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Almohammed EK, Hadi A, Al-Asmakh M, Lazim H. The Qatari population's genetic structure and gene flow as revealed by the Y chromosome. PLoS One 2023; 18:e0290844. [PMID: 37656680 PMCID: PMC10473524 DOI: 10.1371/journal.pone.0290844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023] Open
Abstract
The Y-chromosome has been widely used in forensic genetic applications and human population genetic studies due to its uniparental origins. A large database on the Qatari population was created for comparison with other databases from the Arabian Peninsula, the Middle East, and Africa. We provide a study of 23 Y-STR loci included in PowerPlex Y23 (Promega, USA) that were genotyped to produce haplotypes in 379 unrelated males from Qatar, a country at the crossroads of migration patterns. Overall, the most polymorphic locus provided by the Promega kit was DYS458, with a genetic diversity value of 0.85 and a haplotype diversity of 0.998924. Athey's Haplogroup Predictor tool was used to predict haplogroups from Y-STR haplotypes in the Qatari population. In a median-joining network, the haplogroup J1 predominance (49%) in Qatar generated a star-like expansion cluster. The graph of population Q-matrix was developed using Y-STR data from 38 Middle Eastern and 97 African populations (11,305 individuals), and it demonstrated a stronger sub-grouping of countries within each ethnic group and showed the effect of Arabs on the indigenous Berbers of North Africa. The estimated migration rate between the Qatari and other Arabian populations was inferred using Bayesian coalescence theory in the Migrate-n program. According to the Gene Flow study, the main migration route was from Yemen to Kuwait through Qatar. Our research, using the PowerPlex Y23 database, shows the importance of gene diversity, as well as regional and social structuring, in determining the utility of demographic and forensic databases.
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Affiliation(s)
- Eida Khalaf Almohammed
- Ministry of Interior of Qatar, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Abdullah Hadi
- University of Central Lancashire Medical School, Preston, United Kingdom
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hayder Lazim
- School of Medicine, Faculty of Health, Social Care and Medicine (FHSCM), Edge Hill University, Ormskirk, United Kingdom
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Almoussa M, Mattei J. Cardiovascular health and risk factors in African refugees and immigrants in the United States: a narrative review. ETHNICITY & HEALTH 2023; 28:399-412. [PMID: 35306946 DOI: 10.1080/13557858.2022.2052712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
OBJECTIVES Refugees and immigrants often experience challenges pre- and post-settlement that expose them to risk factors of cardiovascular disease (CVD). Literature on CVD among the growing population of African refugees and immigrants in the United States (US) is scant. This narrative review aimed to evaluate existing studies reporting on CVD and its risk factors among African refugees and immigrants in the US, and to recognize limitations in the current research, policy, and healthcare for adequate CVD-related care for African refugees and immigrants. DESIGN Articles on African refugee and/or immigrant health were searched on PubMed using multiple key search terms. Studies conducted between 1995 and 2020 and reporting on CVD-related measures in individuals from African countries of origin were included. Six articles were found discussing refugee health only and seven articles discussed refugee and immigrant health together. RESULTS Overall, the studies showed the varying prevalence of CVD risk factors, mostly depending on the country of origin. Worsening cardiometabolic health with longer residency in the US was generally reported. Refugee-only studies relied mostly on medical records data, while refugee and immigrant studies used both medical records and primary data collection. Limitations in data pertain to the geographical representation of both African countries (predominantly from Somalia despite migrants arriving from diverse African countries) and of regions of settling in the US (predominantly the north/northeast), scarce longitudinal studies, and lack of distinction between refugees and immigrants. Multiple social and structural barriers to cardiovascular health were identified, mostly related to cultural and linguistic challenges and to inadequate or complex health insurance and healthcare systems. CONCLUSION The cardiovascular health of African refugees and immigrants remains understudied and underserved. Further research and interventions to alleviate barriers and improve cardiovascular health in African refugees and immigrants in the US should be developed using culturally appropriate, accessible, flexible, and multifaceted strategies.
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Affiliation(s)
- Maya Almoussa
- Department of Molecular and Cellular Biology, Harvard College Faculty of Arts and Sciences, Cambridge, MA, USA
| | - Josiemer Mattei
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Diakite M, Shaw-Saliba K, Lau CY. Malignancy and viral infections in Sub-Saharan Africa: A review. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2023; 3:1103737. [PMID: 37476029 PMCID: PMC10358275 DOI: 10.3389/fviro.2023.1103737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The burden of malignancy related to viral infection is increasing in Sub-Saharan Africa (SSA). In 2018, approximately 2 million new cancer cases worldwide were attributable to infection. Prevention or treatment of these infections could reduce cancer cases by 23% in less developed regions and about 7% in developed regions. Contemporaneous increases in longevity and changes in lifestyle have contributed to the cancer burden in SSA. African hospitals are reporting more cases of cancer related to infection (e.g., cervical cancer in women and stomach and liver cancer in men). SSA populations also have elevated underlying prevalence of viral infections compared to other regions. Of 10 infectious agents identified as carcinogenic by the International Agency for Research on Cancer, six are viruses: hepatitis B and C viruses (HBV and HCV, respectively), Epstein-Barr virus (EBV), high-risk types of human papillomavirus (HPV), Human T-cell lymphotropic virus type 1 (HTLV-1), and Kaposi's sarcoma herpesvirus (KSHV, also known as human herpesvirus type 8, HHV-8). Human immunodeficiency virus type 1 (HIV) also facilitates oncogenesis. EBV is associated with lymphomas and nasopharyngeal carcinoma; HBV and HCV are associated with hepatocellular carcinoma; KSHV causes Kaposi's sarcoma; HTLV-1 causes T-cell leukemia and lymphoma; HPV causes carcinoma of the oropharynx and anogenital squamous cell cancer. HIV-1, for which SSA has the greatest global burden, has been linked to increasing risk of malignancy through immunologic dysregulation and clonal hematopoiesis. Public health approaches to prevent infection, such as vaccination, safer injection techniques, screening of blood products, antimicrobial treatments and safer sexual practices could reduce the burden of cancer in Africa. In SSA, inequalities in access to cancer screening and treatment are exacerbated by the perception of cancer as taboo. National level cancer registries, new screening strategies for detection of viral infection and public health messaging should be prioritized in SSA's battle against malignancy. In this review, we discuss the impact of carcinogenic viruses in SSA with a focus on regional epidemiology.
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Affiliation(s)
- Mahamadou Diakite
- University Clinical Research Center, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | - Kathryn Shaw-Saliba
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
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Lucas-Sánchez M, Fadhlaoui-Zid K, Comas D. The genomic analysis of current-day North African populations reveals the existence of trans-Saharan migrations with different origins and dates. Hum Genet 2023; 142:305-320. [PMID: 36441222 PMCID: PMC9918576 DOI: 10.1007/s00439-022-02503-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/28/2022] [Indexed: 11/29/2022]
Abstract
The Sahara Desert has acted as a barrier to human gene-flow between the northern and central parts of Africa since its aridification. Nonetheless, some contacts between both sides of the desert have occurred throughout history, mainly driven by commercial activity. Part of this was the infamous trans-Saharan slave trade, which forcedly brought peoples from south of the Sahara to North Africa from Roman times until the nineteenth century. Although historical records exist, the genetic aspects of these trans-Saharan migrations have not been deeply studied. In the present study, we assess the genetic influence of trans-Saharan migrations in current-day North Africa and characterize its amount, geographical origin, and dates. We confirm the heterogeneous and generally low-frequency presence of genomic segments of sub-Saharan origin in present-day North Africans acquired in recent historical times, and we show evidence of at least two admixture events: one dated around the thirteenth-fourteenth centuries CE between North Africans and a Western-sub-Saharan-like source similar to current-day Senegambian populations, and another one dated around the seventeenth century CE involving Tunisians and an Eastern-sub-Saharan-like source related to current-day south-Sudan and Kenyan populations. Time and location coincide with the peak of trans-Saharan slave-trade activity between Western African empires and North African powers, and are also concordant with the possibility of continuous recent south-to-north gene-flow. These findings confirm the trans-Saharan human genetic contacts, providing new and precise evidence about its possible dates and geographical origins, which are pivotal to understanding the genomic composition of an underrepresented region such as North Africa.
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Affiliation(s)
- Marcel Lucas-Sánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia ,College of Science, Department of Biology, Taibah University, Al Madinah Al Monawarah, Saudi Arabia
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Barcelona, Spain.
