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Litz Philipsborn S, Hartmajer S, Shtorch Asor A, Vinovezky M, Regev M, Singer A, Reinstein E. A founder mutation in TCTN2 causes Meckel-Gruber syndrome type 8 among Jews of Ethiopian and Yemenite origin. Am J Med Genet A 2021; 185:1610-1613. [PMID: 33590725 DOI: 10.1002/ajmg.a.62119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/18/2021] [Accepted: 01/24/2021] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | - Mika Vinovezky
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel
| | - Miriam Regev
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Israel
| | - Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Eyal Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel.,Sackler School of Medicine, Tel Aviv University, Israel
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Kelemu T, Erlandsson L, Seifu D, Hansson E, Abebe M, Teklu S, Girma S, Traherne JA, Moffett A, Hansson SR. Polymorphism in killer cell immunoglobulin-like receptors and human leukocyte antigen-c and predisposition to preeclampsia in Ethiopian pregnant women population. J Reprod Immunol 2020; 141:103169. [PMID: 32603992 DOI: 10.1016/j.jri.2020.103169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/29/2020] [Accepted: 06/15/2020] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Preeclampsia (PE) is a human specific pregnancy-related syndrome of unknown etiology that affects 2-8 % of pregnancies. Polymorphism in maternal Killer Cell Immunoglobulin-like Receptors (KIRs) and the ligand fetal Human Leukocyte Antigen-C (HLA-C) may predispose pregnant mothers for PE due to defective trophoblast invasion into the maternal decidua. Our study aimed to investigate the association between maternal KIR and fetal HLA-C polymorphism and PE in Ethiopian pregnant women. METHODS We included a total of 288 (157 controls and 131 PE cases) in a case-controls study at Adama Regional Referral Hospital, Ethiopia. The KIR and HLA-C genotyping was done using traditional polymerase chain reaction on genomic DNA extracted form maternal venous and cord blood followed by 2% agarose gel electrophoresis. RESULTS The statistical associations between variables were evaluated using Pearson's Chi-square test. P < 0.05, with 95 % confidence interval was considered statistically significant. A significant association was observed between the KIR2DS1 and PE, with a higher frequency (60.5 %) of the gene in the control group. Similarly, a significant association was observed between KIR AA genotype and PE, with a higher frequency (38.2 %) of this genotype in the PE group. Ethiopians share the same risk genotype for PE as seen in previous African and European studies, namely homozygosity of a maternal KIR AA genotype. However, Ethiopians differ from other East African populations by sharing the same protective KIR2DS1 gene as Europeans.
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Affiliation(s)
- Tsehayneh Kelemu
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, Ethiopia.
| | - Lena Erlandsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Sweden.
| | - Daniel Seifu
- Department of Biochemistry, College of Health Sciences, Addis Ababa University, Ethiopia; Department of Biochemistry, Division of Biomedical Sciences, University of Global Health Equity, Rwanda.
| | - Eva Hansson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Sweden.
| | | | - Sisay Teklu
- Department of Obstetrics and Gynecology, College of Health Sciences, Addis Ababa University, Ethiopia.
| | - Selfu Girma
- Armauer Hanson Research Institute, Ethiopia.
| | - James A Traherne
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Stefan R Hansson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences Lund, Lund University, Sweden.
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3
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Kiros YK, Elinav H, Gebreyesus A, Gebremeskel H, Azar J, Chemtob D, Abreha H, Elbirt D, Shahar E, Chowers M, Turner D, Grossman Z, Haile A, Sutton RE, Maayan SL, Wolday D. Identification and characterization of HIV positive Ethiopian elite controllers in both Africa and Israel. HIV Med 2019; 20:33-37. [PMID: 30318718 PMCID: PMC6510948 DOI: 10.1111/hiv.12680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVES HIV elite controllers (ECs) are a unique subgroup of HIV-positive patients who are long-term virologically suppressed in the absence of antiretroviral treatment (ART). The prevalence of this subgroup is estimated to be < 1%. Various cohorts of ECs have been described in developed countries, most of which have been demographically heterogeneous. The aim of this study was to identify ECs in two large African cohorts and to estimate their prevalence in a relatively genetically homogenous population. METHODS We screened two cohorts of HIV-positive Ethiopian patients. The first cohort resided in Mekelle, Ethiopia. The second was comprised of HIV-positive Ethiopian immigrants in Israel. In the Mekelle cohort, ART-naïve subjects with stable CD4 counts were prospectively screened using two measurements of viral load 6 months apart. Subjects were defined as ECs when both measurements were undetectable. In the Israeli cohort, subjects with consistently undetectable viral loads (mean of 17 viral load measurements/patient) and stable CD4 count > 500 cells/μL were defined as ECs. RESULTS In the Mekelle cohort, 16 of 9515 patients (0.16%) fitted the definition of EC, whereas seven of 1160 (0.6%) in the Israeli cohort were identified as ECs (P = 0.011). CONCLUSIONS This is the first large-scale screening for HIV-positive ECs to be performed in entirely African cohorts. The overall prevalence of ECs is within the range of that previously described in developing countries. The significant difference in prevalence between the two cohorts of similar genetic background is probably a consequence of selection bias but warrants further investigation into possible environmental factors which may underlie the EC state.
