, Barca KG, Sedig J, Sirak K, Olalde I, Adamski N, Bernardos R, Broomandkhoshbacht N, Ferry M, Qiu L, Stewardson K, Workman JN, Zalzala F, Mallick S, Micco A, Mah M, Zhang Z, Rohland N, Mountain JL, Owsley DW, Reich D. The genetic legacy of African Americans from Catoctin Furnace. Science 2023; 381:eade4995. [PMID: 37535739 PMCID: PMC10958645 DOI: 10.1126/science.ade4995] [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: 08/22/2022] [Accepted: 06/20/2023] [Indexed: 08/05/2023]
Abstract
Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland's Catoctin Furnace African American Cemetery (1774-1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.'s genetic database. One of the highest concentrations of close relatives is in Maryland, suggesting that descendants of the Catoctin individuals remain in the area. We find that many of the Catoctin individuals derived African ancestry from the Wolof or Kongo groups and European ancestry from Great Britain and Ireland. This study demonstrates the power of joint analysis of historical DNA and large datasets generated through direct-to-consumer ancestry testing.
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Affiliation(s)
- Éadaoin Harney
- 23andMe, Inc.; Sunnyvale, CA 94043, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
| | | | - Karin S. Bruwelheide
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | | | | | - Ali Akbari
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Elizabeth Comer
- Catoctin Furnace Historical Society; Thurmont, MD, 21788, USA
| | - Henry Louis Gates
- Hutchins Center for African and African American Research, Harvard University; Cambridge, MA 02138, USA
| | - Linda Heywood
- Department of History/African American Studies, Boston University; Brookline, MA 02446, USA
| | - John Thornton
- Department of History/African American Studies, Boston University; Brookline, MA 02446, USA
| | - Roslyn Curry
- 23andMe, Inc.; Sunnyvale, CA 94043, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
| | | | - Kathryn G. Barca
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | - Jakob Sedig
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | - Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | - Iñigo Olalde
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - J. Noah Workman
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
| | - Shop Mallick
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Adam Micco
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
| | | | - Douglas W. Owsley
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution; Washington DC 20560, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School; Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
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Neuhaus C, Crane J, Pacia D. Special Considerations When Research is Embedded within Community Health Centers. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:55-58. [PMID: 37450533 PMCID: PMC10542914 DOI: 10.1080/15265161.2023.2217112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
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Cakici JA, Dimmock D, Caylor S, Gaughran M, Clarke C, Triplett C, Clark MM, Kingsmore SF, Bloss CS. Assessing Diversity in Newborn Genomic Sequencing Research Recruitment: Race/Ethnicity and Primary Spoken Language Variation in Eligibility, Enrollment, and Reasons for Declining. Clin Ther 2023; 45:736-744. [PMID: 37429778 DOI: 10.1016/j.clinthera.2023.06.014] [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: 01/26/2023] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 07/12/2023]
Abstract
PURPOSE Diagnostic genomic research has the potential to directly benefit participants. This study sought to identify barriers to equitable enrollment of acutely ill newborns into a diagnostic genomic sequencing research study. METHODS We reviewed the 16-month recruitment process of a diagnostic genomic research study enrolling newborns admitted to the neonatal intensive care unit at a regional pediatric hospital that primarily serves English- and Spanish-speaking families. Differences in eligibility, enrollment, and reasons for not enrolling were examined as functions of race/ethnicity and primary spoken language. FINDINGS Of the 1248 newborns admitted to the neonatal intensive care unit, 46% (n = 580) were eligible, and 17% (n = 213) were enrolled. Of the 16 languages represented among the newborns' families, 4 (25%) had translated consent documents. Speaking a language other than English or Spanish increased a newborn's likelihood of being ineligible by 5.9 times (P < 0.001) after controlling for race/ethnicity. The main reason for ineligibility was documented as the clinical team declined having their patient recruited (41% [51 of 125]). This reason significantly affected families who spoke languages other than English or Spanish and was able to be remediated with training of the research staff. Stress (20% [18 of 90]) and the study intervention(s) (20% [18 of 90]) were the main reasons given for not enrolling. IMPLICATIONS This analysis of eligibility, enrollment, and reasons for not enrolling in a diagnostic genomic research study found that recruitment generally did not differ as a function of a newborn's race/ethnicity. However, differences were observed depending on the parent's primary spoken language. Regular monitoring and training can improve equitable enrollment into diagnostic genomic research. There are also opportunities at the federal level to improve access to those with limited English proficiency and thus decrease disparities in representation in research participation.