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Korunes KL, Soares-Souza GB, Bobrek K, Tang H, Araújo II, Goldberg A, Beleza S. Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans. G3 GENES|GENOMES|GENETICS 2022; 12:6647844. [PMID: 35861404 PMCID: PMC9526050 DOI: 10.1093/g3journal/jkac183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022]
Abstract
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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Affiliation(s)
| | | | - Katherine Bobrek
- Department of Anthropology, Emory University , Atlanta, GA 30322, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Isabel Inês Araújo
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde (Uni-CV) , Praia, Ilha de Santiago CP 379C, Cabo Verde
| | - Amy Goldberg
- Evolutionary Anthropology, Duke University , Durham, NC 27705, USA
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester , Leicester LE1 7RH, UK
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Mohottige D, Boulware LE, Ford CL, Jones C, Norris KC. Use of Race in Kidney Research and Medicine: Concepts, Principles, and Practice. Clin J Am Soc Nephrol 2022; 17:314-322. [PMID: 34789476 PMCID: PMC8823929 DOI: 10.2215/cjn.04890421] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Black Americans and other racially and ethnically minoritized individuals are disproportionately burdened by higher morbidity and mortality from kidney disease when compared with their White peers. Yet, kidney researchers and clinicians have struggled to fully explain or rectify causes of these inequalities. Many studies have sought to identify hypothesized genetic and/or ancestral origins of biologic or behavioral deficits as singular explanations for racial and ethnic inequalities in kidney health. However, these approaches reinforce essentialist beliefs that racial groups are inherently biologically and behaviorally different. These approaches also often conflate the complex interactions of individual-level biologic differences with aggregated population-level disparities that are due to structural racism (i.e., sociopolitical policies and practices that created and perpetuate harmful health outcomes through inequities of opportunities and resources). We review foundational misconceptions about race, racism, genetics, and ancestry that shape research and clinical practice with a focus on kidney disease and related health outcomes. We also provide recommendations on how to embed key equity-enhancing concepts, terms, and principles into research, clinical practice, and medical publishing standards.
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Affiliation(s)
- Dinushika Mohottige
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
- Center for Community and Population Health Improvement, Duke Clinical and Translational Science Institute, Duke University School of Medicine, Durham, North Carolina
| | - L. Ebony Boulware
- Center for Community and Population Health Improvement, Duke Clinical and Translational Science Institute, Duke University School of Medicine, Durham, North Carolina
- Division of General Internal Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Chandra L. Ford
- Department of Community Health Science, University of California, Los Angeles School of Public Health, Los Angeles, California
- Center for the Study of Racism, Social Justice & Health, University of California, Los Angeles School of Public Health, Los Angeles, California
| | - Camara Jones
- Department of Community Health and Preventive Medicine, Morehouse School of Medicine, Atlanta, Georgia
- Department of Epidemiology, Rollins School of Public Health at Emory University, Atlanta, Georgia
- Department of Behavioral Sciences and Health Education, Rollins School of Public Health at Emory University, Atlanta, Georgia
| | - Keith C. Norris
- Center for the Study of Racism, Social Justice & Health, University of California, Los Angeles School of Public Health, Los Angeles, California
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California
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7
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Djomkam Zune AL, Olwal CO, Tapela K, Owoicho O, Nganyewo NN, Lyko F, Paemka L. Pathogen-Induced Epigenetic Modifications in Cancers: Implications for Prevention, Detection and Treatment of Cancers in Africa. Cancers (Basel) 2021; 13:cancers13236051. [PMID: 34885162 PMCID: PMC8656768 DOI: 10.3390/cancers13236051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer is a major public health burden worldwide. Tumor formation is caused by multiple intrinsic and extrinsic factors. Many reports have demonstrated a positive correlation between the burden of infectious pathogens and the occurrence of cancers. However, the mechanistic link between pathogens and cancer development remains largely unclear and is subject to active investigations. Apart from somatic mutations that have been widely linked with various cancers, an appreciable body of knowledge points to alterations of host epigenetic patterns as key triggers for cancer development. Several studies have associated various infectious pathogens with epigenetic modifications. It is therefore plausible to assume that pathogens induce carcinogenesis via alteration of normal host epigenetic patterns. Thus, Africa with its disproportionate burden of infectious pathogens is threatened by a dramatic increase in pathogen-mediated cancers. To curb the potential upsurge of such cancers, a better understanding of the role of tropical pathogens in cancer epigenetics could substantially provide resources to improve cancer management among Africans. Therefore, this review discusses cancer epigenetic studies in Africa and the link between tropical pathogens and cancer burden. In addition, we discuss the potential mechanisms by which pathogens induce cancers and the opportunities and challenges of tropical pathogen-induced epigenetic changes for cancer prevention, detection and management.
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Affiliation(s)
- Alexandra Lindsey Djomkam Zune
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana; (C.O.O.); (K.T.); (O.O.); (N.N.N.)
- Correspondence: (A.L.D.Z.); (L.P.); Tel.: +233-205652619 (L.P.)
| | - Charles Ochieng’ Olwal
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana; (C.O.O.); (K.T.); (O.O.); (N.N.N.)
| | - Kesego Tapela
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana; (C.O.O.); (K.T.); (O.O.); (N.N.N.)
| | - Oloche Owoicho
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana; (C.O.O.); (K.T.); (O.O.); (N.N.N.)
- Department of Biological Sciences, Benue State University, Makurdi P.M.B. 102119, Benue State, Nigeria
| | - Nora Nghochuzie Nganyewo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana; (C.O.O.); (K.T.); (O.O.); (N.N.N.)
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul P.O. Box 273, The Gambia
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany;
| | - Lily Paemka
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana; (C.O.O.); (K.T.); (O.O.); (N.N.N.)
- Correspondence: (A.L.D.Z.); (L.P.); Tel.: +233-205652619 (L.P.)
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8
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Adadey SM, Wonkam-Tingang E, Aboagye ET, Quaye O, Awandare GA, Wonkam A. Hearing loss in Africa: current genetic profile. Hum Genet 2021; 141:505-517. [PMID: 34609590 PMCID: PMC9034983 DOI: 10.1007/s00439-021-02376-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023]
Abstract
Hearing impairment (HI) is highly heterogeneous with over 123 associated genes reported to date, mostly from studies among Europeans and Asians. Here, we performed a systematic review of literature on the genetic profile of HI in Africa. The study protocol was registered on PROSPERO, International Prospective Register of Systematic Reviews with the registration number “CRD42021240852”. Literature search was conducted on PubMed, Scopus, Africa-Wide Information, and Web of Science databases. A total of 89 full-text records was selected and retrieved for data extraction and analyses. We found reports from only 17/54 (31.5%) African countries. The majority (61/89; 68.5%) of articles were from North Africa, with few reports found from sub-Saharan Africa. The most common method used in these publications was targeted gene sequencing (n = 66/111; 59.5%), and only 13.5% (n = 15/111) used whole-exome sequencing. More than half of the studies were performed in families segregating HI (n = 51/89). GJB2 was the most investigated gene, with GJB2: p.(R143W) founder variant only reported in Ghana, while GJB2: c.35delG was common in North African countries. Variants in MYO15A were the second frequently reported in both North and Central Africa, followed by ATP6V1B1 only reported from North Africa. Usher syndrome was the main syndromic HI molecularly investigated, with variants in five genes reported: USH2A, USH1G, USH1C, MYO7A, and PCDH15. MYO7A: p.(P1780S) founder variant was reported as the common Usher syndrome variant among Black South Africans. This review provides the most comprehensive data on HI gene variants in the largely under-investigated African populations. Future exomes studies particularly in multiplex families will likely provide opportunities for the discovery of the next sets of novel HI genes, and well as unreported variants in known genes to further our understanding of HI pathobiology, globally.
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Affiliation(s)
- Samuel Mawuli Adadey
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana.,Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Elvis Twumasi Aboagye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Gordon A Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.
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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] [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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10
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Crooks L, Cooper-Knock J, Heath PR, Bouhouche A, Elfahime M, Azzouz M, Bakri Y, Adnaoui M, Ibrahimi A, Amzazi S, Tazi-Ahnini R. Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing. BMC Genet 2020; 21:111. [PMID: 32957965 PMCID: PMC7507649 DOI: 10.1186/s12863-020-00917-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 09/08/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact that genetic diversity is expected to be highest in Africa where Homo sapiens evolved and has maintained a large population for the longest time. The African Genome Variation Project examined several African populations but these were all located south of the Sahara. Morocco is on the northwest coast of Africa and mostly lies north of the Sahara, which makes it very attractive for studying genetic diversity. The ancestry of present-day Moroccans is unknown and may be substantially different from Africans found South of the Sahara desert, Recent genomic data of Taforalt individuals in Eastern Morocco revealed 15,000-year-old modern humans and suggested that North African individuals may be genetically distinct from previously studied African populations. RESULTS We present SNVs discovered by whole genome sequencing (WGS) of three Moroccans. From a total of 5.9 million SNVs detected, over 200,000 were not identified by 1000G and were not in the extensive gnomAD database. We summarise the SNVs by genomic position, type of sequence gene context and effect on proteins encoded by the sequence. Analysis of the overall genomic information of the Moroccan individuals to individuals from 1000G supports the Moroccan population being distinct from both sub-Saharan African and European populations. CONCLUSIONS We conclude that Moroccan samples are genetically distinct and lie in the middle of the previously observed cline between populations of European and African ancestry. WGS of Moroccan individuals can identify a large number of novel SNVs and aid in functional characterisation of the genome.
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Affiliation(s)
- Lucy Crooks
- Centre for Mass Spectrometry Imaging, Biomolecular Sciences Research Centre, Sheffield Hallam University, Howard Street, Sheffield,, S1 1WB, UK
| | - Johnathan Cooper-Knock
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Paul R Heath
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Ahmed Bouhouche
- Neurology and Neurogenetics, Genomic of Human Pathlogies Center, Medical School and Pharmacy, Mohammed-V University, Rabat, Morocco
| | | | - Mimoun Azzouz
- Neuroscience (SITraN), Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
| | - Youssef Bakri
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Mohammed Adnaoui
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Lab (MedBiotech), Medical School and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Saaïd Amzazi
- Laboratory of human pathologies Biology BioPatH-Faculty of science-Center of human pathologies Genomics, GenoPatH- Faculty of Medicine- Mohammed V University in Rabat, Rabat, Morocco
| | - Rachid Tazi-Ahnini
- Medical School and Pharmacy, Mohammed V University, Rabat, Morocco.
- Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, S10 2RX, UK.
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11
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Aljasmi FA, Vijayan R, Sudalaimuthuasari N, Souid AK, Karuvantevida N, Almaskari R, Mohammed Abdul Kader H, Kundu B, Michel Hazzouri K, Amiri KMA. Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population. Genes (Basel) 2020; 11:genes11080876. [PMID: 32752197 PMCID: PMC7464197 DOI: 10.3390/genes11080876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.
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Affiliation(s)
- Fatma A Aljasmi
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Ranjit Vijayan
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Abdul-Kader Souid
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Raja Almaskari
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Biduth Kundu
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled M A Amiri
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
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12
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Omenka OI, Watson DP, Hendrie HC. Understanding the healthcare experiences and needs of African immigrants in the United States: a scoping review. BMC Public Health 2020; 20:27. [PMID: 31914960 PMCID: PMC6950921 DOI: 10.1186/s12889-019-8127-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Africans immigrants in the United States are the least-studied immigrant group, despite the research and policy efforts to address health disparities within immigrant communities. Although their healthcare experiences and needs are unique, they are often included in the "black" category, along with other phenotypically-similar groups. This process makes utilizing research data to make critical healthcare decisions specifically targeting African immigrants, difficult. The purpose of this Scoping Review was to examine extant information about African immigrant health in the U.S., in order to develop lines of inquiry using the identified knowledge-gaps. METHODS Literature published in the English language between 1980 and 2016 were reviewed in five stages: (1) identification of the question and (b) relevant studies, (c) screening, (d) data extraction and synthesis, and (e) results. Databases used included EBSCO, ProQuest, PubMed, and Google Scholar (hand-search). The articles were reviewed according to title and abstract, and studies deemed relevant were reviewed as full-text articles. Data was extracted from the selected articles using the inductive approach, which was based on the comprehensive reading and interpretive analysis of the organically emerging themes. Finally, the results from the selected articles were presented in a narrative format. RESULTS Culture, religion, and spirituality were identified as intertwined key contributors to the healthcare experiences of African immigrants. In addition, lack of culturally-competent healthcare, distrust, and complexity, of the U.S. health system, and the exorbitant cost of care, were identified as major healthcare access barriers. CONCLUSION Knowledge about African immigrant health in the U.S. is scarce, with available literature mainly focusing on databases, which make it difficult to identify African immigrants. To our knowledge, this is the first Scoping Review pertaining to the healthcare experiences and needs of African immigrants in the U.S.
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Affiliation(s)
- Ogbonnaya I Omenka
- College of Pharmacy and Health Sciences, Butler University, 4600 Sunset Avenue, PHSB 404E, Indianapolis, IN, 46208, USA.
| | - Dennis P Watson
- Center for Dissemination and Implementation Science, Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Hugh C Hendrie
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
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13
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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] [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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14
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Misganaw B, Guffanti G, Lori A, Abu-Amara D, Flory JD, Mueller S, Yehuda R, Jett M, Marmar CR, Ressler KJ, Doyle FJ. Polygenic risk associated with post-traumatic stress disorder onset and severity. Transl Psychiatry 2019; 9:165. [PMID: 31175274 PMCID: PMC6555815 DOI: 10.1038/s41398-019-0497-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/07/2019] [Indexed: 01/14/2023] Open
Abstract
Post-traumatic stress disorder (PTSD) is a psychiatric illness with a highly polygenic architecture without large effect-size common single-nucleotide polymorphisms (SNPs). Thus, to capture a substantial portion of the genetic contribution, effects from many variants need to be aggregated. We investigated various aspects of one such approach that has been successfully applied to many traits, polygenic risk score (PRS) for PTSD. Theoretical analyses indicate the potential prediction ability of PRS. We used the latest summary statistics from the largest published genome-wide association study (GWAS) conducted by Psychiatric Genomics Consortium for PTSD (PGC-PTSD). We found that the PRS constructed for a cohort comprising veterans of recent wars (n = 244) explains a considerable proportion of PTSD onset (Nagelkerke R2 = 4.68%, P = 0.003) and severity (R2 = 4.35%, P = 0.0008) variances. However, the performance on an African ancestry sub-cohort was minimal. A PRS constructed with schizophrenia GWAS also explained a significant fraction of PTSD diagnosis variance (Nagelkerke R2 = 2.96%, P = 0.0175), confirming previously reported genetic correlation between the two psychiatric ailments. Overall, these findings demonstrate the important role polygenic analyses of PTSD will play in risk prediction models as well as in elucidating the biology of the disorder.
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Affiliation(s)
- Burook Misganaw
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Guia Guffanti
- Department of Psychiatry, Harvard Medical School and McLean Hospital, Belmont, MA, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Duna Abu-Amara
- Steven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury; and Department of Psychiatry, NYU School of Medicine, New York, NY, USA
| | - Janine D Flory
- Department of Psychiatry, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susanne Mueller
- Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel Yehuda
- Department of Psychiatry, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
- The Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marti Jett
- Integrative Systems Biology, United States Army Medical Research and Material Command, United States Army Center for Environmental Health Research, Frederick, MD, USA
| | - Charles R Marmar
- Steven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury; and Department of Psychiatry, NYU School of Medicine, New York, NY, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School and McLean Hospital, Belmont, MA, USA
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
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15
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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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16
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Velkov S, Ott JJ, Protzer U, Michler T. The Global Hepatitis B Virus Genotype Distribution Approximated from Available Genotyping Data. Genes (Basel) 2018; 9:genes9100495. [PMID: 30326600 PMCID: PMC6210291 DOI: 10.3390/genes9100495] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is divided into nine genotypes, A to I. Currently, it remains unclear how the individual genotypes contribute to the estimated 250 million chronic HBV infections. We performed a literature search on HBV genotyping data throughout the world. Over 900 publications were assessed and data were extracted from 213 records covering 125 countries. Using previously published HBV prevalence, and population data, we approximated the number of infections with each HBV genotype per country and the genotype distribution among global chronic HBV infections. We estimated that 96% of chronic HBV infections worldwide are caused by five of the nine genotypes: genotype C is most common (26%), followed by genotype D (22%), E (18%), A (17%) and B (14%). Genotypes F to I together cause less than 2% of global chronic HBV infections. Our work provides an up-to-date analysis of global HBV genotyping data and an initial approach to estimate how genotypes contribute to the global burden of chronic HBV infection. Results highlight the need to provide HBV cell culture and animal models that cover at least genotypes A to E and represent the vast majority of global HBV infections to test novel treatment strategies.
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Affiliation(s)
- Stoyan Velkov
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Trogerstrasse 30, D-81675 München, Germany.
| | - Jördis J Ott
- Department of Epidemiology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany; Hannover Medical School, D-30625 Hannover, Germany.
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Trogerstrasse 30, D-81675 München, Germany.
- German Center for Infection Research (DZIF), Munich Partner Site.
| | - Thomas Michler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Trogerstrasse 30, D-81675 München, Germany.
- German Center for Infection Research (DZIF), Munich Partner Site.
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17
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Retshabile G, Mlotshwa BC, Williams L, Mwesigwa S, Mboowa G, Huang Z, Rustagi N, Swaminathan S, Katagirya E, Kyobe S, Wayengera M, Kisitu GP, Kateete DP, Wampande EM, Maplanka K, Kasvosve I, Pettitt ED, Matshaba M, Nsangi B, Marape M, Tsimako-Johnstone M, Brown CW, Yu F, Kekitiinwa A, Joloba M, Mpoloka SW, Mardon G, Anabwani G, Hanchard NA. Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. Am J Hum Genet 2018; 102:731-743. [PMID: 29706352 DOI: 10.1016/j.ajhg.2018.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/26/2018] [Indexed: 01/08/2023] Open
Abstract
Large-scale, population-based genomic studies have provided a context for modern medical genetics. Among such studies, however, African populations have remained relatively underrepresented. The breadth of genetic diversity across the African continent argues for an exploration of local genomic context to facilitate burgeoning disease mapping studies in Africa. We sought to characterize genetic variation and to assess population substructure within a cohort of HIV-positive children from Botswana-a Southern African country that is regionally underrepresented in genomic databases. Using whole-exome sequencing data from 164 Batswana and comparisons with 150 similarly sequenced HIV-positive Ugandan children, we found that 13%-25% of variation observed among Batswana was not captured by public databases. Uncaptured variants were significantly enriched (p = 2.2 × 10-16) for coding variants with minor allele frequencies between 1% and 5% and included predicted-damaging non-synonymous variants. Among variants found in public databases, corresponding allele frequencies varied widely, with Botswana having significantly higher allele frequencies among rare (<1%) pathogenic and damaging variants. Batswana clustered with other Southern African populations, but distinctly from 1000 Genomes African populations, and had limited evidence for admixture with extra-continental ancestries. We also observed a surprising lack of genetic substructure in Botswana, despite multiple tribal ethnicities and language groups, alongside a higher degree of relatedness than purported founder populations from the 1000 Genomes project. Our observations reveal a complex, but distinct, ancestral history and genomic architecture among Batswana and suggest that disease mapping within similar Southern African populations will require a deeper repository of genetic variation and allelic dependencies than presently exists.