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Affiliation(s)
- Y K Kiros
- Mekelle University College of Health Sciences, Mekelle, Tigray, Ethiopia
| | - H Elinav
- Clinical Microbiology and Infectious Diseases Department, Hadassah University Medical Center, Jerusalem, Israel
| | - A Gebreyesus
- Mekelle University College of Health Sciences, Mekelle, Tigray, Ethiopia
| | - H Gebremeskel
- Mekelle University College of Health Sciences, Mekelle, Tigray, Ethiopia
| | - J Azar
- Internal Medicine Division, Hadassah University Medical Center, Jerusalem, Israel
| | - D Chemtob
- Department of Tuberculosis and AIDS, Ministry of Health, Jerusalem, Israel
| | - H Abreha
- Mekelle University College of Health Sciences, Mekelle, Tigray, Ethiopia
| | - D Elbirt
- The Allergy, Clinical Immunology and AIDS Unit, Kaplan Medical Center, Rehovot, Israel
| | - E Shahar
- Institute of Allergy, Immunology and AIDS Rambam Medical Center, Haifa, Israel
| | - M Chowers
- Infectious Diseases Unit, Meir Medical Center, Kfar Saba, Israel
| | - D Turner
- Crusaid Kobler AIDS Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Z Grossman
- Clinical Microbiology and Infectious Diseases Department, Hadassah University Medical Center, Jerusalem, Israel
| | - A Haile
- Mekelle University College of Health Sciences, Mekelle, Tigray, Ethiopia
| | - R E Sutton
- Division of Infectious Diseases, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - S L Maayan
- Division of Infectious Diseases, Barzilai Medical Center, Ashkelon, Israel
| | - D Wolday
- Mekelle University College of Health Sciences, Mekelle, Tigray, Ethiopia
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4
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Mekonnen E, Bekele E, Stein CM. Novel polymorphisms in TICAM2 and NOD1 associated with tuberculosis progression phenotypes in Ethiopian populations. Glob Health Epidemiol Genom 2018; 3:e1. [PMID: 29868226 PMCID: PMC5870410 DOI: 10.1017/gheg.2017.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Infection by Mycobacterium tuberculosis (Mtb) is a necessary but not sufficient cause for tuberculosis (TB). Although numerous studies suggest human genetic variation may influence TB pathogenesis, there is a conspicuous lack of replication, likely due to imprecise phenotype definition. We aimed to replicate novel findings from a Ugandan cohort in Ethiopian populations. METHOD We ascertained TB cases and household controls (n = 292) from three different ethnic groups. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of TICAM2 and NOD1. RESULT Significant novel associations were observed between two variants in NOD1 and TB: rs751770147 [unadjusted p = 7.28 × 10-5] and chr7:30477156(T), a novel variant, [unadjusted p = 1.04 × 10-4]. Two SNPs in TICAM2 were nominally associated with TB, including rs2288384 [unadjusted p = 0.003]. Haplotype-based association tests supported the SNP-based results. CONCLUSION We replicated the association of TICAM2 and NOD1 with TB and identified novel genetic associations with TB in Ethiopian populations.