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Affiliation(s)
- Julie A Cakici
- The Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, California, USA; School of Public Health, San Diego State University, San Diego, California, USA
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Mary Gaughran
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Christina Clarke
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | | | - Michelle M Clark
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Cinnamon S Bloss
- The Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, California, USA.
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Scodellaro S, Cohn RD, Cohn I. Urgent call for guidance supporting gene-based drug dosing in children and adolescents. Paediatr Child Health 2023; 28:205-245. [PMID: 37287475 PMCID: PMC10243970 DOI: 10.1093/pch/pxad003] [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: 05/04/2022] [Accepted: 01/12/2023] [Indexed: 06/09/2023] Open
Abstract
In the past decade, there have been tremendous advancements in the field of genomics that have led to significant progress in redefining the concept of precision medicine. Pharmacogenetics (PGx) is one of the most promising areas of precision medicine and is the 'low hanging fruit' of this individualized approach to medication dosing and selection. Although a variety of regulatory health agencies and professional consortia have established PGx clinical practice guidelines, implementation has been slow given numerous barriers faced by health care professionals. Many lack the training needed to interpret PGx and there are no paediatric specific guidelines. As the field of PGx continues to grow, an emphasis on collaborative inter-professional education, coupled with ongoing efforts to increase accessibility to advancing testing technology are necessary to translate this branch of precision medicine from the bench to the bedside.
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Affiliation(s)
- Sierra Scodellaro
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ronald D Cohn
- Genetics and Genome Biology Program, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto and The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Clinical and Metabolic and Genetics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology and Toxicology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Program in Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto and The Hospital for Sick Children, Toronto, Ontario, Canada
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, Ontario, Canada
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Boyd AD, Gonzalez-Guarda R, Lawrence K, Patil CL, Ezenwa MO, O'Brien EC, Paek H, Braciszewski JM, Adeyemi O, Cuthel AM, Darby JE, Zigler CK, Ho PM, Faurot KR, Staman K, Leigh JW, Dailey DL, Cheville A, Del Fiol G, Knisely MR, Marsolo K, Richesson RL, Schlaeger JM. Equity and bias in electronic health records data. Contemp Clin Trials 2023; 130:107238. [PMID: 37225122 PMCID: PMC10330606 DOI: 10.1016/j.cct.2023.107238] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023]
Abstract
Embedded pragmatic clinical trials (ePCTs) are conducted during routine clinical care and have the potential to increase knowledge about the effectiveness of interventions under real world conditions. However, many pragmatic trials rely on data from the electronic health record (EHR) data, which are subject to bias from incomplete data, poor data quality, lack of representation from people who are medically underserved, and implicit bias in EHR design. This commentary examines how the use of EHR data might exacerbate bias and potentially increase health inequities. We offer recommendations for how to increase generalizability of ePCT results and begin to mitigate bias to promote health equity.
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Affiliation(s)
- Andrew D Boyd
- Department of Biomedical and Health Information Sciences, University of Illinois Chicago, Chicago, IL, United States of America.
| | | | - Katharine Lawrence
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Crystal L Patil
- University of Illinois Chicago, College of Nursing, Chicago, IL, United States of America
| | - Miriam O Ezenwa
- University of Florida College of Nursing, Gainesville, FL, United States of America
| | - Emily C O'Brien
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States of America
| | - Hyung Paek
- Yale University, New Haven, CT, United States of America
| | | | - Oluwaseun Adeyemi
- New York University Grossman School of Medicine, Ronald O. Perelman Department of Emergency Medicine, New York, NY, United States of America
| | - Allison M Cuthel
- New York University Grossman School of Medicine, Ronald O. Perelman Department of Emergency Medicine, New York, NY, United States of America
| | - Juanita E Darby
- University of Illinois Chicago, College of Nursing, Chicago, IL, United States of America
| | - Christina K Zigler
- Duke University School of Medicine, Durham, NC, United States of America
| | - P Michael Ho
- Division of Cardiology, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Keturah R Faurot
- Department of Physical Medicine and Rehabilitation, University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Karen Staman
- Duke University School of Medicine, Durham, NC, United States of America
| | - Jonathan W Leigh
- University of Illinois Chicago, College of Nursing, Chicago, IL, United States of America
| | - Dana L Dailey
- St. Ambrose University, Davenport, IA, United States of America; University of Iowa, Iowa City, IA, United States of America
| | - Andrea Cheville
- Mayo Clinic Comprehensive Cancer Center, Rochester, MN, United States of America
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, United States of America
| | | | - Keith Marsolo
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States of America
| | - Rachel L Richesson
- Department of Learning Health Sciences, University of Michigan Medical School
| | - Judith M Schlaeger
- University of Illinois Chicago, College of Nursing, Chicago, IL, United States of America
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Suliman S, Nieto-Caballero VE, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Gutierrez-Arcelus M. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.20.23291558. [PMID: 37425785 PMCID: PMC10327177 DOI: 10.1101/2023.06.20.23291558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
A quarter of humanity is estimated to be latently infected with Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n=63) or did not progress to TB (controls, n=63). Transcriptomic profiling of monocyte-derived dendritic cells (DCs) and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Five genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.
