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Padilla-Iglesias C, Derkx I. Hunter-gatherer genetics research: Importance and avenues. Evol Hum Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Kiran A, Hanachi M, Alsayed N, Fassatoui M, Oduaran OH, Allali I, Maslamoney S, Meintjes A, Zass L, Rocha JD, Kefi R, Benkahla A, Ghedira K, Panji S, Mulder N, Fadlelmola FM, Souiai O. The African Human Microbiome Portal: a public web portal of curated metagenomic metadata. Database (Oxford) 2024; 2024:baad092. [PMID: 38204360 PMCID: PMC10782148 DOI: 10.1093/database/baad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/07/2023] [Revised: 11/03/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.
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Affiliation(s)
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
- Faculty of Science of Bizerte, University of Carthage, Tunis, Tunisia
| | - Nihad Alsayed
- Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum, Sudan
| | - Meriem Fassatoui
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Ovokeraye H Oduaran
- The Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Imane Allali
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Suresh Maslamoney
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Ayton Meintjes
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Jorge Da Rocha
- The Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Rym Kefi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
| | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Faisal M Fadlelmola
- Kush Centre for Genomics and Biomedical Informatics, Biotechnology Perspectives Organization, Khartoum, Sudan
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar, Tunis 1002, Tunisia
- Malawi-Liverpool-Wellcome Trust, Blantyre 3, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
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Affiliation(s)
- Segun Fatumo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
- Department of Non-communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
- H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria.
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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Petersen DC, Steyl C, Scholtz D, Baker B, Abdullah I, Uren C, Möller M. African Genetic Representation in the Context of SARS-CoV-2 Infection and COVID-19 Severity. Front Genet 2022; 13:909117. [PMID: 35620464 PMCID: PMC9127354 DOI: 10.3389/fgene.2022.909117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Desiree C Petersen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Chrystal Steyl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Denise Scholtz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Bienyameen Baker
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ibtisam Abdullah
- Division of Haematological Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University and NHLS Tygerberg Hospital, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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Amanzougaghene N, Drali R, Shako JC, Davoust B, Fenollar F, Raoult D, Mediannikov O. High Genetic Diversity and Rickettsia felis in Pediculus humanus Lice Infesting Mbuti (pygmy people), -Democratic Republic of Congo. Front Cell Infect Microbiol 2022; 12:834388. [PMID: 35310843 PMCID: PMC8924665 DOI: 10.3389/fcimb.2022.834388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Received: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
Pediculus humanus is an obligate bloodsucking parasite of humans that has two ecotypes, the head louse and the body louse, which share an intimate history of coevolution with their human host. In the present work, we obtained and analysed head and body lice collected from Mbuti pygmies living in the Orientale province of the Democratic Republic of the Congo. Cytochrome b DNA analysis was performed in order to type the six known lice clades (A, D, B, F, C and E). The results revealed the presence of two mitochondrial clades. Clade D was the most frequent (61.7% of 47), followed by clade A (38.3% of 47). Sixteen haplotypes were found in 47 samples, of which thirteen were novel haplotypes, indicating an unusually high genetic diversity that closely mirrors the diversity of their hosts. Moreover, we report for the first time the presence of the DNA of R. felis in three (6.4% of 47) head and body lice belonging to both clades A and D. Additional studies are needed to clarify whether the Pediculus lice can indeed transmit this emerging zoonotic bacterium to their human hosts.
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Affiliation(s)
- Nadia Amanzougaghene
- Aix Marseille Univ Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Microbes, Evolution (MEPHI), Phylogénie et Infection, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Rezak Drali
- Aix Marseille Univ Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Microbes, Evolution (MEPHI), Phylogénie et Infection, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Plateforme Génomique - Bioinformatique, Institut Pasteur d’Algérie, Rue du Petit Staouéli, Algiers, Algeria
| | | | - Bernard Davoust
- Aix Marseille Univ Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Microbes, Evolution (MEPHI), Phylogénie et Infection, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Florence Fenollar
- Aix Marseille Univ Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Microbes, Evolution (MEPHI), Phylogénie et Infection, Marseille, France
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Vecteurs – Infections Tropicales et Méditeranéennes (VITROME), Marseille, France
| | - Didier Raoult
- Aix Marseille Univ Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Microbes, Evolution (MEPHI), Phylogénie et Infection, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- Aix Marseille Univ Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (APHM), Microbes, Evolution (MEPHI), Phylogénie et Infection, Marseille, France
- Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- *Correspondence: Oleg Mediannikov,
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Meeks KAC, Adeyemo A, Agyemang C. Beta-cell dysfunction and insulin resistance in relation to abnormal glucose tolerance in African populations: can we afford to ignore the diversity within African populations? BMJ Open Diabetes Res Care 2022; 10:10/1/e002685. [PMID: 35210285 PMCID: PMC8883230 DOI: 10.1136/bmjdrc-2021-002685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/05/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
- Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles Agyemang
- Department of Public and Occupational Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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Nakanishi G, Bertagnolli LS, Pita-Oliveira M, Scudeler MM, Torres-Loureiro S, Almeida-Dantas T, Alves MLC, Cirino HS, Rodrigues-Soares F. GSTM1 and GSTT1 polymorphisms in healthy volunteers - a worldwide systematic review. Drug Metab Rev 2022; 54:37-45. [PMID: 35103568 DOI: 10.1080/03602532.2022.2036996] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/29/2022] [Indexed: 02/06/2023]
Abstract
The GSTM1 and GSTT1 genes encode homonymous enzymes, which are responsible for the detoxification of several substances potentially harmful to the human body, such as air pollution, drugs, pesticides, and tobacco. However, some individuals may present a complete deletion of these genes and, consequently, an enzyme deficiency leading to an inadequate metabolism and, therefore, a higher susceptibility to some clinical conditions. Interethnic variations have also been described for both genes, making necessary the study of the deletion frequencies of GSTM1 and GSTT1 in different populations around the world. So, the aim of this study was to enable the synthesis and discussion of the main population differences of GSTM1 and GSTT1 polymorphisms in healthy volunteers. Searches were performed in the PubMed database, including 533 articles and 178,566 individuals in the analyses. We found an overrepresentation of European individuals and studies, and an underrepresentation of non-European ethnicities. Moreover, there are significant frequency differences among distinct ethnic groups: East Asians present the highest frequencies worldwide for GSTM1 and GSTT1 deletions, which could suggest higher disorders risk for this population; in contrast, Sub-Saharan Africans presented the lowest frequency of GSTM1 worldwide, corroborating evolution inferences performed previously for other genes codifying metabolism enzymes. Also, admixture is a relevant component when analyzing frequency values for both genes, but further studies focusing on this subject are warranted.
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Affiliation(s)
- Giovana Nakanishi
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Laísa S Bertagnolli
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Murilo Pita-Oliveira
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Mariana M Scudeler
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Sabrina Torres-Loureiro
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Thaís Almeida-Dantas
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Maria Laura C Alves
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Heithor S Cirino
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Fernanda Rodrigues-Soares
- Departamento de Patologia, Genética e Evolução, Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
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Marima R, Hull R, Mbeje M, Molefi T, Mathabe K, Elbagory AM, Demetriou D, Dlamini Z. Role of Precision Oncology in Type II Endometrial and Prostate Cancers in the African Population: Global Cancer Genomics Disparities. Int J Mol Sci 2022; 23:628. [PMID: 35054814 DOI: 10.3390/ijms23020628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
Precision oncology can be defined as molecular profiling of tumors to identify targetable alterations. Emerging research reports the high mortality rates associated with type II endometrial cancer in black women and with prostate cancer in men of African ancestry. The lack of adequate genetic reference information from the African genome is one of the major obstacles in exploring the benefits of precision oncology in the African context. Whilst external factors such as the geography, environment, health-care access and socio-economic status may contribute greatly towards the disparities observed in type II endometrial and prostate cancers in black populations compared to Caucasians, the contribution of African ancestry to the contribution of genetics to the etiology of these cancers cannot be ignored. Non-coding RNAs (ncRNAs) continue to emerge as important regulators of gene expression and the key molecular pathways involved in tumorigenesis. Particular attention is focused on activated/repressed genes and associated pathways, while the redundant pathways (pathways that have the same outcome or activate the same downstream effectors) are often ignored. However, comprehensive evidence to understand the relationship between type II endometrial cancer, prostate cancer and African ancestry remains poorly understood. The sub-Saharan African (SSA) region has both the highest incidence and mortality of both type II endometrial and prostate cancers. Understanding how the entire transcriptomic landscape of these two reproductive cancers is regulated by ncRNAs in an African cohort may help elucidate the relationship between race and pathological disparities of these two diseases. This review focuses on global disparities in medicine, PCa and ECa. The role of precision oncology in PCa and ECa in the African population will also be discussed.
