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Díaz-Matallana M, Briceño I, Benavides-Benítez E, Bernal JE, Martínez-Lozano JC. Molecular characterisation of sickle cell disease and classification of major haplotypes associated with the β-globin cluster (HBB gene) by means of SNP marker sequencing in a group of samples from Bolívar, Colombia. Ann Hum Biol 2024; 51:2308714. [PMID: 38378484 DOI: 10.1080/03014460.2024.2308714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Colombia has a mestizo population and the prevalence of haemoglobin variants varies according to each region, but heterozygous carriers can be found in all of them. AIM To characterise sickle cell disease (SCD) haematologically, biochemically, and molecularly, and detect classic haplotypes by DNA sequencing in a group of samples from Bolívar, Colombia. SUBJECTS AND METHODS Blood samples were collected after informed consent from volunteers from eight communities in the Bolívar department, plus samples from the Pacific region, Providencia Island, and Bogotá were included. Data were obtained from: (1) haematological analyses; (2) biochemical tests: dHPLC was used to determine haemoglobin (Hb); and (3) DNA sequencing data through five SNPs. RESULTS 101 samples were identified by rs334 through Sanger's Sequencing, structural haemoglobinopathies HbAS (34.65%), HbSS (2.97%) and HbAC (1.98%) were found. When contrasting the Hb identification results between SNP rs334 Vs. dHPLC/Isoelectric Focusing (IEF), a coincidence was found in 39/43 samples analysed, therefore, when comparing these techniques, a significant correlation was found (Pearson's correlation coefficient r = 0.998). 26 samples previously analysed by rs334 were classified into classical haplotypes CAR (50.0%), BEN (30.76%), CAM (7.69%), SEN (3.84%), and ATP-I (7.69%). CONCLUSIONS SCD characterisation and SNPs-based classification through Sanger's DNA sequencing have not been performed before in Colombia. The results of this work will make it possible to expand the data or records of carriers and those affected, which will benefit patients and their families.
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Affiliation(s)
- Marcela Díaz-Matallana
- Faculty of Medicine, Human Genetics Laboratory, Universidad de La Sabana, Chía, Colombia
| | - Ignacio Briceño
- Faculty of Medicine, Human Genetics Laboratory, Universidad de La Sabana, Chía, Colombia
| | | | - Jaime E Bernal
- Medicine Program, Universidad del Sinú Elías Bechara Zainúm, Cartagena, Colombia
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Esoh K, Wonkam A. Evolutionary history of sickle-cell mutation: implications for global genetic medicine. Hum Mol Genet 2021; 30:R119-R128. [PMID: 33461216 PMCID: PMC8117455 DOI: 10.1093/hmg/ddab004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
Resistance afforded by the sickle-cell trait against severe malaria has led to high frequencies of the sickle-cell mutation [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)] in most parts of Africa. High-coverage sequencing and genotype data have now confirmed the single African origin of the sickle-cell gene variant [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)]. Nevertheless, the classical HBB-like genes cluster haplotypes remain a rich source of HBB-βS evolutionary information. The overlapping distribution of HBB-βS and other disease-associated variants means that their evolutionary genetics must be investigated concurrently. In this review: (1) we explore the evolutionary history of HBB-βS and its implications in understanding human migration within and out of Africa: e.g. HBB haplotypes and recent migration paths of the Bantu expansion, occurrence of ~7% of the Senegal haplotype in Angola reflecting changes in population/SCD dynamics, and existence of all five classical HBB haplotype in Cameroon and Egypt suggesting a much longer presence of HBB-βS in these regions; (2) we discuss the time estimates of the emergence of HBB-βS in Africa and finally, (3) we discuss implications for genetic medicine in understanding complex epistatic interactions between HBB-βS and other gene variants selected under environmental pressure in Africa e.g. variants in HBB, HBA, G6PD, APOL1, APOE, OSBPL10 and RXRA.
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Affiliation(s)
- Kevin Esoh
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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3
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Ngo-Bitoungui VJ, Belinga S, Mnika K, Masekoameng T, Nembaware V, Essomba RG, Ngo-Sack F, Awandare G, Mazandu GK, Wonkam A. Investigations of Kidney Dysfunction-Related Gene Variants in Sickle Cell Disease Patients in Cameroon (Sub-Saharan Africa). Front Genet 2021; 12:595702. [PMID: 33790942 PMCID: PMC8005585 DOI: 10.3389/fgene.2021.595702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 02/19/2021] [Indexed: 12/29/2022] Open
Abstract
Background Renal dysfunctions are associated with increased morbidity and mortality in sickle cell disease (SCD). Early detection and subsequent management of SCD patients at risk for renal failure and dysfunctions are essential, however, predictors that can identify patients at risk of developing renal dysfunction are not fully understood. Methods In this study, we have investigated the association of 31 known kidney dysfunctions-related variants detected in African Americans from multi-ethnic genome wide studies (GWAS) meta-analysis, to kidney-dysfunctions in a group of 413 Cameroonian patients with SCD. Systems level bioinformatics analyses were performed, employing protein-protein interaction networks to further interrogate the putative associations. Results Up to 61% of these patients had micro-albuminuria, 2.4% proteinuria, 71% glomerular hyperfiltration, and 5.9% had renal failure. Six variants are significantly associated with the two quantifiable phenotypes of kidney dysfunction (eGFR and crude-albuminuria): A1CF-rs10994860 (P = 0.02020), SYPL2-rs12136063 (P = 0.04208), and APOL1 (G1)-rs73885319 (P = 0.04610) are associated with eGFR; and WNT7A-rs6795744 (P = 0.03730), TMEM60-rs6465825 (P = 0.02340), and APOL1 (G2)-rs71785313 (P = 0.03803) observed to be protective against micro-albuminuria. We identified a protein-protein interaction sub-network containing three of these gene variants: APOL1, SYPL2, and WNT7A, connected to the Nuclear factor NF-kappa-B p105 subunit (NFKB1), revealed to be essential and might indirectly influence extreme phenotypes. Interestingly, clinical variables, including body mass index (BMI), systolic blood pressure, vaso-occlusive crisis (VOC), and haemoglobin (Hb), explain better the kidney phenotypic variations in this SCD population. Conclusion This study highlights a strong contribution of haematological indices (Hb level), anthropometric variables (BMI, blood pressure), and clinical events (i.e., vaso-occlusive crisis) to kidney dysfunctions in SCD, rather than known genetic factors. Only 6/31 characterised gene-variants are associated with kidney dysfunction phenotypes in SCD samples from Cameroon. The data reveal and emphasise the urgent need to extend GWAS studies in populations of African ancestries living in Africa, and particularly for kidney dysfunctions in SCD.