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Affiliation(s)
- Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Zuckerberg San Francisco General Hospital, Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Initiative Biohub, San Francisco, CA, USA
| | - Victor E. Nieto-Caballero
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samira Asgari
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kattya Lopez
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Socios En Salud Sucursal Peru, Lima, Peru
| | - Sarah K. Iwany
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Luo
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Aparna Nathan
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniela Fernandez-Salinas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marcos Chiñas
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chuan-Chin Huang
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Zibiao Zhang
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Segundo R León
- Socios En Salud Sucursal Peru, Lima, Peru
- Medical Technology School and Global Health Research Institute, San Juan Bautista Private University, Lima, Perú
| | | | | | - Megan Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - D. Branch Moody
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Allen CG, Jefferson M, Magwood G, Melvin C, Babatunde OA, Halbert CH. Understanding men's beliefs and concerns about linking health data in the context of precision medicine. J Clin Transl Sci 2023; 7:e150. [PMID: 37456269 PMCID: PMC10346034 DOI: 10.1017/cts.2023.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023] Open
Abstract
Background/Objective Linking data is a critical feature of precision medicine initiatives that involves integrating information from multiple sources to improve researchers' and clinicians' ability to deliver care. We have limited understanding of how individuals perceive linking data as it relates to precision medicine. The aim of this study was to identify how sociodemographics, comorbidities, and beliefs about precision medicine influence two outcomes related to linking data: beliefs about linking data and concerns about linking data among men. Methods We recruited 124 adult men from primary care practices at a large clinical research university to complete a cross-sectional survey that included questions about sociodemographic characteristics, comorbidities, beliefs, benefits, and limitations of precision medicine, and two outcomes of interest: beliefs about the value of linking data and concerns about linking data. Descriptive statistics, bivariate associations, and multivariable regression were conducted. Results Participants had positive beliefs about linking data for precision medicine (M = 4.05/5) and average concern about linking data (M = 2.1/5). Final multivariable models revealed that higher levels of loneliness are associated with more positive beliefs about linking data (β = 0.41, p = 0.027). Races other than African American (β = -0.64, p = 0.009) and those with lower perceived limitations of precision medicine were less likely to be concerned about linking data (β = -0.75, p = 0.0006). Conclusion Our results advance the literature about perceptions of linking data for use in clinical and research studies among men. Better understanding of factors associated with more positive perceptions of data linkages could help improve how researchers recruit and engage participants.
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Affiliation(s)
- Caitlin G. Allen
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Melanie Jefferson
- Department of Psychiatry and Behavioral Sciences, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Gayenell Magwood
- Department of Biobehavioral Health and Nursing Science, College of Nursing, University of South Carolina, Charleston, SC, USA
| | - Cathy Melvin
- Department of Public Health Sciences, College of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Oluwole Adeyemi Babatunde
- Department of Psychiatry and Behavioral Sciences, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Chanita Hughes Halbert
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
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Ferryman K. Bounded Justice, Inclusion, and the Hyper/Invisibility of Race in Precision Medicine. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023:1-7. [PMID: 37220019 DOI: 10.1080/15265161.2023.2207515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
I take up the call for a more nuanced engagement with race in bioethics by using Creary's analytic of bounded justice and argue that it helps illuminate processes of racialization, or racial formation, specifically Blackness, as a dialectical processes of both invisibility and hyper-visibility. This dialectical view of race provides a lens through which the ethical, legal, and social implications (ELSI) of genetics and genomics field can reflect on fraught issues such as inclusion in genomic and biomedical research. Countering or interrupting racialization in precision medicine can involve asking how marginalized groups are made invisible or hyper-visible in various aspects of the research process. Incorporating these kinds of questions into biomedical research inclusion efforts could lead to potentially powerful engagements with marginalized groups and could provide the opportunity for stakeholders to engage with the ways that racialization can happen in real-time and might undermine good intentions.