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Abstract
The remarkable mutualism between humans and greater honeyguides (Indicator indicator) is known still to thrive in only a few places in Africa. Here, we report on the honey-hunting culture of the marginalised Awer people in Kenya, historically a hunter-gatherer culture who today practise a mixed economy including significant amounts of foraging for wild foods. As part of a larger effort to document cross-cultural honey-hunting traditions in Africa, we interviewed six Awer honey-hunters to document their cultural practices. The interviewees reported that they depend on wild honey as a source of income, and that they readily seek the cooperation of honeyguides. Honey-hunting skills and the calls/whistles used to communicate with honeyguides are learnt from their fathers and other elders in village. The best time to honey-hunt is in the months following the big rains (August–December), when interviewees go out honey-hunting once a week on average. Honeyguides are not actively rewarded with wax, as it is believed that once a bird is fed it will not cooperate again for some time, and therefore after the honey harvest is complete, all remaining wax comb is buried. Honey-hunting practices are declining in this region, which interviewees attributed to drought and a lack of interest by the youth. These findings expand our understanding of how human-honeyguide mutualism persists across a range of human cultural variation.
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Maseme M. Commodification of biomaterials and data when funding is contingent to transfer in biobank research. Med Health Care Philos 2021; 24:667-675. [PMID: 34286415 DOI: 10.1007/s11019-021-10042-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/15/2021] [Indexed: 05/23/2023]
Abstract
It is common practice for biobanks and biobank researchers to seek funding from agencies that are independent of the biobank that often stipulate conditions requiring researchers to grant access and share biomaterials and data as part of the agreement, in particular, in international collaborative health research. As yet, to the author's knowledge, there has been no study conducted to examine whether these conditions could result in the commercialization of biomaterials and data and whether such practice is considered ethical. This paper therefore seeks to answer the question of whether such sharing of biomaterials and data for biobank research in exchange for funding from sponsors and funders in collaborative health research is ethically justified. The central idea of this paper is based on an argument against commodification of the body and its parts, which includes biomaterials and data and holds that it is ethically wrong to commodify humans and their body parts. The arguments against commodification of biomaterials and data explored are the Kantian approach argument as it relates to interference of commodification with human dignity which is linked to a diminished sense of personhood, an argument against commodification that is based on a dilution of altruism and lastly the communitarian approach anti-commodification argument which emphasizes a social responsibility to the common good. Arguments in support of commodification based on liberal individualism and consequentialism are also discussed.
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Affiliation(s)
- Mantombi Maseme
- National Health Laboratory Service (NHLS), Biobank, 25 Hospital Street, Constitution Hill, Johannesburg, South Africa.
- Steve Biko Centre for Bioethics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Velazquez-Roman J, Angulo-Zamudio UA, León-Sicairos N, Medina-Serrano J, DeLira-Bustillos N, Villamil-Ramírez H, Canizales-Quinteros S, Macías-Kauffer L, Campos-Romero A, Alcántar-Fernández J, Canizalez-Roman A. Association of FTO, ABCA1, ADRB3, and PPARG variants with obesity, type 2 diabetes, and metabolic syndrome in a Northwest Mexican adult population. J Diabetes Complications 2021; 35:108025. [PMID: 34420811 DOI: 10.1016/j.jdiacomp.2021.108025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 11/28/2022]
Abstract
AIM To identify associations among allelic variants of the genes FTO, ABCA1, ADRB3, and PPARG with anthropometric and biochemical traits, metabolic diseases (obesity, T2D or metabolic syndrome) in an adult population from Northwest Mexico. METHODS Blood samples were collected from 846 subjects including 266 normal weight subjects, 285 with obesity, and 295 with T2D. Of the 846 persons in the study, 365 presented metabolic syndrome diagnostic criteria. Anthropometric and biochemical traits were recorded and 4 single nucleotide polymorphisms (SNPs): FTO rs9939609 A-allele, ABCA1 rs9282541 A-allele, ADRB3 rs4994 G-allele, and PPARG rs1801282 G-allele were genotyped by real-time PCR. RESULTS FTO rs9939609 A-allele was significantly associated with obesity (p: 8.3 × 10-4), and metabolic syndrome (p: 0.001), but no individual SNPs were significantly associated with T2D. Finally, the cumulative risk of the four SNPs was significantly associated with obesity (p: 1.95 × 10-4). CONCLUSION Associations in FTO, ABCA, ADRB3, and PPARG SNPs presented in this study with obesity and metabolic syndrome could represent a risk for developing metabolic diseases in Northwest Mexican adult subjects.
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Affiliation(s)
- Jorge Velazquez-Roman
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico
| | - Uriel A Angulo-Zamudio
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico
| | - Nidia León-Sicairos
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico; Pediatric Hospital of Sinaloa, 80200 Culiacan, Sinaloa, Mexico
| | - Julio Medina-Serrano
- Programa de Maestría en Ciencias en Biomedicina Molecular, UAS, 80246 Culiacan, Sinaloa, Mexico; Coordinación de Planeación y Enlace Institucional, Órgano de Operación Administrativa Desconcentrada (OOAD) de Sinaloa, Instituto Mexicano del Seguro Social (IMSS), Culiacan Sinaloa, Mexico
| | - Nora DeLira-Bustillos
- Programa de Maestría en Ciencias en Biomedicina Molecular, UAS, 80246 Culiacan, Sinaloa, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | - Luis Macías-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | | | | | - Adrian Canizalez-Roman
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico; The Women's Hospital, Secretariat of Health, 80020 Culiacan, Sinaloa, Mexico.
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Gopalan S, Atkinson EG, Buck LT, Weaver TD, Henn BM. Inferring archaic introgression from hominin genetic data. Evol Anthropol 2021; 30:199-220. [PMID: 33951239 PMCID: PMC8360192 DOI: 10.1002/evan.21895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 08/03/2020] [Accepted: 03/29/2021] [Indexed: 01/05/2023]
Abstract
Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.
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Affiliation(s)
- Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Elizabeth G Atkinson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Stanley Center for Psychiatric Research, Broad Institute, Boston, Massachusetts, USA
| | - Laura T Buck
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Timothy D Weaver
- Department of Anthropology, University of California, Davis, California, USA
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Department of Anthropology, University of California, Davis, California, USA.,UC Davis Genome Center, University of California, Davis, California, USA
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13
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Andras P, Stanton A. Where do successful populations originate from? J Theor Biol 2021; 524:110734. [PMID: 33940036 DOI: 10.1016/j.jtbi.2021.110734] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/01/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 11/28/2022]
Abstract
In order to understand the dynamics of emergence and spreading of socio-technical innovations and population moves it is important to determine the place of origin of these populations. Here we focus on the role of geographical factors, such as land fertility and mountains in the context of human population evolution and distribution dynamics. We use a constrained diffusion-based computational model, computer simulations and the analysis of geographical and land-quality data. Our analysis shows that successful human populations, i.e. those which become dominant in their socio - geographical environment, originate from lands of many valleys with relatively low land fertility, which are close to areas of high land fertility. Many of the homelands predicted by our analysis match the assumed homelands of known successful populations (e.g. Bantus, Turkic, Maya). We also predict other likely homelands as well, where further archaeological, linguistic or genetic exploration may confirm the place of origin for populations with no currently identified urheimat. Our work is significant because it advances the understanding of human population dynamics by guiding the identification of the origin locations of successful populations.
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Affiliation(s)
- Peter Andras
- School of Computing and Mathematics, Keele University, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK.
| | - Adam Stanton
- School of Computing and Mathematics, Keele University, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK
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14
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Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
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Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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15
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Turbón D, Rebato E, Salicrú M. Phenotypic diversity and history of the Congo Basin populations: Equatorial Guinea, Bantu Speaking Central Africans and African Pygmies. Ann Hum Biol 2021; 48:119-132. [PMID: 33821699 DOI: 10.1080/03014460.2021.1909136] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 10/21/2022]
Abstract
BACKGROUND African Pygmy Populations (APP) are believed to be one of the first groups of the Congo Basin rainforest peoples to separate from the rest of modern humanity. The arrival of Bantu speaking agriculturalists from 5,000 BP led to the formation of a large number of ethnic complexes in Central Africa and the Atlantic coastal area, mainly due to a one-way flow of pygmy women. There are now only a few small contingents of African Pygmy population groups who are mixed or who have almost disappeared as a result of migratory flows from Cameroon. AIMS We analysed the adult phenotypic diversity of 9 populations (17 groups of both sexes) of the Congo basin and Bioko Island, which were anthropometrically characterised in 1948. The phenotypic clusters that we detected, which we interpret as likely mixing of local Pygmy populations and Bantus, may be useful as references for future studies, particularly genetics. SUBJECTS AND METHODS The matrix of inter-distances between populations was generated, using the 21 variables, with the Euclidean distance between the mean vectors relating to the standardised variables. When the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) was used separately in men and women, the phylogenetic trees showed a clear separation between populations. RESULTS The body measurements that most effectively distinguished the groups are linear dimensions and the width of the hips and mean thoracic circumference. In this study, the cephalo-facial dimensions were of little value in identifying the groups. CONCLUSIONS The samples of Equatorial Guinea show a major inter-group overlap, and considerable intra-group variations. There are also notable differences amongst African Pygmy populations in terms of height, but not in body proportions.