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Affiliation(s)
- Gaone Retshabile
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Zhuoyi Huang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Navin Rustagi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shanker Swaminathan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Katagirya
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - David P Kateete
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie M Wampande
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda; Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Koketso Maplanka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Edward D Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Betty Nsangi
- Baylor College of Medicine Children's Foundation, Kampala, Uganda
| | - Marape Marape
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | | | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children's Foundation, Kampala, Uganda; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
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18
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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19
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Hollfelder N, Schlebusch CM, Günther T, Babiker H, Hassan HY, Jakobsson M. Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genet 2017; 13:e1006976. [PMID: 28837655 PMCID: PMC5587336 DOI: 10.1371/journal.pgen.1006976] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/06/2017] [Accepted: 08/13/2017] [Indexed: 12/26/2022] Open
Abstract
Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa. Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation, correlated with geography, and likely driven by Eurasian admixture in the wake of migrations along the Nile. This admixture process largely coincides with the time of the Arab conquest, spreading in a southbound direction along the Nile and the Blue Nile. Nilotic populations occupying the region around the White Nile show long-term continuity, genetic isolation and genetic links to ancestral East African people. Compared to current times, groups that are ancestral to the current-day Nilotes likely inhabited a larger area of northeast Africa prior to the migration from the Middle East as their ancestry component can still be found in a large area. Our findings reveal the genetic history of Sudanese and South Sudanese people, broaden our knowledge on demographic history of humans, and quantify the impact of large-scale historic migration events in northeast Africa.
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Affiliation(s)
- Nina Hollfelder
- Dept. of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Torsten Günther
- Dept. of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Hiba Babiker
- Dept. of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hisham Y. Hassan
- Banoon ART and Cytogenetics Centre, Bahrain Defense Force Hospital, Manama, Kingdom of Bahrain
| | - Mattias Jakobsson
- Dept. of Organismal Biology, Uppsala University, Uppsala, Sweden
- SciLife Lab, Uppsala University, Uppsala, Sweden
- * E-mail:
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20
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Reiner WB, Masao F, Sholts SB, Songita AV, Stanistreet I, Stollhofen H, Taylor RE, Hlusko LJ. OH 83: A new early modern human fossil cranium from the Ndutu beds of Olduvai Gorge, Tanzania. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:533-545. [PMID: 28786473 DOI: 10.1002/ajpa.23292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 05/02/2017] [Accepted: 07/23/2017] [Indexed: 01/23/2023]
Abstract
OBJECTIVE Herein we introduce a newly recovered partial calvaria, OH 83, from the upper Ndutu Beds of Olduvai Gorge, Tanzania. We present the geological context of its discovery and a comparative analysis of its morphology, placing OH 83 within the context of our current understanding of the origins and evolution of Homo sapiens. MATERIALS AND METHODS We comparatively assessed the morphology of OH 83 using quantitative and qualitative data from penecontemporaneous fossils and the W.W. Howells modern human craniometric dataset. RESULTS OH 83 is geologically dated to ca. 60-32 ka. Its morphology is indicative of an early modern human, falling at the low end of the range of variation for post-orbital cranial breadth, the high end of the range for bifrontal breadth, and near average in frontal length. DISCUSSION There have been numerous attempts to use cranial anatomy to define the species Homo sapiens and identify it in the fossil record. These efforts have not met wide agreement by the scientific community due, in part, to the mosaic patterns of cranial variation represented by the fossils. The variable, mosaic pattern of trait expression in the crania of Middle and Late Pleistocene fossils implies that morphological modernity did not occur at once. However, OH 83 demonstrates that by ca. 60-32 ka modern humans in Africa included individuals that are at the fairly small and gracile range of modern human cranial variation.
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Affiliation(s)
- Whitney B Reiner
- Department of Integrative Biology, University of California Berkeley, MC 3140, Berkeley, California, 94720
| | - Fidelis Masao
- University of Dar es Salaam, Dar es Salaam, TZ, 35091.,Conservation Olduvai Project, Dar es Salaam, TZ, 35091
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560
| | | | - Ian Stanistreet
- University of Liverpool, Liverpool, L69 3GP, UK.,The Stone Age Institute, Bloomington, Indiana, 47407
| | - Harald Stollhofen
- GeoZentrum Nordbayern, Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - R E Taylor
- University of California Riverside, Riverside, California, 92521
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley, MC 3140, Berkeley, California, 94720
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21
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Tracing the peopling of the world through genomics. Nature 2017; 541:302-310. [PMID: 28102248 DOI: 10.1038/nature21347] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions. Our interpretation of the evolutionary history and adaptation of humans is being transformed by analyses of these new genomic data.
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López S, van Dorp L, Hellenthal G. Human Dispersal Out of Africa: A Lasting Debate. Evol Bioinform Online 2016; 11:57-68. [PMID: 27127403 PMCID: PMC4844272 DOI: 10.4137/ebo.s33489] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/21/2016] [Accepted: 02/21/2016] [Indexed: 01/01/2023] Open
Abstract
Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.
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Affiliation(s)
- Saioa López
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London, UK
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23
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Padayatty SJ, Levine M. Vitamin C: the known and the unknown and Goldilocks. Oral Dis 2016; 22:463-93. [PMID: 26808119 DOI: 10.1111/odi.12446] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 12/11/2022]
Abstract
Vitamin C (Ascorbic Acid), the antiscorbutic vitamin, cannot be synthesized by humans and other primates, and has to be obtained from diet. Ascorbic acid is an electron donor and acts as a cofactor for fifteen mammalian enzymes. Two sodium-dependent transporters are specific for ascorbic acid, and its oxidation product dehydroascorbic acid is transported by glucose transporters. Ascorbic acid is differentially accumulated by most tissues and body fluids. Plasma and tissue vitamin C concentrations are dependent on amount consumed, bioavailability, renal excretion, and utilization. To be biologically meaningful or to be clinically relevant, in vitro and in vivo studies of vitamin C actions have to take into account physiologic concentrations of the vitamin. In this paper, we review vitamin C physiology; the many phenomena involving vitamin C where new knowledge has accrued or where understanding remains limited; raise questions about the vitamin that remain to be answered; and explore lines of investigations that are likely to be fruitful.
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Affiliation(s)
- S J Padayatty
- Molecular and Clinical Nutrition Section, Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - M Levine
- Molecular and Clinical Nutrition Section, Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Schmidt K, Noureen A, Kronenberg F, Utermann G. Structure, function, and genetics of lipoprotein (a). J Lipid Res 2016; 57:1339-59. [PMID: 27074913 DOI: 10.1194/jlr.r067314] [Citation(s) in RCA: 305] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Indexed: 12/29/2022] Open
Abstract
Lipoprotein (a) [Lp(a)] has attracted the interest of researchers and physicians due to its intriguing properties, including an intragenic multiallelic copy number variation in the LPA gene and the strong association with coronary heart disease (CHD). This review summarizes present knowledge of the structure, function, and genetics of Lp(a) with emphasis on the molecular and population genetics of the Lp(a)/LPA trait, as well as aspects of genetic epidemiology. It highlights the role of genetics in establishing Lp(a) as a risk factor for CHD, but also discusses uncertainties, controversies, and lack of knowledge on several aspects of the genetic Lp(a) trait, not least its function.
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Affiliation(s)
- Konrad Schmidt
- Divisions of Human Genetics Medical University of Innsbruck, Innsbruck, Austria Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Asma Noureen
- Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerd Utermann
- Divisions of Human Genetics Medical University of Innsbruck, Innsbruck, Austria
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25
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Stewart C, Pepper MS. Cystic fibrosis on the African continent. Genet Med 2015; 18:653-62. [DOI: 10.1038/gim.2015.157] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/17/2015] [Indexed: 01/11/2023] Open
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26
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Hefke G, Davison S, D'Amato ME. Forensic performance of Investigator DIPplex indels genotyping kit in native, immigrant, and admixed populations in South Africa. Electrophoresis 2015; 36:3018-25. [DOI: 10.1002/elps.201500243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/09/2015] [Accepted: 08/27/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Gwynneth Hefke
- Forensic DNA Laboratory, Department of Biotechnology; University of the Western Cape; Bellville South Africa
- South African Police Service Forensic Science Laboratory; Biology Unit; Panorama South Africa
| | - Sean Davison
- Forensic DNA Laboratory, Department of Biotechnology; University of the Western Cape; Bellville South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology; University of the Western Cape; Bellville South Africa
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27
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Sewali B, Harcourt N, Everson-Rose SA, Leduc RE, Osman S, Allen ML, Okuyemi KS. Prevalence of cardiovascular risk factors across six African Immigrant Groups in Minnesota. BMC Public Health 2015; 15:411. [PMID: 25895917 PMCID: PMC4409770 DOI: 10.1186/s12889-015-1740-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 04/08/2015] [Indexed: 11/17/2022] Open
Abstract
Background Although African immigrants represent a large and growing segment of the U.S. population, there are little or no data available on the prevalence of cardiovascular disease (CVD) risk factors among this diverse population. This study compared the prevalence of self-reported CVD risk factors and health behaviors and examined the associations between immigration related characteristics and CVD risk factors and health behaviors across six African immigrants groups. Methods Data were from 996 African immigrants in the U.S., (37.9% Somalis; 26.8% Ethiopians; 14% Liberians; 8.5% Sudanese; 5.1% Kenyans and 7.8% others group) from a cross-sectional survey conducted in the Twin cities of Minnesota. Logistic regression models estimated the associations of demographic characteristics, and immigration-related factors (length of stay in the United states, English proficiency, income and health insurance) with prevalence of CVD risk factors (overweight/obese; hypertension and diabetes mellitus) and self-reported health behaviors (cigarette smoking, physical inactivity, conscious effort to exercise and eating a healthy diet). Results We found a relatively low self-reported prevalence of diabetes, hypertension, and smoking. However, significant differences were noted by country of origin. Using Somalis as our referent country of origin group, we found that Liberians and Kenyans were more likely to report having diabetes or hypertension. On all measures of health behaviors, Liberians were more likely to engage in more health protective behaviors than other individuals. Conclusions Although African immigrants have different prevalence rates for CVD risk factors and health behaviors, there is a need to further explore the differences observed by country of emigration.