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Gooden A, Thaldar D. Toward an open access genomics database of South Africans: ethical considerations. Front Genet 2023; 14:1166029. [PMID: 37260770 PMCID: PMC10228717 DOI: 10.3389/fgene.2023.1166029] [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: 02/14/2023] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Genomics research holds the potential to improve healthcare. Yet, a very low percentage of the genomic data used in genomics research internationally relates to persons of African origin. Establishing a large-scale, open access genomics database of South Africans may contribute to solving this problem. However, this raises various ethics concerns, including privacy expectations and informed consent. The concept of open consent offers a potential solution to these concerns by (a) being explicit about the research participant's data being in the public domain and the associated privacy risks, and (b) setting a higher-than-usual benchmark for informed consent by making use of the objective assessment of prospective research participants' understanding. Furthermore, in the South African context-where local culture is infused with Ubuntu and its relational view of personhood-community engagement is vital for establishing and maintaining an open access genomics database of South Africans. The South African National Health Research Ethics Council is called upon to provide guidelines for genomics researchers-based on open consent and community engagement-on how to plan and implement open access genomics projects.
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Affiliation(s)
- Amy Gooden
- School of Law, University of KwaZulu-Natal, Durban, South Africa
| | - Donrich Thaldar
- School of Law, University of KwaZulu-Natal, Durban, South Africa
- Petrie-Flom Center for Health Law Policy, Biotechnology and Bioethics, Harvard Law School, Cambridge, MA, United States
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Baine-Savanhu F, Macaulay S, Louw N, Bollweg A, Flynn K, Molatoli M, Nevondwe P, Seymour H, Carstens N, Krause A, Lombard Z. Identifying the genetic causes of developmental disorders and intellectual disability in Africa: a systematic literature review. Front Genet 2023; 14:1137922. [PMID: 37234869 PMCID: PMC10208355 DOI: 10.3389/fgene.2023.1137922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Objective: Genetic variants cause a significant portion of developmental disorders and intellectual disabilities (DD/ID), but clinical and genetic heterogeneity makes identification challenging. Compounding the issue is a lack of ethnic diversity in studies into the genetic aetiology of DD/ID, with a dearth of data from Africa. This systematic review aimed to comprehensively describe the current knowledge from the African continent on this topic. Method: Applicable literature published up until July 2021 was retrieved from PubMed, Scopus and Web of Science databases, following PRISMA guidelines, focusing on original research reports on DD/ID where African patients were the focus of the study. The quality of the dataset was assessed using appraisal tools from the Joanna Briggs Institute, whereafter metadata was extracted for analysis. Results: A total of 3,803 publications were extracted and screened. After duplicate removal, title, abstract and full paper screening, 287 publications were deemed appropriate for inclusion. Of the papers analysed, a large disparity was seen between work emanating from North Africa compared to sub-Saharan Africa, with North Africa dominating the publications. Representation of African scientists on publications was poorly balanced, with most research being led by international researchers. There are very few systematic cohort studies, particularly using newer technologies, such as chromosomal microarray and next-generation sequencing. Most of the reports on new technology data were generated outside Africa. Conclusion: This review highlights how the molecular epidemiology of DD/ID in Africa is hampered by significant knowledge gaps. Efforts are needed to produce systematically obtained high quality data that can be used to inform appropriate strategies to implement genomic medicine for DD/ID on the African continent, and to successfully bridge healthcare inequalities.
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Affiliation(s)
- Fiona Baine-Savanhu
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shelley Macaulay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadja Louw
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alanna Bollweg
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kaitlyn Flynn
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mhlekazi Molatoli
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Peng W, Chuan CH, Morgan SE. Assessing the role of interactivity: An evaluation of information aids to support the enrollment of precision medicine research programs. PATIENT EDUCATION AND COUNSELING 2023; 110:107648. [PMID: 36753934 DOI: 10.1016/j.pec.2023.107648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE Recruiting diverse participants for precision medicine (PM) research programs should overcome low literacy and varied expectations. Information aids (IA) can address these barriers through patient-centered education. The purpose of this study was to evaluate the effectiveness of three information aids (IA) on participating in PM. METHODS An experiment with 290 U.S. participants recruited from Mturk was conducted to compare the effects of three IAs on the outcomes related to participation. Three conditions included an interactive IA (i.e., providing PM-related information responding to each participant's questions), a static IA (i.e., providing uniform PM-related information), and a control condition (i.e., providing non-interactive information irrelevant to PM). RESULTS Both interactive and non-interactive IAs increased attitudes and information-seeking intentions, but not knowledge or participation intention. Perceived control and responsiveness mediated the effects of interactive IA. CONCLUSION Both interactive and static IAs supported enrollment efforts for PM through fostering attitudes and follow-up information-seeking. Increased perceived control and responsiveness are key to the effects of interactive IA. PRACTICE IMPLICATIONS IAs provide effective education and enrollment support for PM. Interactive IA can respond to individuals' inquiries and control the learning process.