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Affiliation(s)
- Daniel Turbón
- Zoology and Anthropology Sub-Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Esther Rebato
- Genetics, Physical Anthropology and Animal Physiology Department of Faculty of Science and Technology, University of the Basque Country-Euskal Herriko Unibertsitatea, (UPV/EHU), Bilbao, Spain
| | - Miquel Salicrú
- Statistics Sub-Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
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16
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Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS 2021; 25:213-233. [PMID: 33794662 DOI: 10.1089/omi.2021.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Chiamaka Jessica Okeke
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Maureen Bilinga Tendwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz-Sidi Mohammed Ben Abdellah University, Fez, Morocco.,University of Mohamed Premier, Oujda, Morocco
| | - Reem Mohamed Sallam
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.,Department of Basic Medical Sciences, Faculty of Medicine, Galala University, Suez, Egypt
| | - Nihad Alsayed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Michael Turkson
- The National Institute for Mathematical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Faisal Mohamed Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samar Kamal Kassim
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Pomeroy E, Stock JT, Wells JCK. Population history and ecology, in addition to climate, influence human stature and body proportions. Sci Rep 2021; 11:274. [PMID: 33431970 DOI: 10.1038/s41598-020-79501-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023] Open
Abstract
Worldwide variation in human stature and limb proportions is widely accepted to reflect thermal adaptation, but the contribution of population history to this variation is unknown. Furthermore, stature and relative lower limb length (LLL) show substantial plastic responses to environmental stressors, e.g., nutrition, pathogen load, which covary with climate. Thus ecogeographic patterns may go beyond temperature-based selection. We analysed global variation in stature, sitting height and absolute and relative LLL using large worldwide samples of published anthropometric data from adult male (n = 571) and female (n = 268) populations in relation to temperature, humidity, and net primary productivity (NPP). Population history was modeled using spatial eigenvector mapping based on geographic distances reflecting the hypothesized pattern for the spread of modern humans out of Africa. Regression models account for ~ 50% of variation in most morphological variables. Population history explains slightly more variation in stature, sitting height and LLL than the environmental/climatic variables. After adjusting for population history, associations between (usually maximum) temperature and LLL are consistent with Allen's "rule" and may drive similar relationships with stature. NPP is a consistent negative predictor of anthropometry, which may reflect the growth-limiting effects of lower environmental resource accessibility (inversely related to NPP) and/or pathogen load.
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18
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Munung NS, Ambele MA, Moela P. Advancing global equity in cancer genomics - challenges and opportunities in Sub-Saharan Africa. Curr Opin Genet Dev 2020; 66:20-24. [PMID: 33373832 DOI: 10.1016/j.gde.2020.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Developments in genomics in the last decade has improved our understanding of the role of genetics in health and disease. One area where the impact of genomics is very noticeable is in oncology, specifically in terms of diagnosis and elucidating genetic predisposition to rare and common cancers. Sub-Saharan Africa (SSA) stands to benefit from cancer genomics, given recent spikes in the incidence of various types of cancers in the region. This mini review presents, from a health and science equity perspective, how genomics could shape cancer research and clinical care in SSA. We highlight some pan-African genomics and cancer initiatives that are facilitating cancer genomics research in SSA. We conclude with recommendations on how the ideals of equity may be advanced in cancer genomics initiatives in SSA.
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Affiliation(s)
- Nchangwi S Munung
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Melvin A Ambele
- Department of Oral Pathology and Oral Biology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, South Africa; Institute for Cellular and Molecular Medicine, Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Pontsho Moela
- Division of Genetics, Department of Biochemistry, Genetics, and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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19
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Taiwo RO, Ipadeola J, Yusuf T, Fagbohunlu F, Jenfa G, Adebamowo SN, Adebamowo CA. Qualitative study of comprehension of heritability in genomics studies among the Yoruba in Nigeria. BMC Med Ethics 2020; 21:124. [PMID: 33298068 PMCID: PMC7726892 DOI: 10.1186/s12910-020-00567-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With growth of genomics research in Africa, concern has arisen about comprehension and adequacy of informed consent given the highly technical terms used in this field. We therefore decided to study whether there are linguistic and cultural concepts used to communicate heritability of characters, traits and diseases in an indigenous African population. METHODS We conducted Focus Group Discussions among 115 participants stratified by sex, age and socio-economic status and Key Informant Interviews among 25 stakeholders and Key Opinion Leaders among Yoruba living in Ibadan, Nigeria. We used Atlas-ti v.8.3.17 software to analyze the data, using thematic approach. RESULTS The study participants identified several linguistic and cultural concepts including words, proverbs, and aphorisms that are used to describe heritable characters, traits and diseases in their local dialect. These included words that can be appropriated to describe dominant and recessive traits, variations in penetrance and dilution of strength of heritable characteristics by time and inter-marriage. They also suggested that these traits are transmitted by "blood", and specific partner's blood may be stronger than the other regardless of sex. CONCLUSIONS Indigenous Yoruba populations have words and linguistic concepts that describe the heritability of characters, traits and diseases which can be appropriated to improve comprehension and adequacy of informed consent in genomics research. Our methods are openly available and can be used by genomic researchers in other African communities.
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Affiliation(s)
- Rasheed O Taiwo
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria
| | - John Ipadeola
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria
| | - Temilola Yusuf
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria
| | - Faith Fagbohunlu
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria
| | - Gbemisola Jenfa
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria
| | - Sally N Adebamowo
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria.,Department of Epidemiology and Public Health, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Clement A Adebamowo
- Division of Research Ethics, Center for Bioethics and Research, Ibadan, Nigeria. .,Department of Epidemiology and Public Health, Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA. .,Institute of Human Virology, Abuja, Nigeria. .,Institute of Human Virology Building, School of Medicine, University of Maryland, 725 West Lombard Street, Baltimore, MD, 21201, USA.
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20
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Černý V, Fortes-Lima C, Tříska P. Demographic history and admixture dynamics in African Sahelian populations. Hum Mol Genet 2020; 30:R29-R36. [PMID: 33105478 DOI: 10.1093/hmg/ddaa239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/18/2023] Open
Abstract
The Sahel/Savannah belt of Africa is a contact zone between two subsistence systems (nomadic pastoralism and sedentary farming) and of two groups of populations, namely Eurasians penetrating from northern Africa southwards and sub-Saharan Africans migrating northwards. Because pastoralism is characterized by a high degree of mobility, it leaves few significant archaeological traces. Demographic history seen through the lens of population genetic studies complements our historical and archaeological knowledge in this African region. In this review, we highlight recent advances in our understanding of demographic history in the Sahel/Savannah belt as revealed by genetic studies. We show the impact of food-producing subsistence strategies on population structure and the somewhat different migration patterns in the western and eastern part of the region. Genomic studies show that the gene pool of various groups of Sahelians consists in a complex mosaic of several ancestries. We also touch upon various signals of genetic adaptations such as lactase persistence, taste sensitivity and malaria resistance, all of which have different distribution patterns among Sahelian populations. Overall, genetic studies contribute to gain a deeper understanding about the demographic and adaptive history of human populations in this specific African region and beyond.
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Affiliation(s)
- Viktor Černý
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Cesar Fortes-Lima
- Subdepartment of Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Petr Tříska
- Archaeogenetics Laboratory, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
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Abstract
BACKGROUND In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history. RESULTS Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens. CONCLUSIONS Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.
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Affiliation(s)
- Sandra Walsh
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Biology, University of Padova, 35131, Padova, Italy
| | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Barcelona, Catalonia, Spain
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88 08003, Barcelona, Catalonia, Spain.