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Affiliation(s)
- Valentina J Ngo-Bitoungui
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon-Accra, Ghana.,Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Microbiology Haematology and Immunology, University of Dschang, Yaoundé, Cameroon
| | | | - Khuthala Mnika
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tshepiso Masekoameng
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Victoria Nembaware
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon-Accra, Ghana
| | - René G Essomba
- National Public Health Laboratory, Yaoundé, Cameroon.,Department of Microbiology, Parasitology, Haematology, Immunology and Infectious Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaounde 1, Yaounde, Cameroon
| | - Francoise Ngo-Sack
- Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon-Accra, Ghana
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,African Institute for Mathematical Sciences, Muizenberg, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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4
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Alpha thalassemia, but not β S-globin haplotypes, influence sickle cell anemia clinical outcome in a large, single-center Brazilian cohort. Ann Hematol 2021; 100:921-931. [PMID: 33586016 DOI: 10.1007/s00277-021-04450-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022]
Abstract
Alpha thalassemia and beta-globin haplotype are considered classical genetic disease modifiers in sickle cell anemia (SCA) causing clinical heterogeneity. Nevertheless, their functional impact on SCA disease emergence and progression remains elusive. To better understand the role of alpha thalassemia and beta-globin haplotype in SCA, we performed a retrospective study evaluating the clinical manifestations of 614 patients. The univariate analysis showed that the presence of alpha-thalassemia -3.7-kb mutation (αα/-α and -α/-α) decreased the risk of stroke development (p = 0.046), priapism (p = 0.033), and cholelithiasis (p = 0.021). Furthermore, the cumulative incidence of stroke (p = 0.023) and cholelithiasis (p = 0.006) was also significantly lower for patients carrying the alpha thalassemia -3.7-kb mutation. No clinical effects were associated with the beta-globin haplotype analysis, which could be explained by the relatively homogeneous haplotype composition in our cohort. Our results reinforce that alpha thalassemia can provide protective functions against hemolysis-related symptoms in SCA. Although, several genetic modifiers can impact the inflammatory state of SCA patients, the alpha thalassemia mutation remains one of the most recurrent genetic aberration and should therefore always be considered first.
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Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, Adebamowo SN, Chimusa ER, Muzny D, Metcalf G, Gibbs RA, Rotimi C, Ramsay M, Adeyemo AA, Lombard Z, Hanchard NA. High-depth African genomes inform human migration and health. Nature 2020; 586:741-748. [PMID: 33116287 PMCID: PMC7759466 DOI: 10.1038/s41586-020-2859-7] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/07/2020] [Indexed: 01/05/2023]
Abstract
The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon-but in other genes, variants denoted as 'likely pathogenic' in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laura R Botigué
- Center for Research in Agricultural Genomics (CRAG), Plant and Animal Genomics Program, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Taoufik Bensellak
- System and Data Engineering Team, Abdelmalek Essaadi University, ENSA, Tangier, Morocco
| | - Gordon Wells
- Centre for Proteomic and Genomic Research (CPGR), Cape Town, South Africa.,South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.,Africa Health Research Institute, Durban, South Africa
| | - Judit Kumuthini
- Centre for Proteomic and Genomic Research (CPGR), Cape Town, South Africa.,South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yasmina J Fakim
- Department of Agriculture and Food Science, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius.,Department of Digital Technologies,Faculty of Information, Communication & Digital Technologies, University of Mauritius, Reduit, Mauritius
| | - Anisah W Ghoorah
- Department of Digital Technologies,Faculty of Information, Communication & Digital Technologies, University of Mauritius, Reduit, Mauritius
| | - Eileen Dareng
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Trust Odia
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Oluwadamilare Falola
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.,Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaston Mazandu
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Oscar A Nyangiri
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Mamana Mbiyavanga
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institute Pasteur of Tunis, Tunis, Tunisia
| | - Samar K Kassim
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo, Egypt
| | - Nicola Mulder
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Sally N Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA.,University of Maryland Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious, Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
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Hassan M, Yaseen N, Al-Mamoori H. Sickle ß-globin haplotypes among patients with sickle cell anemia in Basra, Iraq: A cross-sectional study. IRAQI JOURNAL OF HEMATOLOGY 2020. [DOI: 10.4103/ijh.ijh_20_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Abstract
Fetal haemoglobin (HbF) levels have a clinically beneficial effect on sickle cell disease (SCD). Patients with SCD demonstrate extreme variability in HbF levels (1-30%), a large part of which is likely genetically determined. The main genetic modifier loci for HbF persistence, HBS1L-MYB, BCL11A and the β-globin gene cluster in adults also act in SCD patients. Their effects are, however, modified significantly by a disease pathology that includes a drastically shortened erythrocyte lifespan with an enhanced survival of those red blood cells that carry HbF (F cells). We propose a model of how HbF modifier genes and disease pathology interact to shape HbF levels measured in patients. We review current knowledge on the action of these loci in SCD, their genetic architecture, and their putative functional components. At each locus, one strong candidate for a causative, functional DNA change has been proposed: Xmn1-HBG2 at the β-globin cluster, rs1427407 at BCL11A and the 3 bp deletion rs66650371 at HBS1L-MYB. These, however, explain only part of the impact of these loci and additional variants are yet to be identified. Further progress in understanding the genetic control of HbF levels requires that confounding factors inherent in SCD, such as ethnic complexity, the role of F cells and the influence of drugs, are suitably addressed. This will depend on international collaboration and on large, well-characterised patient cohorts with genome-wide single-nucleotide polymorphism or sequence data.