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Affiliation(s)
- Wei Peng
- Edward R. Murrow College of Communication, Washington State University, Pullman, WA 99164, USA.
| | - Ching-Hua Chuan
- Department of Interactive Media, University of Miami, Coral Gables, FL 33146, USA
| | - Susan E Morgan
- Department of Communication Studies, University of Miami, Coral Gables, FL 33146, USA
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Neuhaus CP, Pacia DM, Crane JT, Maschke KJ, Berlinger N. All of Us and the Promise of Precision Medicine: Achieving Equitable Access for Federally Qualified Health Center Patients. J Pers Med 2023; 13:615. [PMID: 37109001 PMCID: PMC10140886 DOI: 10.3390/jpm13040615] [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: 12/31/2022] [Revised: 03/16/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
The United States National Institutes of Health's (NIH) All of Us (AoU) initiative recruits participants from diverse backgrounds to improve the makeup of biobanks, considering nearly all biospecimens used in research come from people of European ancestry. Participants who join AoU consent to provide samples of blood, urine, and/or saliva and to submit their electronic health record to the program. In addition to diversifying precision medicine research studies, AoU will return genetic results back to many participants, which may require further follow-up care (i.e., more frequent cancer screening or mastectomy after a BRCA result). To help achieve its goals, AoU has partnered with Federally Qualified Health Centers (FQHCs), which is a type of community health center whose patient base is comprised largely of people who are uninsured, underinsured, or on Medicaid. Our NIH-funded study convened FQHC providers involved in AoU to better understand precision medicine in community health settings. Drawing from our findings, we present barriers community health patients and their providers face when accessing diagnostics and specialty care after genetic results necessitate medical follow-up care. We also propose several policy and financial recommendations to help overcome the challenges discussed, stemming from a commitment to equitable access to precision medicine advances.
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Affiliation(s)
| | | | - Johanna T. Crane
- Alden March Bioethics Institute, Albany Medical College, Albany, NY 12208-3478, USA
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Priolo M, Tartaglia M. The Right to Ask, the Need to Answer-When Patients Meet Research: How to Cope with Time. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:4573. [PMID: 36901584 PMCID: PMC10002068 DOI: 10.3390/ijerph20054573] [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: 01/10/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Reaching a diagnosis and its communication are two of the most meaningful events in the physician-patient relationship. When facing a disease, most of the patients' expectations rely on the hope that their clinicians would be able to understand the cause of their illness and eventually end it. Rare diseases are a peculiar subset of conditions in which the search for a diagnosis might reveal a long and painful journey scattered by doubts and requiring, in most cases, a long waiting time. For many individuals affected by a rare disease, turning to research might represent their last chance to obtain an answer to their questions. Time is the worst enemy, threatening to disrupt the fragile balance among affected individuals, their referring physicians, and researchers. It is consuming at all levels, draining economic, emotional, and social resources, and triggering unpredictable reactions in each stakeholder group. Managing waiting time is one of the most burdensome tasks for all the parties playing a role in the search for a diagnosis: the patients and their referring physicians urge to obtain a diagnosis in order to know the condition they are dealing with and establish proper management, respectively. On the other hand, researchers need to be objective and scientifically act to give a rigorous answer to their demands. While moving towards the same goal, patients, clinicians, and researchers might have different expectations and perceive the same waiting time as differently hard or tolerable. The lack of information on mutual needs and the absence of effective communication among the parties are the most common mechanisms of the failure of the therapeutic alliance that risk compromising the common goal of a proper diagnosis. In the landscape of modern medicine that goes faster and claims high standards of cure, rare diseases represent an exception where physicians and researchers should learn to cope with time in order to care for patients.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, 89124 Reggio Calabria, Italy
| | - Marco Tartaglia
- Genetica Molecolare e Genomica Funzionale, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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Meyer MN, Appelbaum PS, Benjamin DJ, Callier SL, Comfort N, Conley D, Freese J, Garrison NA, Hammonds EM, Harden KP, Lee SSJ, Martin AR, Martschenko DO, Neale BM, Palmer RHC, Tabery J, Turkheimer E, Turley P, Parens E. Wrestling with Social and Behavioral Genomics: Risks, Potential Benefits, and Ethical Responsibility. Hastings Cent Rep 2023; 53 Suppl 1:S2-S49. [PMID: 37078667 PMCID: PMC10433733 DOI: 10.1002/hast.1477] [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] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
In this consensus report by a diverse group of academics who conduct and/or are concerned about social and behavioral genomics (SBG) research, the authors recount the often-ugly history of scientific attempts to understand the genetic contributions to human behaviors and social outcomes. They then describe what the current science-including genomewide association studies and polygenic indexes-can and cannot tell us, as well as its risks and potential benefits. They conclude with a discussion of responsible behavior in the context of SBG research. SBG research that compares individuals within a group according to a "sensitive" phenotype requires extra attention to responsible conduct and to responsible communication about the research and its findings. SBG research (1) on sensitive phenotypes that (2) compares two or more groups defined by (a) race, (b) ethnicity, or (c) genetic ancestry (where genetic ancestry could easily be misunderstood as race or ethnicity) requires a compelling justification to be conducted, funded, or published. All authors agree that this justification at least requires a convincing argument that a study's design could yield scientifically valid results; some authors would additionally require the study to have a socially favorable risk-benefit profile.