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Affiliation(s)
- E. Mekonnen
- Microbial, Cellular, Molecular Biology Department, Addis Ababa University, P.O.Box:17087, Addis Ababa, Ethiopia
- Health Biotechnology Department, Institute of Biotechnology, Addis Ababa University, P.O.Box:17087, Addis Ababa, Ethiopia
| | - E. Bekele
- Microbial, Cellular, Molecular Biology Department, Addis Ababa University, Ethiopia
| | - C. M. Stein
- Department of Population & Quantitative Health Sciences, Center for Proteomics & Bioinformatics, and Tuberculosis Research Unit, Case Western Reserve University, USA
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5
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Genetic portrait of Jewish populations based on three sets of X-chromosome markers: Indels, Alu insertions and STRs. Forensic Sci Int Genet 2017; 31:e5-e11. [DOI: 10.1016/j.fsigen.2017.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/25/2017] [Accepted: 09/12/2017] [Indexed: 12/19/2022]
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Berg S, Schelling E, Hailu E, Firdessa R, Gumi B, Erenso G, Gadisa E, Mengistu A, Habtamu M, Hussein J, Kiros T, Bekele S, Mekonnen W, Derese Y, Zinsstag J, Ameni G, Gagneux S, Robertson BD, Tschopp R, Hewinson G, Yamuah L, Gordon SV, Aseffa A. Investigation of the high rates of extrapulmonary tuberculosis in Ethiopia reveals no single driving factor and minimal evidence for zoonotic transmission of Mycobacterium bovis infection. BMC Infect Dis 2015; 15:112. [PMID: 25886866 PMCID: PMC4359574 DOI: 10.1186/s12879-015-0846-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/19/2015] [Indexed: 11/14/2022] Open
Abstract
Background Ethiopia, a high tuberculosis (TB) burden country, reports one of the highest incidence rates of extra-pulmonary TB dominated by cervical lymphadenitis (TBLN). Infection with Mycobacterium bovis has previously been excluded as the main reason for the high rate of extrapulmonary TB in Ethiopia. Methods Here we examined demographic and clinical characteristics of 953 pulmonary (PTB) and 1198 TBLN patients visiting 11 health facilities in distinct geographic areas of Ethiopia. Clinical characteristics were also correlated with genotypes of the causative agent, Mycobacterium tuberculosis. Results No major patient or bacterial strain factor could be identified as being responsible for the high rate of TBLN, and there was no association with HIV infection. However, analysis of the demographic data of involved patients showed that having regular and direct contact with live animals was more associated with TBLN than with PTB, although no M. bovis was isolated from patients with TBLN. Among PTB patients, those infected with Lineage 4 reported “contact with other TB patient” more often than patients infected with Lineage 3 did (OR = 1.6, CI 95% 1.0-2.7; p = 0.064). High fever, in contrast to low and moderate fever, was significantly associated with Lineage 4 (OR = 2.3; p = 0.024). On the other hand, TBLN cases infected with Lineage 4 tended to get milder symptoms overall for the constitutional symptoms than those infected with Lineage 3. Conclusions The study suggests a complex role for multiple interacting factors in the epidemiology of extrapulmonary TB in Ethiopia, including factors that can only be derived from population-based studies, which may prove to be significant for TB control in Ethiopia. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-0846-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Berg
- Animal and Plant Health Agency, TB Research Group, New Haw, Addlestone, Surrey, KT15 3NB, UK.
| | - Esther Schelling
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Elena Hailu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Rebuma Firdessa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia. .,University of Würzburg, Institute for Molecular Infection Biology, Würzburg, Germany.
| | - Balako Gumi
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Girume Erenso
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Endalamaw Gadisa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Araya Mengistu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Meseret Habtamu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Jemal Hussein
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Teklu Kiros
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Shiferaw Bekele
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Wondale Mekonnen
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Yohannes Derese
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia.
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Brian D Robertson
- Center for Molecular Bacteriology and Infection, Department of Medicine, Flowers building, South Kensington, Imperial College London, London, SW7 2AZ, UK.
| | - Rea Tschopp
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia. .,University of Basel, Basel, Switzerland.
| | - Glyn Hewinson
- Animal and Plant Health Agency, TB Research Group, New Haw, Addlestone, Surrey, KT15 3NB, UK.
| | - Lawrence Yamuah
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Stephen V Gordon
- UCD Schools of Veterinary Medicine, Medicine and Medical Science, Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, Dublin, Republic of Ireland.
| | - Abraham Aseffa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
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Labuda D, Yotova V, Lefebvre JF, Moreau C, Utermann G, Williams SM. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations. PLoS One 2013; 8:e80710. [PMID: 24282552 PMCID: PMC3839994 DOI: 10.1371/journal.pone.0080710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/07/2013] [Indexed: 01/04/2023] Open
Abstract
The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ∼500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.