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Affiliation(s)
- Stephan Menzel
- School of Cancer and Pharmaceutical Sciences, King's College London, The Rayne Institute, 123 Coldharbour Lane, London, SE5 9NU, UK.
| | - Swee Lay Thein
- Sickle Cell Branch, National Heart, Lung and Blood Institute, The National Institutes of Health, Building 10, Room 5-5142, 10 Center Drive, Bethesda, MD, 20814, USA.
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Atypical β-S haplotypes: classification and genetic modulation in patients with sickle cell anemia. J Hum Genet 2019; 64:239-248. [DOI: 10.1038/s10038-018-0554-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 12/05/2018] [Accepted: 12/14/2018] [Indexed: 12/24/2022]
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Fong C, Barreto G. Presencia de haplotipos no africanos incrementa la diversidad genética en pacientes con anemia falciforme en Colombia. ACTA BIOLÓGICA COLOMBIANA 2018. [DOI: 10.15446/abc.v23n3.69218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El objetivo de este estudio fue identificar la frecuencia de haplotipos dentro del cluster de Beta globina presente en pacientes con anemia falciforme en Colombia, establecer la presencia de haplotipos no africanos en esta población, así como verificar variaciones en el patrón de desequilibrio de ligamiento dentro del cluster de Beta globina. Se analizaron 83 individuos con anemia falciforme, los haplotipos se formaron utilizando cinco sitios de restricción dentro del cluster de Beta globina, se estableció la frecuencia de haplotipos, se calculó el grado de desequilibrio de ligamiento entre los sitios de restricción, así como la similitud genética de esta población con otra de afectados en América. Los haplotipos más frecuentes en la población fueron Benín ( 35,1 %) y Bantú (26, 5 %), ambos africanos. Sin embargo, haplotipos presentes en poblaciones indígenas americanas y europeas alcanzaron frecuencias entre el 2 – 10 %, así como haplotipos que no han sido reportados en otras poblaciones. Los sitios de restricción presentaron bajo o nulo desequilibrio de ligamiento entre ellos. Al compararse con otras poblaciones, la población colombiana presentó mayor similitud con la población de Venezuela en donde Benin y Bantú son también predominantes. Nuestros resultados muestran que el mestizaje ha facilitado el paso de la mutación para la anemia falciforme a un contexto genético no africano (amerindio y europeo). Además, el mestizaje también ha alterado el patrón de desequilibrio de ligamiento dentro del cluster de Beta globina generando modificaciones que pueden tener influencia en estudios de asociación dentro de esta población de afectados.
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Hsu L, Nnodu OE, Brown BJ, Tluway F, King S, Dogara LG, Patil C, Shevkoplyas SS, Lettre G, Cooper RS, Gordeuk VR, Tayo BO. White Paper: Pathways to Progress in Newborn Screening for Sickle Cell Disease in Sub-Saharan Africa. JOURNAL OF TROPICAL DISEASES & PUBLIC HEALTH 2018; 6:260. [PMID: 30505949 PMCID: PMC6261323 DOI: 10.4172/2329-891x.1000260] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Sickle Cell Disease (SCD) is among the most common single-gene diseases in the world but evidence-based comprehensive health care has not been implemented where the highest prevalence of SCD occurs, in sub-Saharan Africa (SSA). It represents an urgent health burden, both in terms of mortality and morbidity with an estimated mortality of 8-16% in children under 5 years in SSA. Addressing the high mortality of SCD in SSA and for effective management of SCD, newborn screening (NBS) should be incorporated with prevention of infections (including pneumococcal septicaemia and malaria), parental education and support at all levels of healthcare provision to enable timely recognition. The NBS working group of the Africa Sickle Cell Research Network (AfroSickleNet) collaboration surveyed current projects in NBS in SSA, and current conditions that hinder more widespread implementation of NBS for SCD. Solutions based on new point-of-care testing technology to disseminate education, and implementation science approaches that leverage existing resources are proposed.