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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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Rashkin M, Kingham K, Lara-Otero K, Mckenna M, Villiers J, Worthington MM, Prince A. How should we address the inevitable harms from non-negligent variant reclassification in predictive genetic testing? J Genet Couns 2023; 32:18-30. [PMID: 36260514 PMCID: PMC10092710 DOI: 10.1002/jgc4.1638] [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: 08/04/2021] [Revised: 08/26/2022] [Accepted: 09/04/2022] [Indexed: 11/12/2022]
Abstract
The process of interpreting genetic variants, in which experts use all available evidence to determine whether an identified variant is associated with a current or future disease, is both scientific and nevertheless subjective. In this paper, we summarize the existing evidence that any given variant could be reclassified and that such a reclassification could lead to harm. Furthermore, the racial gap in genetic databases could lead to a higher likelihood of harm for non-white patients. We also review recent legal analyses indicating it is unlikely that an individual who sues for restitution would be successful, especially in the absence of evidence of lab negligence. We then propose a compensation program for medical genetic tests to ensure that individuals who experience demonstrable harm due to a variant reclassification can be made whole financially. We conclude by discussing outstanding questions that must be answered for such a program to be feasible.
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Affiliation(s)
| | | | | | | | | | | | - Anya Prince
- The University of Iowa, Iowa City, Iowa, USA
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Dauda B, Molina SJ, Allen DS, Fuentes A, Ghosh N, Mauro M, Neale BM, Panofsky A, Sohail M, Zhang SR, Lewis ACF. Ancestry: How researchers use it and what they mean by it. Front Genet 2023; 14:1044555. [PMID: 36755575 PMCID: PMC9900027 DOI: 10.3389/fgene.2023.1044555] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Background: Ancestry is often viewed as a more objective and less objectionable population descriptor than race or ethnicity. Perhaps reflecting this, usage of the term "ancestry" is rapidly growing in genetics research, with ancestry groups referenced in many situations. The appropriate usage of population descriptors in genetics research is an ongoing source of debate. Sound normative guidance should rest on an empirical understanding of current usage; in the case of ancestry, questions about how researchers use the concept, and what they mean by it, remain unanswered. Methods: Systematic literature analysis of 205 articles at least tangentially related to human health from diverse disciplines that use the concept of ancestry, and semi-structured interviews with 44 lead authors of some of those articles. Results: Ancestry is relied on to structure research questions and key methodological approaches. Yet researchers struggle to define it, and/or offer diverse definitions. For some ancestry is a genetic concept, but for many-including geneticists-ancestry is only tangentially related to genetics. For some interviewees, ancestry is explicitly equated to ethnicity; for others it is explicitly distanced from it. Ancestry is operationalized using multiple data types (including genetic variation and self-reported identities), though for a large fraction of articles (26%) it is impossible to tell which data types were used. Across the literature and interviews there is no consistent understanding of how ancestry relates to genetic concepts (including genetic ancestry and population structure), nor how these genetic concepts relate to each other. Beyond this conceptual confusion, practices related to summarizing patterns of genetic variation often rest on uninterrogated conventions. Continental labels are by far the most common type of label applied to ancestry groups. We observed many instances of slippage between reference to ancestry groups and racial groups. Conclusion: Ancestry is in practice a highly ambiguous concept, and far from an objective counterpart to race or ethnicity. It is not uniquely a "biological" construct, and it does not represent a "safe haven" for researchers seeking to avoid evoking race or ethnicity in their work. Distinguishing genetic ancestry from ancestry more broadly will be a necessary part of providing conceptual clarity.