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Affiliation(s)
- Barrett Sewali
- Program in Health Disparities Research, University of Minnesota Medical School, Minneapolis, MN, 55414, USA. .,Department of Family Medicine and Community Health, University of Minnesota Medical School, 717 Delaware St. SE. Ste. 166, Minneapolis, MN, 55414, USA.
| | - Nonyelum Harcourt
- Program in Health Disparities Research, University of Minnesota Medical School, Minneapolis, MN, 55414, USA. .,Department of Medicine, Cardiology Division, University of Minnesota, Minneapolis, MN, 55414, USA.
| | - Susan A Everson-Rose
- Program in Health Disparities Research, University of Minnesota Medical School, Minneapolis, MN, 55414, USA. .,Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, 55414, USA.
| | - Robert E Leduc
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, 55414, USA.
| | - Sirad Osman
- New American Community Services, Minneapolis, MN, 55104, USA.
| | - Michele L Allen
- Program in Health Disparities Research, University of Minnesota Medical School, Minneapolis, MN, 55414, USA. .,Department of Family Medicine and Community Health, University of Minnesota Medical School, 717 Delaware St. SE. Ste. 166, Minneapolis, MN, 55414, USA.
| | - Kolawole S Okuyemi
- Program in Health Disparities Research, University of Minnesota Medical School, Minneapolis, MN, 55414, USA. .,Department of Family Medicine and Community Health, University of Minnesota Medical School, 717 Delaware St. SE. Ste. 166, Minneapolis, MN, 55414, USA. .,Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55414, USA.
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Saab KR, Kendrick J, Yracheta JM, Lanaspa MA, Pollard M, Johnson RJ. New insights on the risk for cardiovascular disease in African Americans: the role of added sugars. J Am Soc Nephrol 2015; 26:247-57. [PMID: 25090991 PMCID: PMC4310665 DOI: 10.1681/asn.2014040393] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 06/30/2014] [Indexed: 12/26/2022] Open
Abstract
African Americans are at increased risk for cardiovascular and metabolic diseases, including obesity, high BP, diabetes, CKD, myocardial infarction, and stroke. Here we summarize the current risks and provide an overview of the underlying risk factors that may account for these associations. By reviewing the relationship between cardiovascular and renal diseases and the African-American population during the early 20th century, the historic and recent associations of African heritage with cardiovascular disease, and modern population genetics, it is possible to assemble strong hypotheses for the primary underlying mechanisms driving the increased frequency of disease in African Americans. Our studies suggest that underlying genetic mechanisms may be responsible for the increased frequency of high BP and kidney disease in African Americans, with particular emphasis on the role of APOL1 polymorphisms in causing kidney disease. In contrast, the Western diet, particularly the relatively high intake of fructose-containing sugars and sweetened beverages, appears to be the dominant force driving the increased risk of diabetes, obesity, and downstream complications. Given that intake of added sugars is a remediable risk factor, we recommend clinical trials to examine the reduction of sweetened beverages as a primary means for reducing cardiovascular risk in African Americans.
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Affiliation(s)
- Karim R Saab
- Renal Division, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Jessica Kendrick
- Renal Division, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado
| | - Joseph M Yracheta
- Department of Pharmaceutics, University of Washington, School of Pharmacy, Seattle, Washington
| | - Miguel A Lanaspa
- Renal Division, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado; Colorado Research Partners LLC, Aurora, Colorado; and
| | | | - Richard J Johnson
- Renal Division, Department of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado; Colorado Research Partners LLC, Aurora, Colorado; and
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Casto AM, Henn BM, Kidd JM, Bustamante CD, Feldman MW. A tale of two haplotypes: the EDA2R/AR Intergenic region is the most divergent genomic segment between Africans and East Asians in the human genome. Hum Biol 2014; 84:641-94. [PMID: 23959643 DOI: 10.3378/027.084.0604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2013] [Indexed: 11/05/2022]
Abstract
Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure of 52 of its highly differentiated SNPs. Using a publicly available data set of 3,000 X chromosomes from 65 human populations, we found that nearly all human X chromosomes carry one of two modal haplotypes for these 52 SNPs. The predominance of two highly divergent haplotypes at this locus was confirmed by use of a subset of individuals sequenced to high coverage. The first of these haplotypes, the α-haplotype is at high frequencies in most of the African populations surveyed and likely arose before the separation of African populations into distinct genetic entities. The second, the β-haplotype, is frequent or fixed in all non-African populations and likely arose in East Africa before the out-of-Africa migration. We also observed a small group or rare haplotypes with no clear relationship to the α- and β-haplotypes. These haplotypes occur at relatively high frequencies in African hunter-gatherer populations, such as the San and Mbuti Pygmies. Our analysis indicates that these haplotypes are part of a pool of diverse, ancestral haplotypes that have now been almost entirely replaced by the α- and β-haplotypes. We suggest that the rise of the α- and β-haplotypes was the result of the demographic forces that human populations experienced during the formation of modern African populations and the out-of-Africa migration. However, we also present evidence that this region is the target of selection in the form of positive selection on the α- and β-haplotypes and of purifying the selection against α/β recombinants.
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Affiliation(s)
- Amanda M Casto
- Department of Genetics, Stanford University, Mail Stop 5120, Stanford, California 94305, USA.
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Sangaré M, Hendrickson B, Sango HA, Chen K, Nofziger J, Amara A, Dutra A, Schindler AB, Guindo A, Traoré M, Harmison G, Pak E, Yaro FN, Bricceno K, Grunseich C, Chen G, Boehm M, Zukosky K, Bocoum N, Meilleur KG, Daou F, Bagayogo K, Coulibaly YI, Diakité M, Fay MP, Lee HS, Saad A, Gribaa M, Singleton AB, Maiga Y, Auh S, Landouré G, Fairhurst RM, Burnett BG, Scholl T, Fischbeck KH. Genetics of low spinal muscular atrophy carrier frequency in sub-Saharan Africa. Ann Neurol 2014; 75:525-32. [PMID: 24515897 PMCID: PMC4112719 DOI: 10.1002/ana.24114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022]
Abstract
Objective Spinal muscular atrophy (SMA) is one of the most common severe hereditary diseases of infancy and early childhood in North America, Europe, and Asia. SMA is usually caused by deletions of the survival motor neuron 1 (SMN1) gene. A closely related gene, SMN2, modifies the disease severity. SMA carriers have only 1 copy of SMN1 and are relatively common (1 in 30–50) in populations of European and Asian descent. SMN copy numbers and SMA carrier frequencies have not been reliably estimated in Malians and other sub‐Saharan Africans. Methods We used a quantitative polymerase chain reaction assay to determine SMN1 and SMN2 copy numbers in 628 Malians, 120 Nigerians, and 120 Kenyans. We also explored possible mechanisms for SMN1 and SMN2 copy number differences in Malians, and investigated their effects on SMN mRNA and protein levels. Results The SMA carrier frequency in Malians is 1 in 209, lower than in Eurasians. Malians and other sub‐Saharan Africans are more likely to have ≥3 copies of SMN1 than Eurasians, and more likely to lack SMN2 than Europeans. There was no evidence of gene conversion, gene locus duplication, or natural selection from malaria resistance to account for the higher SMN1 copy numbers in Malians. High SMN1 copy numbers were not associated with increased SMN mRNA or protein levels in human cell lines. Interpretation SMA carrier frequencies are much lower in sub‐Saharan Africans than in Eurasians. This finding is important to consider in SMA genetic counseling in individuals with black African ancestry. Ann Neurol 2014;75:525–532
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Affiliation(s)
- Modibo Sangaré
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD; Institute of Biomedical Sciences, George Washington University, Washington, DC
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Skelton MM, Kampira EE, Wonkam AA, Mhandire KK, Kumwenda JJ, Duri KK, Dandara CC. Frequency variation among sub-Saharan populations in virus restriction gene, BST-2 proximal promoter polymorphisms: implications for HIV-1 prevalence differences among African countries. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:461-71. [PMID: 24601767 DOI: 10.1089/omi.2013.0127] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The present study reports promoter variants in four sub-Saharan African populations that may affect BST-2 gene regulation. Recently, an in/del within the BST-2 promoter has been associated with HIV-1 disease progression in a Spanish cohort. Hence, we sequenced the proximal promoter region of the BST-2 gene in 581 individuals from South Africa, Zimbabwe, Malawi, and Cameroon. Seven SNPs were identified: rs28413176 (+26i6/Δ6); rs28413175 (-160i1/Δ1), -187A>G (nucleotide position -17516614); rs28413174 (-193G>A); rs73921425 (-199G>A); rs12609479 (-201C>T); and rs112492472 (-225C>T). The -199A and -225T alleles showed interesting trends across the sub-Saharan continent. Using predictive bioinformatics tools, we show that allelic variation at -199 and -201 potentially affect key transcription factor binding sites including bHLH, c-Myb, and E47. Importantly, data available from the ENCODE study gave further credence to our hypothesis of transcriptional regulation of BST-2 by a bHLH TF such as Mxi1. The possible repressive transcriptional effect of Mxi1 combined with the allelic frequency trend seen at -199 between African populations overlays well with current HIV-1 prevalence data, and may be a contributing factor to this phenomenon. The differences in HIV-1 prevalence in African countries could be, in part, due to distribution of genetic variants that affect susceptibility to HIV-1. Our findings therefore have substantive value for the design of future diagnostics for global health oriented diagnostics for HIV-1 susceptibility, and rational therapeutics on the critical path to personalized medicine in the African continent. As HIV-1 epidemiology vastly impacts human populations around the world, the population genomics strategy we have utilized herein can have value for other global regions as well.