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Shi H, Burch KS, Johnson R, Freund MK, Kichaev G, Mancuso N, Manuel AM, Dong N, Pasaniuc B. Localizing Components of Shared Transethnic Genetic Architecture of Complex Traits from GWAS Summary Data. Am J Hum Genet 2020; 106:805-817. [PMID: 32442408 PMCID: PMC7273527 DOI: 10.1016/j.ajhg.2020.04.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 12/19/2022] Open
Abstract
Despite strong transethnic genetic correlations reported in the literature for many complex traits, the non-transferability of polygenic risk scores across populations suggests the presence of population-specific components of genetic architecture. We propose an approach that models GWAS summary data for one trait in two populations to estimate genome-wide proportions of population-specific/shared causal SNPs. In simulations across various genetic architectures, we show that our approach yields approximately unbiased estimates with in-sample LD and slight upward-bias with out-of-sample LD. We analyze nine complex traits in individuals of East Asian and European ancestry, restricting to common SNPs (MAF > 5%), and find that most common causal SNPs are shared by both populations. Using the genome-wide estimates as priors in an empirical Bayes framework, we perform fine-mapping and observe that high-posterior SNPs (for both the population-specific and shared causal configurations) have highly correlated effects in East Asians and Europeans. In population-specific GWAS risk regions, we observe a 2.8× enrichment of shared high-posterior SNPs, suggesting that population-specific GWAS risk regions harbor shared causal SNPs that are undetected in the other GWASs due to differences in LD, allele frequencies, and/or sample size. Finally, we report enrichments of shared high-posterior SNPs in 53 tissue-specific functional categories and find evidence that SNP-heritability enrichments are driven largely by many low-effect common SNPs.
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Affiliation(s)
- Huwenbo Shi
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Kathryn S Burch
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Ruth Johnson
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Malika K Freund
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Astrid M Manuel
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Natalie Dong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS. Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa. Cell 2020; 179:984-1002.e36. [PMID: 31675503 DOI: 10.1016/j.cell.2019.10.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/03/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.
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Affiliation(s)
- Deepti Gurdasani
- William Harvey Research Institute, Queen Mary's University of London, London, UK
| | | | - Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI)/National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | | | | | | | - Marc Haber
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ioanna Tachmazidou
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY, UK
| | - Iain Mathieson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth Ekoru
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Chris Finan
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Li Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Yuan Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Alex J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Georg Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Charles L Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Dermot Maher
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Stephen B Montgomery
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet Seeley
- London School of Hygiene and Tropical Medicine, London, UK; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Elizabeth H Young
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew P Morris
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Biostatistics, University of Liverpool, Liverpool, UK
| | | | | | - Ayesha A Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa.
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA.
| | - Pontiano Kaleebu
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda.
| | - Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Manj S Sandhu
- Department of Medicine, University of Cambridge, Cambridge, UK.
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Hackman JV, Hruschka DJ. Disentangling basal and accrued height‐for‐age for cross‐population comparisons. Am J Phys Anthropol 2019; 171:481-495. [DOI: 10.1002/ajpa.23990] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/28/2019] [Accepted: 12/13/2019] [Indexed: 11/07/2022]
Affiliation(s)
| | - Daniel J. Hruschka
- School of Human Evolution and Social Change Arizona State University Tempe Arizona
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25
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Sallé G, Doyle SR, Cortet J, Cabaret J, Berriman M, Holroyd N, Cotton JA. The global diversity of Haemonchus contortus is shaped by human intervention and climate. Nat Commun 2019; 10:4811. [PMID: 31641125 DOI: 10.1038/s41467-019-12695-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 09/23/2019] [Indexed: 12/14/2022] Open
Abstract
Haemonchus contortus is a haematophagous parasitic nematode of veterinary interest. We have performed a survey of its genome-wide diversity using single-worm whole genome sequencing of 223 individuals sampled from 19 isolates spanning five continents. We find an African origin for the species, together with evidence for parasites spreading during the transatlantic slave trade and colonisation of Australia. Strong selective sweeps surrounding the β-tubulin locus, a target of benzimidazole anthelmintic drug, are identified in independent populations. These sweeps are further supported by signals of diversifying selection enriched in genes involved in response to drugs and other anthelmintic-associated biological functions. We also identify some candidate genes that may play a role in ivermectin resistance. Finally, genetic signatures of climate-driven adaptation are described, revealing a gene acting as an epigenetic regulator and components of the dauer pathway. These results begin to define genetic adaptation to climate in a parasitic nematode. Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.
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Chaichoompu K, Abegaz F, Cavadas B, Fernandes V, Müller-Myhsok B, Pereira L, Van Steen K. A different view on fine-scale population structure in Western African populations. Hum Genet 2019; 139:45-59. [PMID: 31630246 PMCID: PMC6942040 DOI: 10.1007/s00439-019-02069-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/09/2019] [Indexed: 01/03/2023]
Abstract
Due to its long genetic evolutionary history, Africans exhibit more genetic variation than any other population in the world. Their genetic diversity further lends itself to subdivisions of Africans into groups of individuals with a genetic similarity of varying degrees of granularity. It remains challenging to detect fine-scale structure in a computationally efficient and meaningful way. In this paper, we present a proof-of-concept of a novel fine-scale population structure detection tool with Western African samples. These samples consist of 1396 individuals from 25 ethnic groups (two groups are African American descendants). The strategy is based on a recently developed tool called IPCAPS. IPCAPS, or Iterative Pruning to CApture Population Structure, is a genetic divisive clustering strategy that enhances iterative pruning PCA, is robust to outliers and does not require a priori computation of haplotypes. Our strategy identified in total 12 groups and 6 groups were revealed as fine-scale structure detected in the samples from Cameroon, Gambia, Mali, Southwest USA, and Barbados. Our finding helped to explain evolutionary processes in the analyzed West African samples and raise awareness for fine-scale structure resolution when conducting genome-wide association and interaction studies.
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Affiliation(s)
- Kridsadakorn Chaichoompu
- GIGA-R Medical Genomics-BIO3, University of Liege, Avenue de l'Hôpital 11, 4000, Liege, Belgium. .,Max Planck Institute of Psychiatry, 80804, Munich, Germany.
| | - Fentaw Abegaz
- GIGA-R Medical Genomics-BIO3, University of Liege, Avenue de l'Hôpital 11, 4000, Liege, Belgium
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Rua Júlio Amaral de Carvalho, 45, 4200-135, Porto, Portugal
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Rua Júlio Amaral de Carvalho, 45, 4200-135, Porto, Portugal
| | | | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Rua Júlio Amaral de Carvalho, 45, 4200-135, Porto, Portugal
| | - Kristel Van Steen
- GIGA-R Medical Genomics-BIO3, University of Liege, Avenue de l'Hôpital 11, 4000, Liege, Belgium. .,WELBIO (Walloon Excellence in Lifesciences and Biotechnology), Avenue Pasteur 6, 1300, Wavre, Belgium.
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27
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Thami PK, Chimusa ER. Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa. Front Genet 2019; 10:905. [PMID: 31611910 PMCID: PMC6777512 DOI: 10.3389/fgene.2019.00905] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequencies across the region. This genetic structure has potential implications on susceptibility and resistance to infectious diseases such as human immunodeficiency virus (HIV) infection. Southern Africa is the region affected worst by HIV. Here, we discuss advances made in genome-wide association studies (GWAS) of HIV-1 in the past 12 years and dissect population diversity within Southern Africa. Our findings accentuate that a plethora of factors such as migration, language and culture, admixture, and natural selection have profiled the genetics of the people of Southern Africa. Genetic structure has been observed among the Khoe-San, among Bantu speakers, and between the Khoe-San, Coloureds, and Bantu speakers. Moreover, Southern African populations have complex admixture scenarios. Few GWAS of HIV-1 have been conducted in Southern Africa, with only one of these identifying two novel variants (HCG22rs2535307 and CCNG1kgp22385164) significantly associated with HIV-1 acquisition and progression. High genetic diversity, multi-wave genetic mixture and low linkage disequilibrium of Southern African populations constitute a challenge in identifying genetic variants with modest risk or protective effect against HIV-1. We therefore posit that it is compelling to assess genome-wide contribution of ancestry to HIV-1 infection. We further suggest robust methods that can pin-point population-specific variants that may contribute to the control of HIV-1 in Southern Africa.
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Affiliation(s)
- Prisca K Thami
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa.,Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
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28
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Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson N, Reich D, Tishkoff SA. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol 2019; 20:82. [PMID: 31023338 PMCID: PMC6485071 DOI: 10.1186/s13059-019-1679-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations. RESULTS Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120-100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 54-16 kya. Eastern and western CRHG lineages diverged by ~ 50-31 kya, and the western CRHG lineages diverged by ~ 18-12 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations. CONCLUSIONS We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.