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Affiliation(s)
- Bege Dauda
- Center for Global Genomics and Health Equity, University of Pennsylvania, Philadelphia, PA, United States
| | - Santiago J. Molina
- Department of Sociology, Northwestern University, Evanston, IL, United States
| | - Danielle S. Allen
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
| | - Agustin Fuentes
- Department of Anthropology, Princeton University, Princeton, NJ, United States
| | - Nayanika Ghosh
- Department of the History of Science, Harvard University, Cambridge, MA, United States
| | - Madelyn Mauro
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
| | - Benjamin M. Neale
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Aaron Panofsky
- Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Public Policy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Sociology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mashaal Sohail
- Centro de Ciencias Genomicas (CCG), Universidad Nacional Autonoma de Mexico (UNAM), Cuernavaca, Morelos, Mexico
| | - Sarah R. Zhang
- University of California, Berkeley, Berkeley, CA, United States
| | - Anna C. F. Lewis
- Edmond & Lily Safra Center for Ethics, Harvard University, Cambridge, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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De Oliveira TC, Secolin R, Lopes-Cendes I. A review of ancestrality and admixture in Latin America and the caribbean focusing on native American and African descendant populations. Front Genet 2023; 14:1091269. [PMID: 36741309 PMCID: PMC9893294 DOI: 10.3389/fgene.2023.1091269] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/09/2023] [Indexed: 01/21/2023] Open
Abstract
Genomics can reveal essential features about the demographic evolution of a population that may not be apparent from historical elements. In recent years, there has been a significant increase in the number of studies applying genomic epidemiological approaches to understand the genetic structure and diversity of human populations in the context of demographic history and for implementing precision medicine. These efforts have traditionally been applied predominantly to populations of European origin. More recently, initiatives in the United States and Africa are including more diverse populations, establishing new horizons for research in human populations with African and/or Native ancestries. Still, even in the most recent projects, the under-representation of genomic data from Latin America and the Caribbean (LAC) is remarkable. In addition, because the region presents the most recent global miscegenation, genomics data from LAC may add relevant information to understand population admixture better. Admixture in LAC started during the colonial period, in the 15th century, with intense miscegenation between European settlers, mainly from Portugal and Spain, with local indigenous and sub-Saharan Africans brought through the slave trade. Since, there are descendants of formerly enslaved and Native American populations in the LAC territory; they are considered vulnerable populations because of their history and current living conditions. In this context, studying LAC Native American and African descendant populations is important for several reasons. First, studying human populations from different origins makes it possible to understand the diversity of the human genome better. Second, it also has an immediate application to these populations, such as empowering communities with the knowledge of their ancestral origins. Furthermore, because knowledge of the population genomic structure is an essential requirement for implementing genomic medicine and precision health practices, population genomics studies may ensure that these communities have access to genomic information for risk assessment, prevention, and the delivery of optimized treatment; thus, helping to reduce inequalities in the Western Hemisphere. Hoping to set the stage for future studies, we review different aspects related to genetic and genomic research in vulnerable populations from LAC countries.
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Affiliation(s)
- Thais C. De Oliveira
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Rodrigo Secolin
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil,The Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, Brazil,*Correspondence: Iscia Lopes-Cendes,
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Lee IH, Kong SW. ADGR: Admixture-Informed Differential Gene Regulation. Genes (Basel) 2023; 14:147. [PMID: 36672888 PMCID: PMC9859415 DOI: 10.3390/genes14010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
The regulatory elements in proximal and distal regions of genes are involved in the regulation of gene expression. Risk alleles in intronic and intergenic regions may alter gene expression by modifying the binding affinity and stability of diverse DNA-binding proteins implicated in gene expression regulation. By focusing on the local ancestral structure of coding and regulatory regions using the paired whole-genome sequence and tissue-wide transcriptome datasets from the Genotype-Tissue Expression project, we investigated the impact of genetic variants, in aggregate, on tissue-specific gene expression regulation. Local ancestral origins of the coding region, immediate and distant upstream regions, and distal regulatory region were determined using RFMix with the reference panel from the 1000 Genomes Project. For each tissue, inter-individual variation of gene expression levels explained by concordant or discordant local ancestry between coding and regulatory regions was estimated. Compared to European, African descent showed more frequent change in local ancestral structure, with shorter haplotype blocks. The expression level of the Adenosine Deaminase Like (ADAL) gene was significantly associated with admixed ancestral structure in the regulatory region across multiple tissue types. Further validations are required to understand the impact of the local ancestral structure of regulatory regions on gene expression regulation in humans and other species.