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Affiliation(s)
- Damian Labuda
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
| | - Vania Yotova
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-François Lefebvre
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Claudia Moreau
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Gerd Utermann
- Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Scott M. Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
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Pagani L, Kivisild T, Tarekegn A, Ekong R, Plaster C, Gallego Romero I, Ayub Q, Mehdi S, Thomas M, Luiselli D, Bekele E, Bradman N, Balding D, Tyler-Smith C. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am J Hum Genet 2012; 91:83-96. [PMID: 22726845 DOI: 10.1016/j.ajhg.2012.05.015] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 05/03/2012] [Accepted: 05/21/2012] [Indexed: 12/30/2022] Open
Abstract
Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ~3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ~60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.
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Yotova V, Lefebvre JF, Moreau C, Gbeha E, Hovhannesyan K, Bourgeois S, Bédarida S, Azevedo L, Amorim A, Sarkisian T, Avogbe PH, Chabi N, Dicko MH, Kou' Santa Amouzou ES, Sanni A, Roberts-Thomson J, Boettcher B, Scott RJ, Labuda D. An X-linked haplotype of Neandertal origin is present among all non-African populations. Mol Biol Evol 2011; 28:1957-62. [PMID: 21266489 DOI: 10.1093/molbev/msr024] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recent work on the Neandertal genome has raised the possibility of admixture between Neandertals and the expanding population of Homo sapiens who left Africa between 80 and 50 Kya (thousand years ago) to colonize the rest of the world. Here, we provide evidence of a notable presence (9% overall) of a Neandertal-derived X chromosome segment among all contemporary human populations outside Africa. Our analysis of 6,092 X-chromosomes from all inhabited continents supports earlier contentions that a mosaic of lineages of different time depths and different geographic provenance could have contributed to the genetic constitution of modern humans. It indicates a very early admixture between expanding African migrants and Neandertals prior to or very early on the route of the out-of-Africa expansion that led to the successful colonization of the planet.
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Affiliation(s)
- Vania Yotova
- Research Center, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
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10
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Listman JB, Hasin D, Kranzler HR, Malison RT, Mutirangura A, Sughondhabirom A, Aharonovich E, Spivak B, Gelernter J. Identification of population substructure among Jews using STR markers and dependence on reference populations included. BMC Genet 2010; 11:48. [PMID: 20546593 PMCID: PMC2896335 DOI: 10.1186/1471-2156-11-48] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 06/14/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detecting population substructure is a critical issue for association studies of health behaviors and other traits. Whether inherent in the population or an artifact of marker choice, determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Jewish populations, among which association studies are often conducted, have a known history of migrations. As a necessary step in understanding population structure to conduct valid association studies of health behaviors among Israeli Jews, we investigated genetic signatures of this history and quantified substructure to facilitate future investigations of these phenotypes in this population. RESULTS Using 32 autosomal STR markers and the program STRUCTURE, we differentiated between Ashkenazi (AJ, N = 135) and non-Ashkenazi (NAJ, N = 226) Jewish populations in the form of Northern and Southern geographic genetic components (AJ north 73%, south 23%, NAJ north 33%, south 60%). The ability to detect substructure within these closely related populations using a small STR panel was contingent on including additional samples representing major continental populations in the analyses. CONCLUSIONS Although clustering programs such as STRUCTURE are designed to assign proportions of ancestry to individuals without reference population information, when Jewish samples were analyzed in the absence of proxy parental populations, substructure within Jews was not detected. Generally, for samples with a given grandparental country of birth, STRUCTURE assignment values to Northern, Southern, African and Asian clusters agreed with mitochondrial DNA and Y-chromosomal data from previous studies as well as historical records of migration and intermarriage.