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Affiliation(s)
- Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Derek E Kelly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: Division of Genetic Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Simon Thompson
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dares Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Bons PD, Bauer CC, Bocherens H, de Riese T, Drucker DG, Francken M, Menéndez L, Uhl A, van Milligen BP, Wißing C. Out of Africa by spontaneous migration waves. PLoS One 2019; 14:e0201998. [PMID: 31013270 DOI: 10.1371/journal.pone.0201998] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 04/09/2019] [Indexed: 01/23/2023] Open
Abstract
Hominin evolution is characterized by progressive regional differentiation, as well as migration waves, leading to anatomically modern humans that are assumed to have emerged in Africa and spread over the whole world. Why or whether Africa was the source region of modern humans and what caused their spread remains subject of ongoing debate. We present a spatially explicit, stochastic numerical model that includes ongoing mutations, demic diffusion, assortative mating and migration waves. Diffusion and assortative mating alone result in a structured population with relatively homogeneous regions bound by sharp clines. The addition of migration waves results in a power-law distribution of wave areas: for every large wave, many more small waves are expected to occur. This suggests that one or more out-of-Africa migrations would probably have been accompanied by numerous smaller migration waves across the world. The migration waves are considered "spontaneous", as the current model excludes environmental or other extrinsic factors. Large waves preferentially emanate from the central areas of large, compact inhabited areas. During the Pleistocene, Africa was the largest such area most of the time, making Africa the statistically most likely origin of anatomically modern humans, without a need to invoke additional environmental or ecological drivers.
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Traore K, Konate S, Thera MA, Niangaly A, Ba A, Niare A, Arama C, Di Cristofaro J, Baby M, Picot S, Chiaroni J, Boetsch G, Doumbo OK. Genetic polymorphisms with erythrocyte traits in malaria endemic areas of Mali. PLoS One 2019; 14:e0209966. [PMID: 30608964 PMCID: PMC6319707 DOI: 10.1371/journal.pone.0209966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 12/16/2018] [Indexed: 11/19/2022] Open
Abstract
African populations are characterized by high degree of genetic diversity. This high genetic diversity could result from the natural selection pressure. Several studies have described an association between some genetic diversities and difference of susceptibility to infectious diseases like malaria. It seems therefore important to consider genetic diversity impact when interpreting results of clinical trials in malaria endemic areas. This study aimed to determine the genetic polymorphism with erythrocyte traits in different populations of malaria endemic area in Mali. The cross-sectional surveys were carried out in different ethnic groups living in malaria endemic areas in Mali. Six milliliters of whole blood were collected in EDTA vials from each participant after informed consent has been obtained. The ABO, RH, Kell, MNSs, Kidd and Duffy systems phenotypes were assessed by the technique of gel filtration. A total of 231 subjects were included from six villages. The blood groups phenotypes O (40.7%) and A (31.2%) were more frequent with respective allele frequencies of 0.65 and 0.21. In the RH system the haplotypes R0 (0.55), r (0.20) and R1 (0.13) were the most frequent. Seven percent (7%) of Duffy positive and 4% of Glycophorin B deficiency (S-s-) were observed among participants. All participants were Kell negative. ABO and RH systems were polymorphic in these ethnic groups in Mali. Their implication in susceptibility to malaria should be taken into account in clinical trials interpretation, and for prevention of blood transfusion risks during anemia frequently caused by malaria in children.
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Affiliation(s)
- Karim Traore
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
- Univ Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR-5246 CNRS-INSA-CPE, Malaria Research Unit, Lyon, France
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
- * E-mail:
| | - Salimata Konate
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
| | - Amadou Niangaly
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Alhassane Ba
- Centre National de Transfusion Sanguine (CNTS), Bamako, Mali
| | - Alassane Niare
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Charles Arama
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | | | - Mounirou Baby
- Centre National de Transfusion Sanguine (CNTS), Bamako, Mali
| | - Stephane Picot
- Univ Lyon, Université Claude Bernard Lyon 1, Institut de Chimie et Biochimie Moléculaire et Supramoléculaire, UMR-5246 CNRS-INSA-CPE, Malaria Research Unit, Lyon, France
| | - Jacques Chiaroni
- Aix-Marseille Université,CNRS, EFS, ADES UMR 7268, Marseille, France
| | - Gilles Boetsch
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, DEAP/FMPOS, UMI3189, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
- Unité Mixte International UMI 3189 –Environnement—Santé—Sociétés, (CNRS/USTTB, CNRST/UGB/UCAD) Université Cheikh Anta Diop, Dakar, Sénégal
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31
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Roberts L, Rebello G, Greenberg J, Ramesar R. Update on Inherited Retinal Disease in South Africa: Encouraging Diversity in Molecular Genetics. Adv Exp Med Biol 2019; 1185:257-261. [PMID: 31884621 DOI: 10.1007/978-3-030-27378-1_42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
There is a glaring disparity in the populations included in genetic research; the majority of work involves European-derived cohorts, while other global populations - including Africans - are underrepresented. This is also true for the study of inherited retinal diseases. Being the most ancient of extant populations, African samples carry more variation than others, making them valuable for novel gene and variant discovery. The inclusion of diverse populations in research is essential to gain a more comprehensive understanding of genetic variation and molecular mechanisms of disease.
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Affiliation(s)
- Lisa Roberts
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - George Rebello
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jacquie Greenberg
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Raj Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Abstract
There is an almost innate urge in human beings to represent reality in a visual form. From rock art in the Paleolithic to images of galaxies, the quotidian and the extraordinary have been visually represented through the ages. Medical and scientific disciplines are no exception. Accurate representation of the human body structures and anatomy based on cadaver dissections was almost not possible up to the Renaissance due to ethical, social, and religious beliefs and objections. The works of Leonardo da Vinci (1452-1519) and others and, later, Andreas Vesalius (1514-1564), who produced De Humanis Corporis Fabrica, are considered landmarks in the history of medicine. During the following centuries medical and scientific illustration relied upon the expertise of physician-artists and scientist-artists until a new paradigm appeared in the realm of scientific (medical) illustration: the invention of photography in the 19th century. Two of the medical disciplines most rapidly influenced by photography were dermatology and pathology, both macro- and microscopic. Physicians rapidly started to use photographs as a tool for consultation, documentation, and education, and large collections of images were amassed by individuals and institutions for these purposes. Photographic images are produced by visible light impressing a light-sensitive material such as a silver halide plate, and nowadays a silicon chip. But photons are reflected by nontransparent objects, including the human skin. Developments in science and technology allowed the use of other types of radiation to reveal internal structures in the human body and, most interestingly, noninvasively. Thus today much of the medical diagnosis and treatment is guided by the so-called medical imaging with the use of these techniques, that is, medical photography, endoscopy, x-ray radiography, computer-aided tomography, magnetic resonance imaging, ultrasonography, thermography, and nuclear medicine functional imaging techniques as positron emission tomography (PET) and single-photon emission computed tomography (SPECT). Some of these techniques are being applied at the microscopic level to study cell structure and even functional changes in real time. All these advancements in science and technology applied to medicine and other disciplines pose the question as to what extent physicians are trading their capabilities as clinicians. Ethics issues add to the complexity of this new era governed by constant changes in scientific paradigms.
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Affiliation(s)
- Fabian Michelangeli
- Biophysics and Biochemistry, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela.
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33
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Bybjerg-Grauholm J, Hagen CM, Gonçalves VF, Bækvad-Hansen M, Hansen CS, Hedley PL, Kanters JK, Nielsen J, Theisen M, Mors O, Kennedy J, Als TD, Demur AB, Nordentoft M, Børglum A, Mortensen PB, Werge TM, Hougaard DM, Christiansen M. Complex spatio-temporal distribution and genomic ancestry of mitochondrial DNA haplogroups in 24,216 Danes. PLoS One 2018; 13:e0208829. [PMID: 30543675 PMCID: PMC6292624 DOI: 10.1371/journal.pone.0208829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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] [Received: 06/21/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroups (hgs) are evolutionarily conserved sets of mtDNA SNP-haplotypes with characteristic geographical distribution. Associations of hgs with disease and physiological characteristics have been reported, but have frequently not been reproducible. Using 418 mtDNA SNPs on the PsychChip (Illumina), we assessed the spatio-temporal distribution of mtDNA hgs in Denmark from DNA isolated from 24,642 geographically un-biased dried blood spots (DBS), collected from 1981 to 2005 through the Danish National Neonatal Screening program. ADMIXTURE was used to establish the genomic ancestry of all samples using a reference of 100K+ autosomal SNPs in 2,248 individuals from nine populations. Median-joining analysis determined that the hgs were highly variable, despite being typically Northern European in origin, suggesting multiple founder events. Furthermore, considerable heterogeneity and variation in nuclear genomic ancestry was observed. Thus, individuals with hg H exhibited 95%, and U hgs 38.2% - 92.5%, Danish ancestry. Significant clines between geographical regions and rural and metropolitan populations were found. Over 25 years, macro-hg L increased from 0.2% to 1.2% (p = 1.1*E-10), and M from 1% to 2.4% (p = 3.7*E-8). Hg U increased among the R macro-hg from 14.1% to 16.5% (p = 1.9*E-3). Genomic ancestry, geographical skewedness, and sub-hg distribution suggested that the L, M and U increases are due to immigration. The complex spatio-temporal dynamics and genomic ancestry of mtDNA in the Danish population reflect repeated migratory events and, in later years, net immigration. Such complexity may explain the often contradictory and population-specific reports of mito-genomic association with disease.