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02215, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02215, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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Khalil D, Giurgescu C, Misra DP, Templin T, Jenuwine E, Drury SS. Psychosocial Factors and Telomere Length Among Parents and Infants of Immigrant Arab American Families. Biol Res Nurs 2023; 25:137-149. [PMID: 36036284 PMCID: PMC10331091 DOI: 10.1177/10998004221124145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background: Immigrant Arab American families face multiple stressors related to migration and resettlement. Telomere length (TL) is an established biomarker of aging and psychosocial stress. No published studies have concurrently examined the association between maternal and paternal psychosocial factors and infants' TL. The purpose of this study was to: (1) compare mother, father, and infant TLs; (2) explore the association of maternal and paternal psychosocial factors (acculturative stress and depressive symptoms) with maternal and paternal TL; and (3) explore the association of maternal and paternal psychosocial factors with infants' TL among Arab American immigrants. Method: Using a cross-sectional exploratory design, a sample of 52 immigrant Arab American mother-father-infant triads were recruited from community centers. Data were collected in a single home visit when the infant was 6-24 months old. Each parent completed the study questionnaires addressing their psychosocial factors (acculturative stress, and depressive symptoms), then parents and infants provided buccal cell for TL measurement. Results: Maternal TL was positively correlated to infants' TL (r = .31, p = .04) and significantly shorter (p < .001). Paternal TL was not correlated with infant TL but was significantly shorter than infant's TL (p < .001). Maternal depression was significantly correlated with mothers' TL (r = .4, p = .007). Higher levels of maternal depressive symptoms were significantly associated with shorter infant TL when controlling for background characteristics. Conclusions: Our pilot study is the first study to examine maternal and paternal psychosocial factors related to migration and infants' TL. More research is needed to advance our understanding of the effects of immigration on the intergenerational transfer of stress and trauma.
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Affiliation(s)
- Dalia Khalil
- College of Nursing, Wayne State University, Detroit, MI, USA
| | - Carmen Giurgescu
- College of Nursing, University of Central Florida, Orlando, FL, USA
| | - Dawn P. Misra
- College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Thomas Templin
- College of Nursing, Wayne State University, Detroit, MI, USA
| | | | - Stacy S. Drury
- The Department of Psychiatry and Behavioral Sciences, Tulane University School of Medicine, New Orleans, LA, USA
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Giudicelli GC, De Souza CMB, Veronese FV, Pereira LV, Hünemeier T, Vianna FSL. Precision medicine implementation challenges for APOL1 testing in chronic kidney disease in admixed populations. Front Genet 2022; 13:1016341. [PMID: 36588788 PMCID: PMC9797503 DOI: 10.3389/fgene.2022.1016341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic Kidney Disease (CKD) is a public health problem that presents genetic and environmental risk factors. Two alleles in the Apolipoprotein L1 (APOL1) gene were associated with chronic kidney disease; these alleles are common in individuals of African ancestry but rare in European descendants. Genomic studies on Afro-Americans have indicated a higher prevalence and severity of chronic kidney disease in people of African ancestry when compared to other ethnic groups. However, estimates in low- and middle-income countries are still limited. Precision medicine approaches could improve clinical outcomes in carriers of risk alleles in the Apolipoprotein L1 gene through early diagnosis and specific therapies. Nevertheless, to enhance the definition of studies on these variants, it would be necessary to include individuals with different ancestry profiles in the sample, such as Latinos, African Americans, and Indigenous peoples. There is evidence that measuring genetic ancestry improves clinical care for admixed people. For chronic kidney disease, this knowledge could help establish public health strategies for monitoring patients and understanding the impact of the Apolipoprotein L1 genetic variants in admixed populations. Therefore, researchers need to develop resources, methodologies, and incentives for vulnerable and disadvantaged communities, to develop and implement precision medicine strategies and contribute to consolidating diversity in science and precision medicine in clinical practice.
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Affiliation(s)
- Giovanna Câmara Giudicelli
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, RS, Brazil
| | - Celia Mariana Barbosa De Souza
- Departamento de Nefrologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Programa de Pós-graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francisco Veríssimo Veronese
- Departamento de Nefrologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Programa de Pós-graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lygia V. Pereira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil,Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain
| | - Fernanda Sales Luiz Vianna
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, RS, Brazil,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil,Programa de Medicina Personalizada Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil,*Correspondence: Fernanda Sales Luiz Vianna,
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