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Affiliation(s)
- Jennifer B Listman
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Deborah Hasin
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, NY, USA
- New York State Psychiatric Institute, NY, USA
- Dept Epidemiology, Mailman School of Public Health, Columbia University, NY, USA
| | - Henry R Kranzler
- Departments of Psychiatry and Genetics and Developmental Biology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Robert T Malison
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
| | | | | | - Efrat Aharonovich
- Department of Psychiatry, Columbia University College of Physicians and Surgeons, NY, USA
| | - Baruch Spivak
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA
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11
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Sex and CYP3A5 genotype influence total CYP3A activity: high CYP3A activity and a unique distribution of CYP3A5 variant alleles in Ethiopians. THE PHARMACOGENOMICS JOURNAL 2010; 11:130-7. [PMID: 20231858 DOI: 10.1038/tpj.2010.16] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The objectives of the this study were to assess the influence of CYP3A5 genotype and sex on the variability in total CYP3A activity and to compare 4β-hydroxycholesterol and omeprazole sulfoxidation as phenotypic markers for CYP3A activity in Ethiopians. Healthy subjects (n=150) were genotyped for CYP3A5*3, *6 and *7 using allele-specific PCR and Taqman genotyping assays. Plasma levels of 4β-hydroxycholesterol, 3 h post-dose omeprazole and omeprazole sulfone, were determined by gas chromatography-mass spectrometry and high performance liquid chromatography, respectively. The frequency of CYP3A5*1, *3, *6 and *7 was 20.5, 67.3, 12.2 and 0%, respectively. The mean plasma 4β-hydroxycholesterol level was 35.4 ng ml⁻¹. The mean 4β-hydroxycholesterol level (P=0.0001) and the 4β-hydroxycholesterol/cholesterol ratio (P=0.004) were higher in women than in men. CYP3A5 genotype significantly correlated with the plasma 4β-hydroxycholesterol concentration (P=0.003) and 4β-hydroxycholesterol/cholesterol ratio (P=0.0002). The omeprazole/omeprazole sulfone ratio was significantly correlated with 4β-hydroxycholesterol and 4β-hydroxycholesterol/cholesterol ratio in CYP3A5*0/*0 genotypes but not in individuals carrying the CYP3A5*1 allele. No correlation of omeprazole/omeprazole sulfone ratio with sex or CYP3A5 genotype was observed. A clear gene-dose effect implies plasma 4β-hydroxycholesterol level as a useful endogenous biomarker for total CYP3A activity (CYP3A5 plus CYP3A4) whereas the omeprazole/omeprazole sulfone ratio reflects mainly CYP3A4 activity. Sex and CYP3A5 genotype influence total CYP3A activity. Ethiopians display high total CYP3A activity and a unique distribution of CYP3A5 variant alleles not described hitherto.
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12
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Bourgeois S, Yotova V, Wang S, Bourtoumieu S, Moreau C, Michalski R, Moisan JP, Hill K, Hurtado AM, Ruiz-Linares A, Labuda D. X-chromosome lineages and the settlement of the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 140:417-28. [PMID: 19425105 DOI: 10.1002/ajpa.21084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Most genetic studies on the origins of Native Americans have examined data from mtDNA and Y-chromosome DNA. To complement these studies and to broaden our understanding of the origin of Native American populations, we present an analysis of 1,873 X-chromosomes representing Native American (n = 438) and other continental populations (n = 1,435). We genotyped 36 polymorphic sites, forming an informative haplotype within an 8-kb DNA segment spanning exon 44 of the dystrophin gene. The data reveal continuity from a common Eurasian ancestry between Europeans, Siberians, and Native Americans. However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians, we also observe a signal of a differentiated ancestry of southern and northern populations that cannot be simply explained by the serial southward dilution of genetic diversity. It is possible that the distribution of X-chromosome lineages reflects the genetic structure of the population of Beringia, itself issued from founder effects and a source of subsequent southern colonization(s).