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Affiliation(s)
- Lewis Hsu
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Illinois at Chicago, Chicago, IL, USA
| | - Obiageli E. Nnodu
- Department of Hematology and Blood Transfusion, University of Abuja, Abuja, Nigeria
- Centre of Excellence for Sickle Cell Disease Research & Training, University of Abuja, Abuja, Nigeria
| | - Biobele J. Brown
- Department of Pediatrics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Furahini Tluway
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dares Salaam, Tanzania
| | - Shonda King
- Department of Health Social Work, University of Illinois Hospital and Health Sciences Systems, Chicago, IL, USA
| | - Livingstone G. Dogara
- Department of Hematology and Blood Transfusion, Ahmadu Bello University Teaching Hospital, Zaria, Nigeria
| | - Crystal Patil
- Department of Women, Children and Family Health Science, University of Illinois at Chicago, College of Nursing, Chicago, IL, USA
| | | | | | - Richard S. Cooper
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
| | - Victor R. Gordeuk
- Division of Hematology and Oncology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Bamidele O. Tayo
- Department of Public Health Sciences, Loyola University Chicago Stritch School of Medicine, Maywood, IL, USA
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Adeyemo TA, Ojewunmi OO, Oyetunji IA, Rooks H, Rees DC, Akinsulie AO, Akanmu AS, Thein SL, Menzel S. A survey of genetic fetal-haemoglobin modifiers in Nigerian patients with sickle cell anaemia. PLoS One 2018; 13:e0197927. [PMID: 29879141 PMCID: PMC5991720 DOI: 10.1371/journal.pone.0197927] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/10/2018] [Indexed: 12/31/2022] Open
Abstract
Genetic variants at three quantitative trait loci (QTL) for fetal haemoglobin (HbF), BCL11A, HBS1L-MYB and the β-globin gene cluster, have attracted interest as potential targets of therapeutic strategies for HbF reactivation in sickle cell anaemia (SCA). We carried out the first systematic evaluation of critical single nucleotide polymorphisms at these disease modifier loci in Nigerian patients with SCA. Common variants for BCL11A and HBS1L-MYB were strongly associated with HbF levels. At both loci, secondary association signals were detected, illustrating the mapping resolution attainable in this population. For BCL11A, the two independent sites of association were represented by rs1427407 (primary site, p = 7.0 x 10(-10)) and rs6545816 (secondary site, conditioned on rs1427407: p = 0.02) and for HBS1L-MYB by rs9402686 (HMIP-2B, p = 1.23 x 10(-4)) and rs66650371 (HMIP-2A, p = 0.002). Haplotype analysis revealed similarities in the genetic architecture of BCL11A and HBS1L-MYB in Nigerian patients. Variants at both loci also alleviated anaemia. The variant allele for the γ globin gene promoter polymorphism XmnI-HBG2 was too infrequent in our patients to be evaluated in this relatively small study. Studying the large and diverse SCA patient populations in African countries such as Nigeria will be key for a clearer understanding of how these loci work and for the discovery of new disease modifier genes.
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Affiliation(s)
- Titilope A. Adeyemo
- Department of Haematology and Blood Transfusion, College of Medicine, University of Lagos, Idi-araba, Lagos, Nigeria
- * E-mail: (TAA); (SM)
| | | | | | - Helen Rooks
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
| | - David C. Rees
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
- King's College Hospital, Paediatric Haematology, London, United Kingdom
| | - Adebola O. Akinsulie
- Department of Paediatrics, College of Medicine, University of Lagos, Idi-araba, Lagos, Nigeria
| | - Alani S. Akanmu
- Department of Haematology and Blood Transfusion, College of Medicine, University of Lagos, Idi-araba, Lagos, Nigeria
| | - Swee Lay Thein
- Sickle Cell Branch, National Heart Lung and Blood Institute, National Institute of Health, Bethesda, MD, United States of America
| | - Stephan Menzel
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, United Kingdom
- * E-mail: (TAA); (SM)
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Shriner D, Rotimi CN. Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase. Am J Hum Genet 2018. [PMID: 29526279 PMCID: PMC5985360 DOI: 10.1016/j.ajhg.2018.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Five classical designations of sickle haplotypes are made on the basis of the presence or absence of restriction sites and are named after the ethno-linguistic groups or geographic regions from which the individuals with sickle cell anemia originated. Each haplotype is thought to represent an independent occurrence of the sickle mutation rs334 (c.20A>T [p.Glu7Val] in HBB). We investigated the origins of the sickle mutation by using whole-genome-sequence data. We identified 156 carriers from the 1000 Genomes Project, the African Genome Variation Project, and Qatar. We classified haplotypes by using 27 polymorphisms in linkage disequilibrium with rs334. Network analysis revealed a common haplotype that differed from the ancestral haplotype only by the derived sickle mutation at rs334 and correlated collectively with the Central African Republic (CAR), Cameroon, and Arabian/Indian haplotypes. Other haplotypes were derived from this haplotype and fell into two clusters, one composed of Senegal haplotypes and the other composed of Benin and Senegal haplotypes. The near-exclusive presence of the original sickle haplotype in the CAR, Kenya, Uganda, and South Africa is consistent with this haplotype predating the Bantu expansions. Modeling of balancing selection indicated that the heterozygote advantage was 15.2%, an equilibrium frequency of 12.0% was reached after 87 generations, and the selective environment predated the mutation. The posterior distribution of the ancestral recombination graph yielded a sickle mutation age of 259 generations, corresponding to 7,300 years ago during the Holocene Wet Phase. These results clarify the origin of the sickle allele and improve and simplify the classification of sickle haplotypes.
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Rotimi CN, Tekola-Ayele F, Baker JL, Shriner D. The African diaspora: history, adaptation and health. Curr Opin Genet Dev 2016; 41:77-84. [PMID: 27644073 DOI: 10.1016/j.gde.2016.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/30/2016] [Accepted: 08/02/2016] [Indexed: 01/13/2023]
Abstract
The trans-Atlantic slave trade brought millions of Africans to the New World. Advances in genomics are providing novel insights into the history and health of Africans and the diasporan populations. Recent examples reviewed here include the unraveling of substantial hunter-gatherer and 'Eurasian' admixtures across sub-Saharan Africa, expanding our understanding of ancestral African genetics; the global ubiquity of mixed ancestry; the revealing of African ancestry in Latin Americans that likely derived from the slave trade; and understanding of the ancestral backgrounds of APOL1 and LPL found to influence kidney disease and lipid levels, respectively, providing specific insights into disease etiology and health disparities.