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Affiliation(s)
- Michelle M Skelton
- 1 Division of Human Genetics, Faculty of Health Sciences, University of Cape Town , Observatory, Cape Town, South Africa
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Moormann A, Skiles J, Koros E, Asirwa FC, Busakhala N, Loehrer P. Mentoring future Kenyan oncology researchers. Infect Agent Cancer 2013; 8:40. [PMID: 24099090 PMCID: PMC3851568 DOI: 10.1186/1750-9378-8-40] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/02/2013] [Indexed: 11/18/2022] Open
Abstract
This is a summary of the 1st Academic Model Providing Access to Healthcare (AMPATH) Oncology Institute research grant writing workshop organized in collaboration with the Kenya Medical Research Institute (KEMRI) and held in Kisumu, Kenya from January 16th to 18th, 2013. The goal of this meeting was to mentor future Kenyan scientists and prioritize research topics that would lead to improved cancer care and survival for the citizens of Kenya.
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Affiliation(s)
- Ann Moormann
- University of Massachusetts Medical School, Biotech II, 373 Plantation Street, Suite 318, Worcester, MA 01605, USA
| | - Jodi Skiles
- Indiana University School of Medicine, 705 Riley Hospital Drive, ROC Room 4340, Indianapolis, IN 46268, USA
| | - Emmanuel Koros
- College of Health Sciences, School of Medicine, Department of Medicine, Moi University, Eldoret, Kenya
| | - Fredrick Chite Asirwa
- Indiana University School of Medicine, 705 Riley Hospital Drive, ROC Room 4340, Indianapolis, IN 46268, USA.,College of Health Sciences, School of Medicine, Department of Medicine, Moi University, Eldoret, Kenya
| | - Naftali Busakhala
- College of Health Sciences, School of Medicine, Department of Medicine, Moi University, Eldoret, Kenya.,Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Patrick Loehrer
- Indiana University School of Medicine, 705 Riley Hospital Drive, ROC Room 4340, Indianapolis, IN 46268, USA
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Detecting Sex-Biased Gene Flow in African-Americans through the Analysis of Intra- and Inter-Population Variation at Mitochondrial DNA and Y- Chromosome Microsatellites. Balkan J Med Genet 2013; 15:7-14. [PMID: 24052726 PMCID: PMC3776662 DOI: 10.2478/bjmg-2013-0001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This study reports on variations at the mitochondrial DNA (mtDNA) hypervariable region 1 (HVR-1) and at seven Y-chromosome microsatellites in an African-American population sample from Chicago, IL, USA. Our results support the hypothesis that the population studied had undergone a European male-biased gene flow. We show that comparisons of intra-and inter-population diversity parameters between African-Americans, Europeans and Africans may help detect sex-biased gene flow, providing a complement to quantitative methods to estimate genetic admixture.
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Budenz DL, Barton K, Whiteside-de Vos J, Schiffman J, Bandi J, Nolan W, Herndon L, Kim H, Hay-Smith G, Tielsch JM. Prevalence of glaucoma in an urban West African population: the Tema Eye Survey. JAMA Ophthalmol 2013; 131:651-8. [PMID: 23538512 PMCID: PMC4139110 DOI: 10.1001/jamaophthalmol.2013.1686] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
IMPORTANCE Multiple studies have found an increased prevalence, younger age at onset, and more severe course of glaucoma in people of African descent, but these findings are based on studies conducted outside Africa. OBJECTIVE To determine the prevalence of glaucoma in an urban West African population of adults. DESIGN AND SETTING A population-based, cross-sectional study of adults 40 years and older conducted from September 1, 2006, through December 31, 2008, from 5 communities in Tema, Ghana. PARTICIPANTS Participants from randomly selected clusters underwent a screening examination that consisted of visual acuity, frequency doubling perimetry, applanation tonometry, and optic disc photography. Participants who failed any of these tests were referred for complete examination, including gonioscopy, standard automated perimetry, and stereoscopic optic disc photography. RESULTS A total of 6806 eligible participants were identified, and 5603 (82.3%) were enrolled in the study. The field examination referred 1869 participants (33.3%) to the clinic examination, and 1538 (82.2%) came for complete examination. A total of 362 participants were identified as having glaucoma of any type and category. Primary open-angle glaucoma was the underlying diagnosis in 342 participants (94.5%). The prevalence of primary open-angle glaucoma was 6.8% overall, increasing from 3.7% among those 40 to 49 years old to 14.6% among those 80 years and older, and was higher in men than in women in all age groups, with an overall male-female prevalence ratio of 1.5. Of the participants with glaucoma, 9 (2.5%) were blind using World Health Organization criteria, and only 12 (3.3%) were aware that they had glaucoma. CONCLUSIONS AND RELEVANCE The prevalence of glaucoma is higher in this urban West African population than in previous studies of people of East or South African and of non-African descent. Strategies to identify affected persons and effectively manage the burden of glaucoma are needed in West Africa.
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Affiliation(s)
- Donald L Budenz
- Department of Ophthalmology, Bascom Palmer Eye Institute, Miller School of Medicine, University of Miami, Department of Ophthalmology, Miami, FL, USA.
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Gómez-Pérez L, Alfonso-Sánchez MA, Dipierri JE, Sánchez D, Espinosa I, De Pancorbo MM, Peña JA. Young Alu insertions within the MHC class I region in native American populations: insights into the origin of the MHC-Alu repeats. Am J Hum Biol 2013; 25:359-65. [PMID: 23564323 DOI: 10.1002/ajhb.22377] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/17/2012] [Accepted: 01/07/2013] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Genetic heterogeneity of two Amerindian populations (Jujuy province, Argentina, and Waorani tribe, Ecuador) was characterized by analyzing data on polymorphic Alu insertions within the human major histocompatibility complex (MHC) class I region (6p21.31), which are completely nonexistent in Native Americans. We further evaluated the haplotype distribution and genetic diversity among continental ancestry groups and their potential implications for the dating of the origin of MHC-Alus. METHODS Five MHC-Alu elements (AluMicB, AluTF, AluHJ, AluHG, and AluHF) were typed in samples from Jujuy (N = 108) and Waorani (N = 36). Allele and haplotype frequency data on worldwide populations were compiled to explore spatial structuring of the MHC-Alu diversity through AMOVA tests. We utilized the median-joining network approach to illustrate the continental distribution of the MHC-Alu haplotypes and their phylogenetic relationships. RESULTS Allele and haplotype distributions differed significantly between Jujuy and Waorani. The Waorani featured a low average heterozygosity attributable to strong population isolation. Overall, Alu markers showed great genetic heterogeneity both within and among populations. The haplotype distribution was distinctive of each continental ancestry group. Contrary to expectations, Africans showed the lowest MHC-Alu diversity. CONCLUSIONS Genetic drift mainly associated to population bottlenecks seems to be reflected in the low MHC-Alu diversity of the Amerindians, mainly in Waorani. Geographical structuring of the haplotype distribution supports the efficiency of the MHC-Alu loci as lineage (ancestry) markers. The markedly low Alu diversity of African populations relative to other continental clusters suggests that these MHC-Alus might have arisen after the anatomically modern humans expanded out of Africa.
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Affiliation(s)
- Luis Gómez-Pérez
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, Spain
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Chen F, Chen GK, Stram DO, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Palmer JR, Hu JJ, Rebbeck TR, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Ruiz-Narvaez EA, Deming SL, Rodriguez-Gil JL, Demichele A, Chanock SJ, Blot W, Signorello L, Cai Q, Li G, Long J, Huo D, Zheng Y, Cox NJ, Olopade OI, Ogundiran TO, Adebamowo C, Nathanson KL, Domchek SM, Simon MS, Hennis A, Nemesure B, Wu SY, Leske MC, Ambs S, Hutter CM, Young A, Kooperberg C, Peters U, Rhie SK, Wan P, Sheng X, Pooler LC, Van Den Berg DJ, Le Marchand L, Kolonel LN, Henderson BE, Haiman CA. A genome-wide association study of breast cancer in women of African ancestry. Hum Genet 2013; 132:39-48. [PMID: 22923054 PMCID: PMC3749077 DOI: 10.1007/s00439-012-1214-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/31/2012] [Indexed: 01/30/2023]
Abstract
Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10(-6) and 10(-5) in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 × 10(-6); rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 × 10(-5)). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.
