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Gombault C, Grenet G, Segurel L, Duret L, Gueyffier F, Cathébras P, Pontier D, Mainbourg S, Sanchez-Mazas A, Lega JC. Population designations in biomedical research: Limitations and perspectives. HLA 2023; 101:3-15. [PMID: 36258305 PMCID: PMC10099491 DOI: 10.1111/tan.14852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/03/2022] [Accepted: 10/14/2022] [Indexed: 12/13/2022]
Abstract
In biomedical research, population differences are of central interest. Variations in the frequency and severity of diseases and in treatment effects among human subpopulation groups are common in many medical conditions. Unfortunately, the practices in terms of subpopulation labeling do not exhibit the level of rigor one would expect in biomedical research, especially when studying multifactorial diseases such as cancer or atherosclerosis. The reporting of population differences in clinical research is characterized by large disparities in practices, and fraught with methodological issues and inconsistencies. The actual designations such as "Black" or "Asian" refer to broad and heterogeneous groups, with a great discrepancy among countries. Moreover, the use of obsolete concepts such as "Caucasian" is unfortunate and imprecise. The use of adequate labeling to reflect the scientific hypothesis needs to be promoted. Furthermore, the use of "race/ethnicity" as a unique cause of human heterogeneity may distract from investigating other factors related to a medical condition, particularly if this label is employed as a proxy for cultural habits, diet, or environmental exposure. In addition, the wide range of opinions among researchers does not facilitate the attempts made for resolving this heterogeneity in labeling. "Race," "ethnicity," "ancestry," "geographical origin," and other similar concepts are saturated with meanings. Even if the feasibility of a global consensus on labeling seems difficult, geneticists, sociologists, anthropologists, and ethicists should help develop policies and practices for the biomedical field.
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Affiliation(s)
- Caroline Gombault
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - Guillaume Grenet
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Pole de Santé Publique, Hospices Civils de Lyon, Service Hospitalo-Universitaire de PharmacoToxicologie, Lyon, France
| | - Laure Segurel
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - François Gueyffier
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Pôle de Santé Publique, Hospices Civils De Lyon, Lyon, France
| | - Pascal Cathébras
- Service de Médecine Interne, Hôpital Nord, CHU de Saint-Etienne, Saint-Etienne, France
| | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France
| | - Sabine Mainbourg
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Service de Médecine Interne et Pathologie Vasculaire, Hôpital Lyon Sud, Hospices Civils De Lyon, Lyon, France
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling history, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Jean-Christophe Lega
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, UMR CNRS 5558, Lyon, France.,Service de Médecine Interne et Pathologie Vasculaire, Hôpital Lyon Sud, Hospices Civils De Lyon, Lyon, France
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3
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Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 2021; 184:2053-2067.e18. [PMID: 33794144 DOI: 10.1016/j.cell.2021.02.052] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/27/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.
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Affiliation(s)
- Mathieu Groussin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ainara Sistiaga
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA; GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Sean M Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katya Moniz
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary Noel
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Chief Dull Knife College, Lame Deer, MT, USA
| | - Jeff Hooker
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Chief Dull Knife College, Lame Deer, MT, USA
| | - Sean M Gibbons
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institute for Systems Biology, Seattle, WA, USA; Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Laure Segurel
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; UMR7206 Eco-anthropologie, CNRS-MNHN-Univ Paris Diderot-Sorbonne, Paris, France
| | - Alain Froment
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement UMR 208, Muséum National d'Histoire Naturelle, Paris, France
| | - Rihlat Said Mohamed
- SA MRC / Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Alain Fezeu
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
| | - Vanessa A Juimo
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
| | - Sophie Lafosse
- UMR7206 Eco-anthropologie, CNRS-MNHN-Univ Paris Diderot-Sorbonne, Paris, France
| | - Francis E Tabe
- Faculté de Médecine et des Sciences Biomédicales, Université Yaoundé 1, Yaoundé, Cameroun
| | - Catherine Girard
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Centre d'études nordiques, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, 1030 rue de la Médecine, Québec, QC, Canada
| | - Deborah Iqaluk
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Resolute Bay, Nunavut, Canada
| | - Le Thanh Tu Nguyen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - B Jesse Shapiro
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; McGill Genome Centre, McGill University, Montreal, QC, Canada
| | - Jenni Lehtimäki
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland; Environmental Policy Centre, Finnish Environment Institute SYKE, Helsinki, Finland
| | - Lasse Ruokolainen
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland
| | - Pinja P Kettunen
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental sciences, University of Helsinki, Helsinki, Finland