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Affiliation(s)
| | - Christian M. Hagen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Christine S. Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Paula L. Hedley
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jimmi Nielsen
- Aalborg Psychiatric Hospital. Aalborg University Hospital, Aalborg, Denmark
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Mors
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - James Kennedy
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Thomas D. Als
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Alfonso B. Demur
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | | | - Anders Børglum
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Preben B. Mortensen
- Center for Register Research, Institute of Economics, Aarhus University, Århus, Denmark
| | - Thomas M. Werge
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | - David M. Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Abstract
Paucity of data from African populations due to under-representation in human genetic studies has impeded detailed understanding of the heritable human genome variation. This is despite the fact that Africa has sizeable genetic, cultural and linguistic diversity. There are renewed efforts to understand health problems relevant to African populations using more comprehensive datasets, and by improving expertise in health-related genomics among African scientists. We emphasise that careful consideration of the sampled populations from national and within-continental cohorts in large multi-ethnic genetic research efforts is required to maximise the prospects of identifying and fine-mapping novel risk variants in indigenous populations. We caution that human demographic history should be taken into consideration in such prospective genetic-association studies.
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Affiliation(s)
- Benard W Kulohoma
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
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35
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Quillen EE, Norton HL, Parra EJ, Lona-Durazo F, Ang KC, Illiescu FM, Pearson LN, Shriver MD, Lasisi T, Gokcumen O, Starr I, Lin YL, Martin AR, Jablonski NG. Shades of complexity: New perspectives on the evolution and genetic architecture of human skin. Am J Phys Anthropol 2018; 168 Suppl 67:4-26. [PMID: 30408154 DOI: 10.1002/ajpa.23737] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Like many highly variable human traits, more than a dozen genes are known to contribute to the full range of skin color. However, the historical bias in favor of genetic studies in European and European-derived populations has blinded us to the magnitude of pigmentation's complexity. As deliberate efforts are being made to better characterize diverse global populations and new sequencing technologies, better measurement tools, functional assessments, predictive modeling, and ancient DNA analyses become more widely accessible, we are beginning to appreciate how limited our understanding of the genetic bases of human skin color have been. Novel variants in genes not previously linked to pigmentation have been identified and evidence is mounting that there are hundreds more variants yet to be found. Even for genes that have been exhaustively characterized in European populations like MC1R, OCA2, and SLC24A5, research in previously understudied groups is leading to a new appreciation of the degree to which genetic diversity, epistatic interactions, pleiotropy, admixture, global and local adaptation, and cultural practices operate in population-specific ways to shape the genetic architecture of skin color. Furthermore, we are coming to terms with how factors like tanning response and barrier function may also have influenced selection on skin throughout human history. By examining how our knowledge of pigmentation genetics has shifted in the last decade, we can better appreciate how far we have come in understanding human diversity and the still long road ahead for understanding many complex human traits.
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Affiliation(s)
- Ellen E Quillen
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.,Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Cincinnati, Ohio
| | - Esteban J Parra
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Frida Lona-Durazo
- Department of Anthropology, University of Toronto - Mississauga, Mississauga, Ontario, Canada
| | - Khai C Ang
- Department of Pathology and Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania
| | - Florin Mircea Illiescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Mark D Shriver
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Tina Lasisi
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Izzy Starr
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
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Atkinson FS, Hancock D, Petocz P, Brand-Miller JC. The physiologic and phenotypic significance of variation in human amylase gene copy number. Am J Clin Nutr 2018; 108:737-748. [PMID: 30239565 DOI: 10.1093/ajcn/nqy164] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/27/2018] [Indexed: 12/15/2022] Open
Abstract
Background Salivary α-amylase gene (AMY1) copy number (CN) correlates with the amount of salivary α-amylase, but beyond this, the physiologic significance is uncertain. Objective We hypothesized that individuals with higher AMY1 CN would digest starchy foods faster and show higher postprandial responses and lower breath hydrogen excretion compared with those with low CN. Design Four linked studies were conducted. In Study 1, we genotyped 201 healthy subjects with the use of real-time quantitative polymerase chain reaction and determined glucose tolerance, insulin sensitivity, salivary α-amylase activity, body mass index (BMI), and macronutrient intake. In Study 2, a pool of 114 subjects tested 6 starchy foods, 3 sugary foods, 1 mixed meal, and 2 reference glucose solutions, containing either 50 or 25 g of available carbohydrate. In Study 3, we compared glycemic and insulin responses to starchy foods with responses to glucose in 40 individuals at extremes of high and low CN. In Study 4, we compared breath hydrogen and methane responses over 8 h in 30 individuals at extremes of CN. Results AMY1 CN correlated positively with salivary α-amylase activity (r = 0.62, P < 0.0001, n = 201) but not with BMI, glucose tolerance, or insulin sensitivity. However, CN was strongly correlated with normalized glycemic responses to all starchy foods (explaining 26-61% of interindividual variation), but not to sucrose or fruit. Individuals in the highest compared with the lowest decile of CN produced modestly higher glycemia (+15%, P = 0.018), but not insulinemia, after consuming 2 starchy foods. Low-CN individuals displayed >6-fold higher breath methane levels in the fasting state and after starch ingestion than high-CN individuals (P = 0.001), whereas hydrogen excretion was similar. Conclusions Starchy foods are digested faster and produce higher postprandial glycemia in individuals with high AMY1 CN. In contrast, having low CN is associated with colonic methane production. This trial was registered at www.anzctr.org.au as ACTRN12617000670370.
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Affiliation(s)
- Fiona S Atkinson
- School of Life and Environmental Sciences and Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Dale Hancock
- School of Life and Environmental Sciences and Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Peter Petocz
- Department of Statistics, Macquarie University, Sydney, New South Wales, Australia
| | - Jennie C Brand-Miller
- School of Life and Environmental Sciences and Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
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37
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Kulohoma BW. Importance of human demographic history knowledge in genetic studies involving multi-ethnic cohorts. Wellcome Open Res 2018; 3:82. [DOI: 10.12688/wellcomeopenres.14692.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Paucity of data from African populations due to under-representation in human genetic studies has impeded detailed understanding of the heritable human genome variation. This is despite the fact that Africa has sizeable genetic, cultural and linguistic diversity. There are renewed efforts to understand health problems relevant to African populations using more comprehensive datasets, and by improving expertise in health-related genomics among African scientists. We emphasise that careful consideration of the sampled populations from national and within-continental cohorts in large multi-ethnic genetic research efforts is required to maximise the prospects of identifying and fine-mapping novel risk variants in indigenous populations. We caution that human demographic history should be taken into consideration in such prospective genetic-association studies.
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38
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Kjeldsen SR, Raadsma HW, Leigh KA, Tobey JR, Phalen D, Krockenberger A, Ellis WA, Hynes E, Higgins DP, Zenger KR. Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments. Heredity (Edinb) 2018; 122:525-544. [PMID: 30209291 PMCID: PMC6461856 DOI: 10.1038/s41437-018-0144-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/07/2018] [Accepted: 08/01/2018] [Indexed: 02/05/2023] Open
Abstract
The Australian koala is an iconic marsupial with highly specific dietary requirements distributed across heterogeneous environments, over a large geographic range. The distribution and genetic structure of koala populations has been heavily influenced by human actions, specifically habitat modification, hunting and translocation of koalas. There is currently limited information on population diversity and gene flow at a species-wide scale, or with consideration to the potential impacts of local adaptation. Using species-wide sampling across heterogeneous environments, and high-density genome-wide markers (SNPs and PAVs), we show that most koala populations display levels of diversity comparable to other outbred species, except for those populations impacted by population reductions. Genetic clustering analysis and phylogenetic reconstruction reveals a lack of support for current taxonomic classification of three koala subspecies, with only a single evolutionary significant unit supported. Furthermore, ~70% of genetic variance is accounted for at the individual level. The Sydney Basin region is highlighted as a unique reservoir of genetic diversity, having higher diversity levels (i.e., Blue Mountains region; AvHecorr=0.20, PL% = 68.6). Broad-scale population differentiation is primarily driven by an isolation by distance genetic structure model (49% of genetic variance), with clinal local adaptation corresponding to habitat bioregions. Signatures of selection were detected between bioregions, with no single region returning evidence of strong selection. The results of this study show that although the koala is widely considered to be a dietary-specialist species, this apparent specialisation has not limited the koala’s ability to maintain gene flow and adapt across divergent environments as long as the required food source is available.