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Affiliation(s)
- Fang Chen
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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Scally A, Durbin R. Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet 2012; 13:745-53. [PMID: 22965354 DOI: 10.1038/nrg3295] [Citation(s) in RCA: 308] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is now possible to make direct measurements of the mutation rate in modern humans using next-generation sequencing. These measurements reveal a value that is approximately half of that previously derived from fossil calibration, and this has implications for our understanding of demographic events in human evolution and other aspects of population genetics. Here, we discuss the implications of a lower-than-expected mutation rate in relation to the timescale of human evolution.
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Blindness and visual impairment in an urban West African population: the Tema Eye Survey. Ophthalmology 2012; 119:1744-53. [PMID: 22677425 DOI: 10.1016/j.ophtha.2012.04.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022] Open
Abstract
OBJECTIVE To determine the prevalence, causes, and risk factors of blindness and visual impairment among persons aged 40 years or older residing in an urban West African location. DESIGN Population-based, cross-sectional study. PARTICIPANTS A total of 5603 participants residing in Tema, Ghana. METHODS Proportionate random cluster sampling was used to select participants aged 40 years or older living in the city of Tema. Presenting distance visual acuity (VA) was measured at 4 and 1 m using a reduced logarithm of the minimum angle of resolution tumbling E chart and then with trial frame based on autorefraction. A screening examination was performed in the field on all participants. Complete clinical examination by an ophthalmologist was performed on participants with best-corrected visual acuity (BCVA) <20/40 or failure of any screening test. MAIN OUTCOME MEASURES Age- and gender-specific prevalence, causes, and risk factors for blindness (VA of <20/400 in the better eye, World Health Organization definition) and visual impairment (VA of <20/40 in the better eye). RESULTS A total of 6806 eligible participants were identified, of whom 5603 (82.3%) participated in the study. The mean age (± standard deviation) of participants was 52.7 ± 1 0.9 years. The prevalence of visual impairment and blindness was 17.1% and 1.2%, respectively. After refraction and spectacle correction, the prevalence of visual impairment and blindness decreased to 6.7% and 0.75%, respectively, suggesting that refractive error is the major correctable cause of visual impairment and blindness in this population. Of 65 subjects with a VA <20/400, 22 (34%) were correctable with refraction, 21 to the level of visual impairment and 1 to normal. The remaining 43 patients (66%) had underlying pathology (cataract in 19, glaucoma in 9, nonglaucomatous optic neuropathy in 3, corneal opacities in 3, retinal disease in 3, and undetermined in 5) that prevented refractive correction. Increased age was a significant risk factor for blindness and visual impairment. CONCLUSIONS There is a high prevalence of blindness and visual impairment among those aged ≥ 40 years in Tema, Ghana, West Africa. Refractive error is a major cause of blindness and visual impairment in this population, followed by cataract, glaucoma, and corneal disease.
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Blome MW, Cohen AS, Tryon CA, Brooks AS, Russell J. The environmental context for the origins of modern human diversity: A synthesis of regional variability in African climate 150,000–30,000 years ago. J Hum Evol 2012; 62:563-92. [DOI: 10.1016/j.jhevol.2012.01.011] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 12/02/2011] [Accepted: 01/24/2012] [Indexed: 11/27/2022]
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Kempińska-Podhorodecka A, Knap O, Drozd A, Kaczmarczyk M, Parafiniuk M, Parczewski M, Ciechanowicz A. Analysis for genotyping Duffy blood group in inhabitants of Sudan, the fourth cataract of the Nile. Malar J 2012; 11:115. [PMID: 22510366 PMCID: PMC3375187 DOI: 10.1186/1475-2875-11-115] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/17/2012] [Indexed: 01/03/2023] Open
Abstract
Background Genetic polymophisms of the Duffy antigen receptor for the chemokines (DARC) gene successfully protected against blood stage infection by Plasmodium vivax infection. The Fy (a-, b-) phenotype is predominant among African populations, particularly those originating from West Africa, and it is rare among non-African populations. The aim of this study was to analyse the frequency of four Duffy blood groups based on SNPs (T-33C, G125A, G298A and C5411T) in two local tribes of Sudanese Arabs, the Shagia and Manasir, which are both from the region of the Fourth Nile cataract in Sudan. Methods An analysis of polymorphisms was performed on 217 individuals (126 representatives of the Shagia tribe and 91 of the Manasir). Real-time PCR and TaqMan Genotyping Assays were used to study the prevalence of alleles and genotypes. Results The analysis of allelic and genotype frequency in the T-33C polymorphisms demonstrated a significant dominance of the C allele and CC genotype (OR = 0.53 [0.32-0.88]; p = 0.02) in both tribes. The G125A polymorphism is associated with phenotype Fy(a-, b-) and was identified in 83% of Shagia and 77% of Manasir. With regard to G298A polymorphisms, the genotype frequencies were different between the tribes (p = 0,002) and no single AA homozygote was found. Based on four SNPs examined, 20 combinations of genotypes for the Shagia and Manasir tribes were determined. The genotype CC/AA/GG/CT occurred most often in Shagia tribe (45.9%) but was rare in the Manasir tribe (6.6%) (p < 0.001 Shagia versus Manasir). The FY*AES allele was identified in both analysed tribes. The presence of individuals with the FY*A/FY*A genotype was demonstrated only in the Shagia tribe. Conclusion This is probably the first report showing genotypically Duffy-negative people who carry both FY*BES and FY*AES. The identification of the FY*AES allele in both tribes may be due to admixture of the non-African genetic background. Taken as a whole, allele and genotype frequencies between the Shagia and the Manasir were statistically different. However, the presence of individuals with the FY*A/FY*A genotype was demonstrated only in the Shagia tribe.
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Torres JB, Doura MB, Keita SOY, Kittles RA. Y chromosome lineages in men of west African descent. PLoS One 2012; 7:e29687. [PMID: 22295064 PMCID: PMC3266241 DOI: 10.1371/journal.pone.0029687] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/01/2011] [Indexed: 11/19/2022] Open
Abstract
The early African experience in the Americas is marked by the transatlantic slave trade from ∼1619 to 1850 and the rise of the plantation system. The origins of enslaved Africans were largely dependent on European preferences as well as the availability of potential laborers within Africa. Rice production was a key industry of many colonial South Carolina low country plantations. Accordingly, rice plantations owners within South Carolina often requested enslaved Africans from the so-called "Grain Coast" of western Africa (Senegal to Sierra Leone). Studies on the African origins of the enslaved within other regions of the Americas have been limited. To address the issue of origins of people of African descent within the Americas and understand more about the genetic heterogeneity present within Africa and the African Diaspora, we typed Y chromosome specific markers in 1,319 men consisting of 508 west and central Africans (from 12 populations), 188 Caribbeans (from 2 islands), 532 African Americans (AAs from Washington, DC and Columbia, SC), and 91 European Americans. Principal component and admixture analyses provide support for significant Grain Coast ancestry among African American men in South Carolina. AA men from DC and the Caribbean showed a closer affinity to populations from the Bight of Biafra. Furthermore, 30-40% of the paternal lineages in African descent populations in the Americas are of European ancestry. Diverse west African ancestries and sex-biased gene flow from EAs has contributed greatly to the genetic heterogeneity of African populations throughout the Americas and has significant implications for gene mapping efforts in these populations.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Menahem B. Doura
- Department of Pharmacology and Physiology, George Washington University, Washington, District of Columbia, United States of America
| | - Shomarka O. Y. Keita
- National Human Genome Center, Howard University, Washington, District of Columbia, United States of America
| | - Rick A. Kittles
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Institute of Human Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Genotype imputation with thousands of genomes. G3-GENES GENOMES GENETICS 2011; 1:457-70. [PMID: 22384356 PMCID: PMC3276165 DOI: 10.1534/g3.111.001198] [Citation(s) in RCA: 716] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 09/19/2011] [Indexed: 12/22/2022]
Abstract
Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package.
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Harvati K, Stringer C, Grün R, Aubert M, Allsworth-Jones P, Folorunso CA. The Later Stone Age calvaria from Iwo Eleru, Nigeria: morphology and chronology. PLoS One 2011; 6:e24024. [PMID: 21949689 PMCID: PMC3174138 DOI: 10.1371/journal.pone.0024024] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/04/2011] [Indexed: 12/04/2022] Open
Abstract
Background In recent years the Later Stone Age has been redated to a much deeper time depth than previously thought. At the same time, human remains from this time period are scarce in Africa, and even rarer in West Africa. The Iwo Eleru burial is one of the few human skeletal remains associated with Later Stone Age artifacts in that region with a proposed Pleistocene date. We undertook a morphometric reanalysis of this cranium in order to better assess its affinities. We also conducted Uranium-series dating to re-evaluate its chronology. Methodology/Principal Findings A 3-D geometric morphometric analysis of cranial landmarks and semilandmarks was conducted using a large comparative fossil and modern human sample. The measurements were collected in the form of three dimensional coordinates and processed using Generalized Procrustes Analysis. Principal components, canonical variates, Mahalanobis D2 and Procrustes distance analyses were performed. The results were further visualized by comparing specimen and mean configurations. Results point to a morphological similarity with late archaic African specimens dating to the Late Pleistocene. A long bone cortical fragment was made available for U-series analysis in order to re-date the specimen. The results (∼11.7–16.3 ka) support a terminal Pleistocene chronology for the Iwo Eleru burial as was also suggested by the original radiocarbon dating results and by stratigraphic evidence. Conclusions/Significance Our findings are in accordance with suggestions of deep population substructure in Africa and a complex evolutionary process for the origin of modern humans. They further highlight the dearth of hominin finds from West Africa, and underscore our real lack of knowledge of human evolution in that region.