| | - Tommi Vatanen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; The Liggins Institute, University of Auckland, Auckland 1023, New Zealand
| | - Shani Sigwazi
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Tumaini University Makumira, Arusha, Tanzania
| | - Audax Mabulla
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Archaeology and Heritage Studies, University of Dar es Salaam, Tanzania
| | - Manuel Domínguez-Rodrigo
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Prehistory Unit, Department of History and Philosophy, University of Alcalá, Alcalá de Henares, Madrid, Spain; Institute of Evolution in Africa, University of Alcalá de Henares, Madrid, Spain
| | - Yvonne A Nartey
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Adwoa Agyei-Nkansah
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine and Therapeutics, University of Ghana Medical School and Korle Bu Teaching Hospital, Accra, Ghana
| | - Amoako Duah
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, St. Dominic Hospital, Akwatia, Ghana
| | - Yaw A Awuku
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Internal Medicine and Therapeutics, School of Medical Sciences University of Cape Coast, Cape Coast, Ghana
| | - Kenneth A Valles
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Medical Scientist Training Program, Mayo Clinic, Rochester, 55905, USA
| | - Shadrack O Asibey
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Catholic University College, Sunyani, Ghana
| | - Mary Y Afihene
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lewis R Roberts
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
| | - Amelie Plymoth
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Charles A Onyekwere
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Lagos State University College of Medicine, Lagos, Nigeria
| | - Roger E Summons
- The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Global Microbiome Conservancy, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Segurel L, Guarino-Vignon P, Marchi N, Lafosse S, Laurent R, Bon C, Fabre A, Hegay T, Heyer E. Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA. PLoS Biol 2020; 18:e3000742. [PMID: 32511234 PMCID: PMC7302802 DOI: 10.1371/journal.pbio.3000742] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/18/2020] [Indexed: 01/22/2023] Open
Abstract
The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?
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Affiliation(s)
- Laure Segurel
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
- * E-mail:
| | - Perle Guarino-Vignon
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Nina Marchi
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Sophie Lafosse
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Romain Laurent
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Céline Bon
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
| | - Alexandre Fabre
- Aix Marseille University, INSERM, MMG, Marseille, France
- APHM, Hôpital de la Timone Enfant, Service de Pédiatrie Multidisciplinaire, Marseille, France
| | - Tatyana Hegay
- Institute of Immunology and Human Genomics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Evelyne Heyer
- Eco-anthropologie, Muséum national d’Histoire naturelle, CNRS, Université de Paris, Paris, France
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6
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Kermany AR, Segurel L, Oliver TR, Przeworski M. TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception. Bioinformatics 2014; 30:2035-42. [PMID: 24659032 PMCID: PMC4080739 DOI: 10.1093/bioinformatics/btu159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 01/15/2014] [Accepted: 03/18/2014] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION An estimated 10-30% of clinically recognized conceptions are aneuploid, leading to spontaneous miscarriages, in vitro fertilization failures and, when viable, severe developmental disabilities. With the ongoing reduction in the cost of genotyping and DNA sequencing, the use of high-density single nucleotide polymorphism (SNP) markers for clinical diagnosis of aneuploidy and biomedical research into its causes is becoming common practice. A reliable, flexible and computationally feasible method for inferring the sources of aneuploidy is thus crucial. RESULTS We propose a new method, TroX, for analyzing human trisomy data using high density SNP markers from a trisomic individual or product of conception and one parent. Using a hidden Markov model, we infer the stage of the meiotic error (I or II) and the individual in which non-disjunction event occurred, as well as the crossover locations on the trisomic chromosome. A novel and important feature of the method is its reliance on data from the proband and only one parent, reducing the experimental cost by a third and enabling a larger set of data to be used. We evaluate our method by applying it to simulated trio data as well as to genotype data for 282 trios that include a child trisomic for chromosome 21. The analyses show the method to be highly reliable even when data from only one parent are available. With the increasing availability of DNA samples from mother and fetus, application of approaches such as ours should yield unprecedented insights into the genetic risk factors for aneuploidy. AVAILABILITY AND IMPLEMENTATION An R package implementing TroX is available for download at http://przeworski.uchicago.edu/.
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Affiliation(s)
- Amir R Kermany
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USADepartment of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USA
| | - Laure Segurel
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USADepartment of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USA
| | - Tiffany R Oliver
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USA
| | - Molly Przeworski
- Department of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USADepartment of Human Genetics and Howard Hughes Medical Institute, University of Chicago, Chicago, IL 60637, USA and Department of Biology, Spelman College, Atlanta, GA 30314, USA
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