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Affiliation(s)
- Charles N Rotimi
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA.
| | - Fasil Tekola-Ayele
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
| | - Jennifer L Baker
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health National Human Genome Research Institute, Building 12A, Room 4047 12 South Drive, Bethesda, MD 20892, USA
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Hockham C, Piel FB, Gupta S, Penman BS. Understanding the contrasting spatial haplotype patterns of malaria-protective β-globin polymorphisms. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 36:174-183. [PMID: 26394108 PMCID: PMC4653953 DOI: 10.1016/j.meegid.2015.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/04/2015] [Accepted: 09/06/2015] [Indexed: 12/24/2022]
Abstract
The malaria-protective β-globin polymorphisms, sickle-cell (β(S)) and β(0)-thalassaemia, are canonical examples of human adaptation to infectious disease. Occurring on distinct genetic backgrounds, they vary markedly in their patterns of linked genetic variation at the population level, suggesting different evolutionary histories. β(S) is associated with five classical restriction fragment length polymorphism haplotypes that exhibit remarkable specificity in their geographical distributions; by contrast, β(0)-thalassaemia mutations are found on haplotypes whose distributions overlap considerably. Here, we explore why these two polymorphisms display contrasting spatial haplotypic distributions, despite having malaria as a common selective pressure. We present a meta-population genetic model, incorporating individual-based processes, which tracks the evolution of β-globin polymorphisms on different haplotypic backgrounds. Our simulations reveal that, depending on the rate of mutation, a large population size and/or high population growth rate are required for both the β(S)- and the β(0)-thalassaemia-like patterns. However, whilst the β(S)-like pattern is more likely when population subdivision is high, migration low and long-distance migration absent, the opposite is true for β(0)-thalassaemia. Including gene conversion has little effect on the overall probability of each pattern; however, when inter-haplotype fitness variation exists, gene conversion is more likely to have contributed to the diversity of haplotypes actually present in the population. Our findings highlight how the contrasting spatial haplotype patterns exhibited by β(S) and β(0)-thalassaemia may provide important indications as to the evolution of these adaptive alleles and the demographic history of the populations in which they have evolved.
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Affiliation(s)
| | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, UK.
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Bitoungui VJN, Pule GD, Hanchard N, Ngogang J, Wonkam A. Beta-globin gene haplotypes among cameroonians and review of the global distribution: is there a case for a single sickle mutation origin in Africa? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:171-9. [PMID: 25748438 DOI: 10.1089/omi.2014.0134] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Studies of hemoglobin S haplotypes in African subpopulations have potential implications for patient care and our understanding of genetic factors that have shaped the prevalence of sickle cell disease (SCD). We evaluated HBB gene cluster haplotypes in SCD patients from Cameroon, and reviewed the literature for a global distribution. We reviewed medical records to obtain pertinent socio-demographic and clinical features for 610 Cameroonian SCD patients, including hemoglobin electrophoresis and full blood counts. RFLP-PCR was used to determine the HBB gene haplotype on 1082 chromosomes. A systematic review of the current literature was undertaken to catalogue HBB haplotype frequencies in SCD populations around the world. Benin (74%; n = 799) and Cameroon (19%; n = 207) were the most prevalent haplotypes observed among Cameroonian patients. There was no significant association between HBB haplotypes and clinical life events, anthropometric measures, hematological parameters, or fetal hemoglobin (HbF) levels. The literature review of the global haplotype distributions was consistent with known historical migrations of the people of Africa. Previously reported data from Sudan showed a distinctly unusual pattern; all four classical haplotypes were reported, with an exceptionally high proportion of the Senegal, Cameroon, and atypical haplotypes. We did not observe any significant associations between HBB haplotype and SCD disease course in this cohort. Taken together, the data from Cameroon and from the wider literature suggest that a careful reassessment of African HBB haplotypes may shed further light on the evolutionary dynamics of the sickle allele, which could suggest a single origin of the sickle mutation.
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Affiliation(s)
- Valentina J Ngo Bitoungui
- 1 Department of Microbiology, Parasitology, and Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaoundé , Yaoundé, Cameroon
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Wang X, Cheng CY, Liao J, Sim X, Liu J, Chia KS, Tai ES, Little P, Khor CC, Aung T, Wong TY, Teo YY. Evaluation of transethnic fine mapping with population-specific and cosmopolitan imputation reference panels in diverse Asian populations. Eur J Hum Genet 2015; 24:592-9. [PMID: 26130488 DOI: 10.1038/ejhg.2015.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 05/13/2015] [Accepted: 05/26/2015] [Indexed: 12/13/2022] Open
Abstract
There has been limited success in identifying causal variants underlying association signals observed in genome-wide association studies (GWAS). The use of 1000 Genomes Project (1KGP) allows the imputation to estimate the genetic information at untyped variants. However, long stretches of high linkage disequilibrium within the genome prevent us from differentiating between causal variants and perfect surrogates, thus limiting our ability to identify causal variants. Transethnic strategies have been proposed as a possible solution to mitigate this. However, these studies generally rely on imputing genotypes from multiple ancestries from 1KGP but not against population-specific reference panels. Here, we perform the first transethnic fine-mapping study across three Asian cohorts from diverse ancestries at the loci implicated with eye and blood lipid traits, using population-specific reference panels that have been generated by whole-genome sequencing samples from the same ancestry groups. Our study outlines several challenges faced in a fine-mapping exercise where one simply aims to meta-analyse existing GWAS that have been imputed against reference haplotypes from the 1KGP.