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Affiliation(s)
- Katerina Harvati
- Paleoanthropology, Senckenberg Center for Human Evolution and Paleoecology, Eberhard Karls Universität Tübingen, Tübingen, Germany.
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Winkler C. Is there a genetic basis for health disparities in human immunodeficiency virus disease? ACTA ACUST UNITED AC 2011; 77:149-59. [PMID: 20309925 DOI: 10.1002/msj.20172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The highest global prevalence rates for human immunodeficiency virus and acquired immune deficiency syndrome have been recorded in southern Africa; in the United States, individuals of African descent are disproportionately affected by human immunodeficiency virus infection. Human immunodeficiency virus-infected individuals with African ancestry are also estimated to have a 17-fold or greater risk for developing human immunodeficiency virus-associated nephropathy in comparison with their counterparts of non-African descent. Several recent studies have implicated genetic alleles that are more frequent in populations of African descent and increase the risk of human immunodeficiency virus infection and the risk of human immunodeficiency virus-associated neuropathy (HIVAN). The supposition that persons of African descent are more susceptible to human immunodeficiency virus infection because of an underlying genetic predisposition is not supported by available evidence. However, strong, replicated data show that the increased risk for human immunodeficiency virus-associated nephropathy, as well as other major forms of kidney disease in individuals of African descent, is due in part to MYH9 (myosin, heavy chain 9, non-muscle) renal disease susceptibility alleles that are very frequent throughout sub-Saharan Africa but are infrequent or absent in non-Africans. Selection, drift, and demographic events shape the allelic architecture of the human genome: it is expected that these events will be reflected in geographic-specific differentiation in allele frequencies for a small subset of alleles that may be associated with either increased or reduced risk for complex and infectious diseases.
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Affiliation(s)
- Cheryl Winkler
- Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD, USA.
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Beyin A. Upper Pleistocene Human Dispersals out of Africa: A Review of the Current State of the Debate. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:615094. [PMID: 21716744 PMCID: PMC3119552 DOI: 10.4061/2011/615094] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/22/2011] [Accepted: 02/24/2011] [Indexed: 12/31/2022]
Abstract
Although there is a general consensus on African origin of early modern humans, there is disagreement about how and when they dispersed to Eurasia. This paper reviews genetic and Middle Stone Age/Middle Paleolithic archaeological literature from northeast Africa, Arabia, and the Levant to assess the timing and geographic backgrounds of Upper Pleistocene human colonization of Eurasia. At the center of the discussion lies the question of whether eastern Africa alone was the source of Upper Pleistocene human dispersals into Eurasia or were there other loci of human expansions outside of Africa? The reviewed literature hints at two modes of early modern human colonization of Eurasia in the Upper Pleistocene: (i) from multiple Homo sapiens source populations that had entered Arabia, South Asia, and the Levant prior to and soon after the onset of the Last Interglacial (MIS-5), (ii) from a rapid dispersal out of East Africa via the Southern Route (across the Red Sea basin), dating to ~74–60 kya.
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Affiliation(s)
- Amanuel Beyin
- Turkana Basin Institute, Stony Brook University, SBS Building 5th Floor, Stony Brook, NY 11794, USA
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CYP1A2 is more variable than previously thought: a genomic biography of the gene behind the human drug-metabolizing enzyme. Pharmacogenet Genomics 2010; 20:647-64. [DOI: 10.1097/fpc.0b013e32833e90eb] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wang Z, Hildesheim A, Wang SS, Herrero R, Gonzalez P, Burdette L, Hutchinson A, Thomas G, Chanock SJ, Yu K. Genetic admixture and population substructure in Guanacaste Costa Rica. PLoS One 2010; 5:e13336. [PMID: 20967209 PMCID: PMC2954167 DOI: 10.1371/journal.pone.0013336] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 08/23/2010] [Indexed: 11/20/2022] Open
Abstract
The population of Costa Rica (CR) represents an admixture of major continental populations. An investigation of the CR population structure would provide an important foundation for mapping genetic variants underlying common diseases and traits. We conducted an analysis of 1,301 women from the Guanacaste region of CR using 27,904 single nucleotide polymorphisms (SNPs) genotyped on a custom Illumina InfiniumII iSelect chip. The program STRUCTURE was used to compare the CR Guanacaste sample with four continental reference samples, including HapMap Europeans (CEU), East Asians (JPT+CHB), West African Yoruba (YRI), as well as Native Americans (NA) from the Illumina iControl database. Our results show that the CR Guanacaste sample comprises a three-way admixture estimated to be 43% European, 38% Native American and 15% West African. An estimated 4% residual Asian ancestry may be within the error range. Results from principal components analysis reveal a correlation between genetic and geographic distance. The magnitude of linkage disequilibrium (LD) measured by the number of tagging SNPs required to cover the same region in the genome in the CR Guanacaste sample appeared to be weaker than that observed in CEU, JPT+CHB and NA reference samples but stronger than that of the HapMap YRI sample. Based on the clustering pattern observed in both STRUCTURE and principal components analysis, two subpopulations were identified that differ by approximately 20% in LD block size averaged over all LD blocks identified by Haploview. We also show in a simulated association study conducted within the two subpopulations, that the failure to account for population stratification (PS) could lead to a noticeable inflation in the false positive rate. However, we further demonstrate that existing PS adjustment approaches can reduce the inflation to an acceptable level for gene discovery.
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Affiliation(s)
- Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, SAIC Frederick, Inc., National Cancer Institute - Frederick, Frederick, Maryland, United States of America
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Sophia S. Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Division of Etiology, Department of Population Sciences, Beckman Research Institute and the City of Hope, Duarte, California, United States of America
| | | | - Paula Gonzalez
- Proyecto Epidemiologico Guanacaste, San Jose, Costa Rica
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, SAIC Frederick, Inc., National Cancer Institute - Frederick, Frederick, Maryland, United States of America
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, SAIC Frederick, Inc., National Cancer Institute - Frederick, Frederick, Maryland, United States of America
| | - Gilles Thomas
- Synergie-Lyon-Cancer, Universite Lyon 1, Lyon, France
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
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Campbell MC, Tishkoff SA. The evolution of human genetic and phenotypic variation in Africa. Curr Biol 2010; 20:R166-73. [PMID: 20178763 DOI: 10.1016/j.cub.2009.11.050] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.
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Affiliation(s)
- Michael C Campbell
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Lambert CA, Tishkoff SA. Genetic structure in African populations: implications for human demographic history. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2010; 74:395-402. [PMID: 20453204 DOI: 10.1101/sqb.2009.74.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The continent of Africa is the source of all anatomically modern humans that dispersed across the planet during the past 100,000 years. As such, African populations are characterized by high genetic diversity and low levels of linkage disequilibrium (LD) among loci, as compared to populations from other continents. African populations also possess a number of genetic adaptations that have evolved in response to the diverse climates, diets, geographic environments, and infectious agents that characterize the African continent. Recently, Tishkoff et al. (2009) performed a genome-wide analysis of substructure based on DNA from 2432 Africans from 121 geographically diverse populations. The authors analyzed patterns of variation at 1327 nuclear microsatellite and insertion/deletion markers and identified 14 ancestral population clusters that correlate well with self-described ethnicity and shared cultural or linguistic properties. The results suggest that African populations may have maintained a large and subdivided population structure throughout much of their evolutionary history. In this chapter, we synthesize recent work documenting evidence of African population structure and discuss the implications for inferences about evolutionary history in both African populations and anatomically modern humans as a whole.
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Affiliation(s)
- C A Lambert
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Abstract
Despite the widespread study of genetic variation in admixed human populations, such as African-Americans, there has not been an evaluation of the effects of recent admixture on patterns of polymorphism or inferences about population demography. These issues are particularly relevant because estimates of the timing and magnitude of population growth in Africa have differed among previous studies, some of which examined African-American individuals. Here we use simulations and single-nucleotide polymorphism (SNP) data collected through direct resequencing and genotyping to investigate these issues. We find that when estimating the current population size and magnitude of recent growth in an ancestral population using the site frequency spectrum (SFS), it is possible to obtain reasonably accurate estimates of the parameters when using samples drawn from the admixed population under certain conditions. We also show that methods for demographic inference that use haplotype patterns are more sensitive to recent admixture than are methods based on the SFS. The analysis of human genetic variation data from the Yoruba people of Ibadan, Nigeria and African-Americans supports the predictions from the simulations. Our results have important implications for the evaluation of previous population genetic studies that have considered African-American individuals as a proxy for individuals from West Africa as well as for future population genetic studies of additional admixed populations.
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