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Affiliation(s)
- Stephane Bourgeois
- Centre de Recherche de l'Hôpital Sainte-Justine, Montréal, QC H3T 1C5, Canada
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Poloni ES, Naciri Y, Bucho R, Niba R, Kervaire B, Excoffier L, Langaney A, Sanchez-Mazas A. Genetic evidence for complexity in ethnic differentiation and history in East Africa. Ann Hum Genet 2009; 73:582-600. [PMID: 19706029 DOI: 10.1111/j.1469-1809.2009.00541.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Afro-Asiatic and Nilo-Saharan language families come into contact in Western Ethiopia. Ethnic diversity is particularly high in the South, where the Nilo-Saharan Nyangatom and the Afro-Asiatic Daasanach dwell. Despite their linguistic differentiation, both populations rely on a similar agripastoralist mode of subsistence. Analysis of mitochondrial DNA extracted from Nyangatom and Daasanach archival sera revealed high levels of diversity, with most sequences belonging to the L haplogroups, the basal branches of the mitochondrial phylogeny. However, in sharp contrast with other Ethiopian populations, only 5% of the Nyangatom and Daasanach sequences belong to haplogroups M and N. The Nyangatom and Daasanach were found to be significantly differentiated, while each of them displays close affinities with some Tanzanian populations. The strong genetic structure found over East Africa was neither associated with geography nor with language, a result confirmed by the analysis of 6711 HVS-I sequences of 136 populations mainly from Africa. Processes of migration, language shift and group absorption are documented by linguists and ethnographers for the Nyangatom and Daasanach, thus pointing to the probably transient and plastic nature of these ethnic groups. These processes, associated with periods of isolation, could explain the high diversity and strong genetic structure found in East Africa.
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Affiliation(s)
- Estella S Poloni
- Département d'Anthropologie et d'Ecologie, Université de Genève, 1211 Geneva 4, Switzerland.
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Kitchen A, Ehret C, Assefa S, Mulligan CJ. Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East. Proc Biol Sci 2009; 276:2703-10. [PMID: 19403539 DOI: 10.1098/rspb.2009.0408] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of languages provides a unique opportunity to study human population history. The origin of Semitic and the nature of dispersals by Semitic-speaking populations are of great importance to our understanding of the ancient history of the Middle East and Horn of Africa. Semitic populations are associated with the oldest written languages and urban civilizations in the region, which gave rise to some of the world's first major religious and literary traditions. In this study, we employ Bayesian computational phylogenetic techniques recently developed in evolutionary biology to analyse Semitic lexical data by modelling language evolution and explicitly testing alternative hypotheses of Semitic history. We implement a relaxed linguistic clock to date language divergences and use epigraphic evidence for the sampling dates of extinct Semitic languages to calibrate the rate of language evolution. Our statistical tests of alternative Semitic histories support an initial divergence of Akkadian from ancestral Semitic over competing hypotheses (e.g. an African origin of Semitic). We estimate an Early Bronze Age origin for Semitic approximately 5750 years ago in the Levant, and further propose that contemporary Ethiosemitic languages of Africa reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago.
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Affiliation(s)
- Andrew Kitchen
- Department of Anthropology, University of Florida, , Gainesville, FL 32610-3610, USA.
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Campbell MC, Tishkoff SA. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 2008; 9:403-33. [PMID: 18593304 DOI: 10.1146/annurev.genom.9.081307.164258] [Citation(s) in RCA: 517] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility.
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Affiliation(s)
- Michael C Campbell
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19107, USA.
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16
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Cerný V, Mulligan CJ, Rídl J, Zaloudková M, Edens CM, Hájek M, Pereira L. Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 136:128-37. [PMID: 18257024 DOI: 10.1002/ajpa.20784] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite its key location for population movements out of and back into Africa, Yemen has not yet been sampled on a regional level for an investigation of sub-Saharan, West Eurasian, and South Asian genetic contributions. In this study, we present mitochondrial DNA (mtDNA) data for regionally distinct Yemeni populations that reveal different distributions of mtDNA lineages. An extensive database of mtDNA sequences from North and East African, Middle Eastern and Indian populations was analyzed to provide a context for the regional Yemeni mtDNA datasets. The groups of western Yemen appear to be most closely related to Middle Eastern and North African populations, while the eastern Yemeni population from Hadramawt is most closely related to East Africa. Furthermore, haplotype matches with Africa are almost exclusively confined to West Eurasian R0a haplogroup in southwestern Yemen, although more sub-Saharan L-type matches appear in more northern Yemeni populations. In fact, Yemeni populations have the highest frequency of R0a haplotypes detected to date, thus Yemen or southern Arabia may be the site of the initial expansion of this haplogroup. Whereas two variants of the sub-Saharan haplogroup M1 were detected only in southwestern Yemen close to the Bab el-Mandeb Strait, different non-African M haplotypes were detected at low frequencies (approximately 2%) in western parts of the country and at a higher frequency (7.5%) in the Hadramawt. We conclude that the Yemeni gene pool is highly stratified both regionally and temporally and that it has received West Eurasian, Northeast African, and South Asian gene flow.