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Affiliation(s)
- Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia.
| | - Herman W Raadsma
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
| | - Kellie A Leigh
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia.,Science for Wildlife, PO Box 286, Cammeray, NSW, 2062, Australia
| | - Jennifer R Tobey
- San Diego Zoo Institute for Conservation Research, Escondido, CA, 92027, USA
| | - David Phalen
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, Private Mail Bag 4003, Narellan, NSW, 2570, Australia
| | - Andrew Krockenberger
- Centre for Tropical Biodiversity and Climate Change, Division of Research and Innovation, James Cook University, Cairns, QLD, 4878, Australia
| | - William A Ellis
- School of Agriculture and Food Science, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Emily Hynes
- Ecoplan Australia, PO Box 968, Torquay, VIC, 3228, Australia
| | - Damien P Higgins
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
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39
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Dnyansagar R, Zimmermann B, Moran Y, Praher D, Sundberg P, Møller LF, Technau U. Dispersal and speciation: The cross Atlantic relationship of two parasitic cnidarians. Mol Phylogenet Evol 2018; 126:346-355. [PMID: 29702219 DOI: 10.1016/j.ympev.2018.04.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/12/2018] [Accepted: 04/23/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Rohit Dnyansagar
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Bob Zimmermann
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Yehu Moran
- Department of Molecular Evolution and Development, University of Vienna, Austria; Department of Ecology, Evolution and Behavior, Hebrew University of Jerusalem, Israel
| | - Daniela Praher
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Per Sundberg
- Department of Marine Sciences, University of Gothenburg, Sweden
| | - Lene Friis Møller
- Danish Shellfish Centre, DTU Aqua, Technical University of Denmark, Denmark
| | - Ulrich Technau
- Department of Molecular Evolution and Development, University of Vienna, Austria.
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40
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Arend P. Position of human blood group O(H) and phenotype-determining enzymes in growth and infectious disease. Ann N Y Acad Sci 2018; 1425:5-18. [PMID: 29754430 PMCID: PMC7676429 DOI: 10.1111/nyas.13694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/22/2018] [Accepted: 03/06/2018] [Indexed: 12/12/2022]
Abstract
The human ABO(H) blood group phenotypes arise from the evolutionarily oldest genetic system found in primate populations. While the blood group antigen A is considered the ancestral primordial structure, under the selective pressure of life‐threatening diseases blood group O(H) came to dominate as the most frequently occurring blood group worldwide. Non‐O(H) phenotypes demonstrate impaired formation of adaptive and innate immunoglobulin specificities due to clonal selection and phenotype formation in plasma proteins. Compared with individuals with blood group O(H), blood group A individuals not only have a significantly higher risk of developing certain types of cancer but also exhibit high susceptibility to malaria tropica or infection by Plasmodium falciparum. The phenotype‐determining blood group A glycotransferase(s), which affect the levels of anti‐A/Tn cross‐reactive immunoglobulins in phenotypic glycosidic accommodation, might also mediate adhesion and entry of the parasite to host cells via trans‐species O‐GalNAc glycosylation of abundantly expressed serine residues that arise throughout the parasite's life cycle, while excluding the possibility of antibody formation against the resulting hybrid Tn antigen. In contrast, human blood group O(H), lacking this enzyme, is indicated to confer a survival advantage regarding the overall risk of developing cancer, and individuals with this blood group rarely develop life‐threatening infections involving evolutionarily selective malaria strains.
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Affiliation(s)
- Peter Arend
- Department of Medicine, Philipps University Marburg, Marburg/Lahn, Germany. Gastroenterology Research Laboratory, College of Medicine, University of Iowa, Iowa City, Iowa. Research Laboratories, Chemie Grünenthal GmbH, Aachen, Germany
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41
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Romero A, Ramirez-Rozzi FV, Pérez-Pérez A. Dental size variability in Central African Pygmy hunter-gatherers and Bantu-speaking farmers. Am J Phys Anthropol 2018; 166:671-681. [PMID: 29566431 DOI: 10.1002/ajpa.23458] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Odontometric studies of African populations show high within-group variation in tooth size. Overall, North Africans exhibit smaller dimensions than groups from eastern and southern sub-Saharan regions, but no previous studies have analyzed the full dental metrics among extant African Pygmy hunter-gatherers and Bantu-speaking farmers. Furthermore, the population variability in tooth crown sizes from equatorial rainforest regions remains to be elucidated. MATERIALS AND METHODS The mesiodistal and buccolingual diameters of the permanent teeth (I1-M2) were measured in vivo using high-resolution replicas from Baka Pygmies and Mvae and Yassa Bantu-speakers from Cameroon (western Africa). Analyses of variance were used to record sex-related and population-level differences in tooth sizes, and a principal component analysis of geometrically scaled measures was used to plot the odontometric variability among groups. RESULTS Cameroonian Baka Pygmies differ in dental size from their Bantu-speaking neighbors. Molar teeth are larger in Pygmies than in Bantu individuals, while the anterior dentition is larger in the Bantu. Baka males exhibit significantly larger teeth than females, whereas sexual dimorphism in non-Pygmies is only present in the anterior dentition. DISCUSSION Odontometric patterns and the degree of sexual dimorphism in dental size differ among Central African groups, indicating adaptation to their different forager and farmer lifestyles. In particular, the admixture of Bantu-speakers in Baka populations is smaller than that in other western Pygmy groups. The greater dental phenetic diversity in Baka compared to that of the smaller-toothed farmers suggests that ecogenetic and microevolutionary factors are influencing a particular divergence scenario.
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Affiliation(s)
- Alejandro Romero
- Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, Alicante, 03080, Spain
| | | | - Alejandro Pérez-Pérez
- Departament de Biologia Evolutiva, Ecologia i Ciencies Ambientals, Secció Zoologia i Antropologia Biològica, Universitat de Barcelona, Barcelona, 08028, Spain
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42
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Tawe L, Motshoge T, Ramatlho P, Mutukwa N, Muthoga CW, Dongho GBD, Martinelli A, Peloewetse E, Russo G, Quaye IK, Paganotti GM. Human cytochrome P450 2B6 genetic variability in Botswana: a case of haplotype diversity and convergent phenotypes. Sci Rep 2018; 8:4912. [PMID: 29559695 PMCID: PMC5861095 DOI: 10.1038/s41598-018-23350-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 03/09/2018] [Indexed: 01/11/2023] Open
Abstract
Identification of inter-individual variability for drug metabolism through cytochrome P450 2B6 (CYP2B6) enzyme is important for understanding the differences in clinical responses to malaria and HIV. This study evaluates the distribution of CYP2B6 alleles, haplotypes and inferred metabolic phenotypes among subjects with different ethnicity in Botswana. A total of 570 subjects were analyzed for CYP2B6 polymorphisms at position 516 G > T (rs3745274), 785 A > G (rs2279343) and 983 T > C (rs28399499). Samples were collected in three districts of Botswana where the population belongs to Bantu (Serowe/Palapye and Chobe) and San-related (Ghanzi) ethnicity. The three districts showed different haplotype composition according to the ethnic background but similar metabolic inferred phenotypes, with 59.12%, 34.56%, 2.10% and 4.21% of the subjects having, respectively, an extensive, intermediate, slow and rapid metabolic profile. The results hint at the possibility of a convergent adaptation of detoxifying metabolic phenotypes despite a different haplotype structure due to the different genetic background. The main implication is that, while there is substantial homogeneity of metabolic inferred phenotypes among the country, the response to drugs metabolized via CYP2B6 could be individually associated to an increased risk of treatment failure and toxicity. These are important facts since Botswana is facing malaria elimination and a very high HIV prevalence.