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Affiliation(s)
- Xu Wang
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Ching-Yu Cheng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore.,Department of Ophthalmology, National University of Singapore, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jiemin Liao
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore
| | - Xueling Sim
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Kee-Seng Chia
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Peter Little
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Chiea-Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore.,Department of Ophthalmology, National University of Singapore, Singapore, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore.,Department of Ophthalmology, National University of Singapore, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Center, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
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17
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Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Hum Genet 2015; 134:375-92. [PMID: 25634076 DOI: 10.1007/s00439-014-1525-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/25/2014] [Indexed: 10/24/2022]
Abstract
The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
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Abstract
Infectious pathogens are among the strongest selective forces that shape the human genome. Migrations and cultural changes in the past 100,000 years exposed populations to dangerous new pathogens. Host genetics influences susceptibility to infectious disease. Evolutionary adaptations for resistance and symbiosis may underlie common immune-mediated diseases. Signatures of selection and methods to detect them vary with the age, geographical spread and virulence of the pathogen. A history of selection on a trait adds power to association studies by driving the emergence of common alleles of strong effect. Combining selection and association metrics can further increase power. Genome-wide association studies (GWASs) of susceptibility to pathogens that are moderately old (1,000–50,000 years ago), geographically limited in history and exerted strong positive selective pressure will have the most power if GWASs can be done in the historically affected population. An understanding of host–pathogen interactions can inform the development of new therapies for both infectious diseases and common immune-mediated diseases.
The impact of various infectious agents on human survival and reproduction over thousands of years has exerted selective pressure on numerous regions of the human genome. This Review describes how such signatures of selection can be detected and integrated with data from complementary approaches, such as genome-wide association studies, to provide biological insights into host–pathogen interactions. The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology.
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Abstract
The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural selection. These methods have been used to investigate the macro- and microevolution of a broad range of organisms, including humans. Here, we provide a comprehensive outline of these methods, explaining their conceptual motivations and statistical interpretations. We highlight areas of recent and future development in evolutionary genomics methods and discuss ongoing challenges for researchers employing such tests. In particular, we emphasize the importance of functional follow-up studies to characterize putative selected alleles and the use of selection scans as hypothesis-generating tools for investigating evolutionary histories.
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Affiliation(s)
- Joseph J Vitti
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138; ,
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20
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Wonkam A, Ngo Bitoungui VJ, Vorster AA, Ramesar R, Cooper RS, Tayo B, Lettre G, Ngogang J. Association of variants at BCL11A and HBS1L-MYB with hemoglobin F and hospitalization rates among sickle cell patients in Cameroon. PLoS One 2014; 9:e92506. [PMID: 24667352 PMCID: PMC3965431 DOI: 10.1371/journal.pone.0092506] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 02/21/2014] [Indexed: 01/03/2023] Open
Abstract
Background Genetic variation at loci influencing adult levels of HbF have been shown to modify the clinical course of sickle cell disease (SCD). Data on this important aspect of SCD have not yet been reported from West Africa. We investigated the relationship between HbF levels and the relevant genetic loci in 610 patients with SCD (98% HbSS homozygotes) from Cameroon, and compared the results to a well-characterized African-American cohort. Methods and Findings Socio-demographic and clinical features were collected and medical records reviewed. Only patients >5 years old, who had not received a blood transfusion or treatment with hydroxyurea were included. Hemoglobin electrophoresis and a full blood count were conducted upon arrival at the hospital. RFLP-PCR was used to describe the HBB gene haplotypes. SNaPshot PCR, Capillary electrophoresis and cycle sequencing were used for the genotyping of 10 selected SNPs. Genetic analysis was performed with PLINK software and statistical models in the statistical package R. Allele frequencies of relevant variants at BCL11A were similar to those detected in African Americans; although the relationships with Hb F were significant (p <.001), they explained substantially less of the variance in HbF than was observed among African Americans (∼ 2% vs 10%). SNPs in HBS1L-MYB region (HMIP) likewise had a significant impact on HbF, however, we did not find an association between HbF and the variations in HBB cluster and OR51B5/6 locus on chromosome 11p, due in part to the virtual absence of the Senegal and Indian Arab haplotypes. We also found evidence that selected SNPs in HBS1L-MYB region (HMIP) and BCL11A affect both other hematological indices and rates of hospitalization. Conclusions This study has confirmed the associations of SNPs in BCL11A and HBS1L-MYB and fetal haemoglobin in Cameroonian SCA patients; hematological indices and hospitalization rates were also associated with specific allelic variants.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
- * E-mail:
| | - Valentina J. Ngo Bitoungui
- Department of Microbiology, Parasitology and Haematology, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Anna A. Vorster
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Raj Ramesar
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Richard S. Cooper
- Department of Public Health Sciences, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Bamidele Tayo
- Department of Public Health Sciences, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Guillaume Lettre
- Montreal Heart Institute and Université de Montréal, Montreal, Quebec, Canada
| | - Jeanne Ngogang
- Department of Microbiology, Parasitology and Haematology, Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
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Bean CJ, Boulet SL, Yang G, Payne AB, Ghaji N, Pyle ME, Hooper WC, Bhatnagar P, Keefer J, Barron-Casella EA, Casella JF, Debaun MR. Acute chest syndrome is associated with single nucleotide polymorphism-defined beta globin cluster haplotype in children with sickle cell anaemia. Br J Haematol 2013; 163:268-76. [PMID: 23952145 DOI: 10.1111/bjh.12507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/24/2013] [Indexed: 12/20/2022]
Abstract
Genetic diversity at the human β-globin locus has been implicated as a modifier of sickle cell anaemia (SCA) severity. However, haplotypes defined by restriction fragment length polymorphism sites across the β-globin locus have not been consistently associated with clinical phenotypes. To define the genetic structure at the β-globin locus more thoroughly, we performed high-density single nucleotide polymorphism (SNP) mapping in 820 children who were homozygous for the sickle cell mutation (HbSS). Genotyping results revealed very high linkage disequilibrium across a large region spanning the locus control region and the HBB (β-globin gene) cluster. We identified three predominant haplotypes accounting for 96% of the β(S) -carrying chromosomes in this population that could be distinguished using a minimal set of common SNPs. Consistent with previous studies, fetal haemoglobin level was significantly associated with β(S) -haplotypes. After controlling for covariates, an association was detected between haplotype and rate of hospitalization for acute chest syndrome (ACS) (incidence rate ratio 0·51, 95% confidence interval 0·29-0·89) but not incidence rate of vaso-occlusive pain or presence of silent cerebral infarct (SCI). Our results suggest that these SNP-defined β(S) -haplotypes may be associated with ACS, but not pain or SCI in a study population of children with SCA.