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Affiliation(s)
- Viktor Cerný
- Institute of Archaeology of Academy of Sciences of Czech Republic, Prague, v.v.i., Prague 118 01, The Czech Republic.
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Cruciani F, Trombetta B, Labuda D, Modiano D, Torroni A, Costa R, Scozzari R. Genetic diversity patterns at the human clock gene period 2 are suggestive of population-specific positive selection. Eur J Hum Genet 2008; 16:1526-34. [PMID: 18575464 DOI: 10.1038/ejhg.2008.105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Period 2 (PER2) is a key component of the mammalian circadian clock machinery. In humans, genetic variation of clock genes or chronic disturbance of circadian rhythmicity has been implied in the onset of several phenotypes, ranging from periodic insomnias to advanced or delayed sleep phases, to more severe disorders. Peculiar geographic diversity patterns in circadian genes might represent an adaptive response to different light/dark cycles or environmental changes to which different human populations are exposed. To investigate the degree and nature of PER2 gene variation in human populations of different geographic origin, and its possible correlation with different latitudes, we sequenced a 7.7 kb portion of the gene in 20 individuals worldwide. In total, 25 variable sites were identified. The geographic distribution of haplotypes defined by five polymorphic sites was analyzed in 499 individuals from 11 populations from four continents. No evidence for latitude-driven selective effects on PER2 genetic variability was found. However, a high and significant difference in the geographic distribution of PER2 polymorphisms was observed between Africans and non-Africans, suggesting a history of geographically restricted natural selection at this locus. In support of this notion, we found several signals for selection in the sequences. The putative selected haplotype showed a recent coalescent age (8.7 Kyr), and an unusually high frequency in non-African populations. Overall, these findings indicate that a human clock-relevant gene, PER2, might have been influenced by positive selection, and offer preliminary insights into the evolution of this functional class of genes.
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Affiliation(s)
- Fulvio Cruciani
- Dipartimento di Genetica e Biologia Molecolare, Sapienza Università di Roma, Rome, Italy
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Yotova V, Lefebvre JF, Kohany O, Jurka J, Michalski R, Modiano D, Utermann G, Williams SM, Labuda D. Tracing genetic history of modern humans using X-chromosome lineages. Hum Genet 2007; 122:431-43. [PMID: 17680273 DOI: 10.1007/s00439-007-0413-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 07/24/2007] [Indexed: 10/23/2022]
Abstract
Genetic variability of the compound interrupted microsatellite DXS1238, in intron 44 of the dystrophin gene, provides evidence for a complex structure of the ancestral population that led to the emergence of modern humans. We sequenced DXS1238 in 600 X-chromosomes from all over the world. Forty four percent of African-specific chromosomes belong to the ancestral lineage that did not participate in the out-of-Africa expansion and subsequent colonization of other continents. Based on the coalescence analysis these lineages separated from those that contributed to the out-of-Africa expansion 366 +/- 136 thousands years ago (Kya). Independently, the analysis of the variance in the repeat length and of the decay of the ancestral alleles of the two DXS1238 repeats, GT and GA, dates this separation at more than 200 Kya. This suggests a complex demographic history and genetic structure of the African melting pot that led to the emergence of modern humans and their out-of-Africa migration. The subsequent subdivisions of human populations among different continents appear to be preceded by even more structured population history within Africa itself, which resulted from a restricted gene flow between lineages allowing for genetic differences to accumulate. If the transition to modern humans occurred during that time, it necessarily follows that genes associated with this transformation spread between subpopulations via gene flow. Otherwise, in spite of subsequent anatomical variation, Homo sapiens as a species could have emerged in Africa already between 300 and 200 Kya, i.e. before the mitochondrial DNA and well before the Y-chromosome most recent common ancestors.
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Affiliation(s)
- Vania Yotova
- Centre de Recherche, Hôpital Sainte-Justine, CHU Mère Enfant, 3175 Côte Sainte-Catherine, Montreal, QC, Canada, H3T 1C5
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