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Affiliation(s)
- Leabaneng Tawe
- University of Botswana, Department of Medical Laboratory Sciences, Gaborone, Botswana.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Sub-Saharan African Network for TB/HIV Research Excellence at Botswana-Harvard Partnership, Gaborone, Botswana
| | - Thato Motshoge
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Pleasure Ramatlho
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Naledi Mutukwa
- University of Botswana, Department of Pathology, Gaborone, Botswana
| | | | - Ghyslaine Bruna Djeunang Dongho
- Sapienza University of Rome, Department of Infectious Diseases and Public Health, Rome, Italy.,Evangelical University of Cameroon, Department of Biomedical Sciences, Bandjoun, Cameroon
| | - Axel Martinelli
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.,King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Thuwal, Saudi Arabia
| | - Elias Peloewetse
- University of Botswana, Department of Biological Sciences, Gaborone, Botswana
| | - Gianluca Russo
- Sapienza University of Rome, Department of Infectious Diseases and Public Health, Rome, Italy
| | - Isaac Kweku Quaye
- University of Namibia, Department of Biochemistry, Windhoek, Namibia
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana. .,University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. .,University of Botswana, Department of Biomedical Sciences, Gaborone, Botswana.
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Pule GD, Chimusa ER, Mnika K, Mhandire K, Kampira E, Dandara C, Wonkam A. Beta-globin gene haplotypes and selected Malaria-associated variants among black Southern African populations. Glob Health Epidemiol Genom 2017; 2:e17. [PMID: 29868223 DOI: 10.1017/gheg.2017.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 09/27/2017] [Accepted: 10/16/2017] [Indexed: 12/16/2022]
Abstract
Partial carrier-resistance to Plasmodium falciparum malaria conferred by the sickle cell (HbS) mutation has resulted in the local amplification and positive selection of sickle cell disease (SCD) in malaria-endemic regions and particularly in sub-Saharan Africa (SSA). The present study investigated the β-globin gene haplotypes, and selected malaria-associated variants among three cohorts of Bantu-speaking individuals from Malawi, Zimbabwe and South Africa compared with reports with data from others SSA populations. The data suggest a south-ward frequency decrease of malaria-associated variants in SSA linked to the evolutionary dynamics of various African populations’ genomes through selective pressure of malaria. These selected genomics differences, positive selection of SCD in malaria-endemic regions among ‘Bantus’ from various part of Africa emphasise the evidence of the dissociation between genetics, anthropology and culture. The present study also showed a relatively prevalent Benin haplotype, which is mostly found in West Africa, among Southern African Blacks and very low Bantu haplotype, which could suggest a major migration route, of Southern Africa Bantu, along the African west coast, post-occurrence of the Sickle cell mutation, which date remain to be fully elucidated.
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Vyas DN, Al‐Meeri A, Mulligan CJ. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. Am J Phys Anthropol 2017; 164:736-749. [DOI: 10.1002/ajpa.23312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
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Roberts L, Ratnapriya R, du Plessis M, Chaitankar V, Ramesar RS, Swaroop A. Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing. Invest Ophthalmol Vis Sci 2017; 57:6374-6381. [PMID: 27898983 PMCID: PMC5132076 DOI: 10.1167/iovs.16-19785] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose A majority of genes associated with inherited retinal diseases (IRDs) have been identified in patients of European origin. Indigenous African populations exhibit rich genomic diversity, and evaluation of reported genetic mutations has yielded low returns so far. Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts. Methods Whole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics). Variants in reported IRD genes were identified using WES and validated by Sanger sequencing. Custom TaqMan assays were used to screen for identified mutations in 193 unrelated indigenous Africans with IRDs. Results A total of 3494 variants were identified in 217 known IRD genes, leading to the identification of seven different mutations (including six novel) in six genes (RHO, PRPF3, PRPF31, ABCA4, CERKL, and PDE6B) in six distinct families. TaqMan screening in additional probands revealed identical homozygous CERKL and PDE6B variants in four more patients. Conclusions This is the first report of WES of patients with IRDs in indigenous African populations. Our study identified genetic defects in almost 40% of the families analyzed, significantly enhancing the molecular diagnosis of IRD in South Africa. Thus, WES of understudied cohorts seems to present an effective strategy for determining novel mutations in heterogeneous retinal diseases.
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Affiliation(s)
- Lisa Roberts
- University of Cape Town/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Morné du Plessis
- University of Cape Town/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vijender Chaitankar
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Raj S Ramesar
- University of Cape Town/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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Ibrahim M, Osman M, Peprah E. Understanding the Evolutionary Biology of CVD From Analysis of Ancestral Population Genomes. Glob Heart 2017; 12:73-75. [PMID: 28302549 DOI: 10.1016/j.gheart.2017.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 01/29/2023] Open
Affiliation(s)
- Muntaser Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.
| | - Maha Osman
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Emmanuel Peprah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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Montinaro F, Busby GB, Gonzalez-Santos M, Oosthuitzen O, Oosthuitzen E, Anagnostou P, Destro-Bisol G, Pascali VL, Capelli C. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations. Genetics 2017; 205:303-16. [PMID: 27838627 DOI: 10.1534/genetics.116.189209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022] Open
Abstract
The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.
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Beltrame MH, Rubel MA, Tishkoff SA. Inferences of African evolutionary history from genomic data. Curr Opin Genet Dev 2016; 41:159-166. [PMID: 27810637 DOI: 10.1016/j.gde.2016.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/29/2016] [Accepted: 10/07/2016] [Indexed: 01/22/2023]
Abstract
Africa is the origin of anatomically modern humans and a continent of linguistic, cultural, environmental, phenotypic, and genetic diversity. However, African populations remain underrepresented in genetic studies, which have largely focused on individuals with European and Asian ancestry. The expansion of high-throughput 'omic' technologies to interrogate multiple tissue types across many biomolecules-DNA, proteins, epigenetic modifications, metabolites, and others-has heralded a new era of investigation into African history. In this review, we summarize how some of these recent advances have been applied to contemporary sub-Saharan African populations to inform studies on human origins and adaptation.
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Affiliation(s)
- Marcia Holsbach Beltrame
- Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Baker JL, Shriner D, Bentley AR, Rotimi CN. Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa. Pharmacogenomics J 2017; 17:112-20. [PMID: 27779243 DOI: 10.1038/tpj.2016.78] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/06/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.
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Carstens N, Williams S, Goolam S, Carmichael T, Cheung MS, Büchmann-Møller S, Sultan M, Staedtler F, Zou C, Swart P, Rice DS, Lacoste A, Paes K, Ramsay M. Novel mutation in the CHST6 gene causes macular corneal dystrophy in a black South African family. BMC Med Genet 2016; 17:47. [PMID: 27439461 PMCID: PMC4955246 DOI: 10.1186/s12881-016-0308-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 06/23/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Macular corneal dystrophy (MCD) is a rare autosomal recessive disorder that is characterized by progressive corneal opacity that starts in early childhood and ultimately progresses to blindness in early adulthood. The aim of this study was to identify the cause of MCD in a black South African family with two affected sisters. METHODS A multigenerational South African Sotho-speaking family with type I MCD was studied using whole exome sequencing. Variant filtering to identify the MCD-causal mutation included the disease inheritance pattern, variant minor allele frequency and potential functional impact. RESULTS Ophthalmologic evaluation of the cases revealed a typical MCD phenotype and none of the other family members were affected. An average of 127 713 variants per individual was identified following exome sequencing and approximately 1.2 % were not present in any of the investigated public databases. Variant filtering identified a homozygous E71Q mutation in CHST6, a known MCD-causing gene encoding corneal N-acetyl glucosamine-6-O-sulfotransferase. This E71Q mutation results in a non-conservative amino acid change in a highly conserved functional domain of the human CHST6 that is essential for enzyme activity. CONCLUSION We identified a novel E71Q mutation in CHST6 as the MCD-causal mutation in a black South African family with type I MCD. This is the first description of MCD in a black Sub-Saharan African family and therefore contributes valuable insights into the genetic aetiology of this disease, while improving genetic counselling for this and potentially other MCD families.
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Affiliation(s)
- Nadia Carstens
- />Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 2050 Johannesburg, Gauteng South Africa
| | - Susan Williams
- />Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Saadiah Goolam
- />Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Trevor Carmichael
- />Division of Ophthalmology, Department of Neurosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ming Sin Cheung
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Stine Büchmann-Møller
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Marc Sultan
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Frank Staedtler
- />Biomarker Development, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Chao Zou
- />Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Peter Swart
- />Division of Anatomical Pathology, National Health Laboratory Services and University of the Witwatersrand, Johannesburg, South Africa
| | - Dennis S. Rice
- />Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Arnaud Lacoste
- />Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Kim Paes
- />Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Michèle Ramsay
- />Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, 2050 Johannesburg, Gauteng South Africa
- />Division of Human Genetics, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, 2050 Johannesburg, Gauteng South Africa
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