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Affiliation(s)
- Christopher J Bean
- Division of Blood Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Liu X, Ong RTH, Pillai EN, Elzein AM, Small KS, Clark TG, Kwiatkowski DP, Teo YY. Detecting and characterizing genomic signatures of positive selection in global populations. Am J Hum Genet 2013; 92:866-81. [PMID: 23731540 DOI: 10.1016/j.ajhg.2013.04.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 04/17/2013] [Accepted: 04/24/2013] [Indexed: 12/20/2022] Open
Abstract
Natural selection is a significant force that shapes the architecture of the human genome and introduces diversity across global populations. The question of whether advantageous mutations have arisen in the human genome as a result of single or multiple mutation events remains unanswered except for the fact that there exist a handful of genes such as those that confer lactase persistence, affect skin pigmentation, or cause sickle cell anemia. We have developed a long-range-haplotype method for identifying genomic signatures of positive selection to complement existing methods, such as the integrated haplotype score (iHS) or cross-population extended haplotype homozygosity (XP-EHH), for locating signals across the entire allele frequency spectrum. Our method also locates the founder haplotypes that carry the advantageous variants and infers their corresponding population frequencies. This presents an opportunity to systematically interrogate the whole human genome whether a selection signal shared across different populations is the consequence of a single mutation process followed subsequently by gene flow between populations or of convergent evolution due to the occurrence of multiple independent mutation events either at the same variant or within the same gene. The application of our method to data from 14 populations across the world revealed that positive-selection events tend to cluster in populations of the same ancestry. Comparing the founder haplotypes for events that are present across different populations revealed that convergent evolution is a rare occurrence and that the majority of shared signals stem from the same evolutionary event.
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Affiliation(s)
- Xuanyao Liu
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117456, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore
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Ghansah A, Rockett KA, Clark TG, Wilson MD, Koram KA, Oduro AR, Amenga-Etego L, Anyorigiya T, Hodgson A, Milligan P, Rogers WO, Kwiatkowski DP. Haplotype analyses of haemoglobin C and haemoglobin S and the dynamics of the evolutionary response to malaria in Kassena-Nankana District of Ghana. PLoS One 2012; 7:e34565. [PMID: 22506028 PMCID: PMC3323552 DOI: 10.1371/journal.pone.0034565] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 03/02/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Haemoglobin S (HbS) and C (HbC) are variants of the HBB gene which both protect against malaria. It is not clear, however, how these two alleles have evolved in the West African countries where they co-exist at high frequencies. Here we use haplotypic signatures of selection to investigate the evolutionary history of the malaria-protective alleles HbS and HbC in the Kassena-Nankana District (KND) of Ghana. METHODOLOGY/PRINCIPAL FINDINGS The haplotypic structure of HbS and HbC alleles was investigated, by genotyping 56 SNPs around the HBB locus. We found that, in the KND population, both alleles reside on extended haplotypes (approximately 1.5 Mb for HbS and 650 Kb for HbC) that are significantly less diverse than those of the ancestral HbA allele. The extended haplotypes span a recombination hotspot that is known to exist in this region of the genome SIGNIFICANCE Our findings show strong support for recent positive selection of both the HbS and HbC alleles and provide insights into how these two alleles have both evolved in the population of northern Ghana.
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Affiliation(s)
- Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
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Elderdery AY, Mills J, Mohamed BA, Cooper AJ, Mohammed AO, Eltieb N, Old J. Molecular analysis of the β-globin gene cluster haplotypes in a Sudanese population with sickle cell anaemia. Int J Lab Hematol 2012; 34:262-6. [PMID: 22260316 DOI: 10.1111/j.1751-553x.2011.01388.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
INTRODUCTION Sudan has a multiethnic population with a high frequency of Hb S, but little is known about the β(S) haplotypes in this population. METHODS Blood samples from Sudanese Hb SS individuals were taken at two locations. Family history, age, ethnicity and clinical symptoms were recorded for each subject. Hb S was investigated using cellulose acetate electrophoresis (CAE) and cation exchange-high performance liquid chromatography. Dried blood samples from 93 individuals were used for β(S) haplotype identification based on restriction fragment length polymorphism analysis for seven restriction sites. RESULTS Haplotypes could be assigned unequivocally to 143 chromosomes. Four of the five typical β(S) -globin haplotypes were identified. The most frequent was the Cameroon (35.0%), followed by the Benin (29.4%), the Senegal (18.2%) and the Bantu (2.8%). The Indian-Arab haplotype was not observed. Three atypical haplotypes were identified in 17 patients, occurring at a combined frequency of 14.6%. One of these, found at the high frequency of 11.8%, possibly represented a new Sudan haplotype. CONCLUSION β(S) Haplotyes were demonstrated successfully from dried blood samples. A new haplotype is apparent in Sudan, in addition to the four African haplotypes.
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Affiliation(s)
- A Y Elderdery
- School of Pharmacy and Biomedical Sciences, Portsmouth University, Portsmouth, UK
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Ramsay M, Tiemessen CT, Choudhury A, Soodyall H. Africa: the next frontier for human disease gene discovery? Hum Mol Genet 2011; 20:R214-20. [PMID: 21908518 DOI: 10.1093/hmg/ddr401] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The populations of Africa harbour the greatest human genetic diversity following an evolutionary history tracing its beginnings on the continent to time before the emergence of Homo sapiens. Signatures of selection are detectable as responses to ancient environments and cultural practices, modulated by more recent events including infectious epidemics, migrations, admixture and, of course, chance. The age of high-throughput biology is not passing Africa by. African-based cohort studies and networks with an African footprint are ideal springboards for disease-related genetic and genomic studies. Initiatives like HapMap, the 1000 Genomes Project, MalariaGEN, the INDEPTH network and Human Heredity and Health in Africa are catalysts to exploring African genetic diversity and its role in the spectrum from health to disease. The challenges are abundant in dissecting biological questions in the light of linguistic, cultural, geographic and political boundaries and their respective roles in shaping health-related profiles. Will studies based on African populations lead to a new wave of discovery of genetic contributors to disease?
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Affiliation(s)
- Michèle Ramsay
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand andNational Health Laboratory Service, Johannesburg, South Africa.
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Abstract
The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane's initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are 'loss-of-function' mutants and appear to be recent polymorphisms from the last 5000-10 000 years or less. I discuss estimation of selection coefficients from case-control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants.
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27
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Saltzman AJ, Mancini-DiNardo D, Li C, Chung WK, Ho CY, Hurst S, Wynn J, Care M, Hamilton RM, Seidman GW, Gorham J, McDonough B, Sparks E, Seidman JG, Seidman CE, Rehm HL. Short communication: the cardiac myosin binding protein C Arg502Trp mutation: a common cause of hypertrophic cardiomyopathy. Circ Res 2010; 106:1549-52. [PMID: 20378854 DOI: 10.1161/circresaha.109.216291] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RATIONALE The myosin-binding protein C isoform 3 (MYBPC3) variant Arg502Trp has been identified in multiple hypertrophic cardiomyopathy (HCM) cases, but compelling evidence to support or refute the pathogenicity of this variant is lacking. OBJECTIVE To determine the prevalence, origin and clinical significance of the MYBPC3 Arg502Trp variant. METHODS AND RESULTS The prevalence of MYBPC3 Arg502Trp was ascertained in 1414 sequential HCM patients of primarily European descent. MYBPC3 Arg502Trp was identified in 34 of these 1414 unrelated HCM patients. Segregation of MYBPC3 Arg502Trp with clinical status was assessed in family members. Disease haplotypes were examined in 17 families using two loci flanking MYBPC3. Family studies identified an additional 43 variant carriers, many with manifest disease, yielding a calculated odds ratio of 11 000:1 for segregation of MYBPC3 Arg502Trp with HCM. Analyses in 17 families showed at least 4 independent haplotypes flanked MYBPC3 Arg502Trp. Eight individuals (4 probands and 4 family members) also had another sarcomere protein gene mutation. Major adverse clinical events occurred in approximately 30% of MYBPC3 Arg502Trp carriers by age 50; these were significantly more likely (P<0.0001) when another sarcomere mutation was present. CONCLUSIONS MYBPC3 Arg502Trp is the most common and recurrent pathogenic mutation in a diverse primarily European descent HCM cohort, occurring in 2.4% of patients. MYBPC3 Arg502Trp conveys a 340-fold increased risk for HCM by 45 years of age, when more than 50% of carriers have overt disease. HCM prognosis worsens when MYBPC3 Arg502Trp occurs in the setting of another sarcomere protein gene mutation.
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Affiliation(s)
- Adam J Saltzman
- Department of Medicine, Columbia University, New York, NY, USA
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28
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Abstract
In population genetics, it is common to represent the haplotype diversity at a genomic region between multiple populations using well-constructed visual representations. This typically requires the chromosomes from these populations to be grouped according to some definition of haplotypic similarity. Here, we introduce a novel algorithm for clustering haplotypes with the specific aim of addressing haplotype diversity within or between populations. The algorithm allows for missing data in the haplotypes and appropriately downweighs single nucleotide polymorphisms with higher extent of missingness. By identifying the canonical haplotypes in a genomic region, defined as the haplotype forms, which most chromosomes are similar to, the algorithm maps each chromosome to either a unique canonical haplotype or as a mosaic of the identified canonical haplotypes. This mapping can subsequently be utilized for producing graphical visualizations of the haplotype clustering for understanding the extent of haplotype diversity in the region. The clustering application has been implemented in R for distribution as haplosim, and we also provide a visualization script hapvisual for graphical display of the clustering results. The outcome of such analysis can be informative in understanding the extent of haplotype diversity between populations, in addressing the reproducibility of established association signals across multiple populations, and also in the investigation of positive selection in the human genome.
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Affiliation(s)
- Yik Y Teo
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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29
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Teo YY, Small KS, Kwiatkowski DP. Methodological challenges of genome-wide association analysis in Africa. Nat Rev Genet 2010; 11:149-60. [PMID: 20084087 PMCID: PMC3769612 DOI: 10.1038/nrg2731] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Medical research in Africa has yet to benefit from the advent of genome-wide association (GWA) analysis, partly because the genotyping tools and statistical methods that have been developed for European and Asian populations struggle to deal with the high levels of genome diversity and population structure in Africa. However, the haplotypic diversity of African populations might help to overcome one of the major roadblocks in GWA research, the fine mapping of causal variants. We review the methodological challenges and consider how GWA studies in Africa will be transformed by new approaches in statistical imputation and large-scale genome sequencing.
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Affiliation(s)
- Yik-Ying Teo
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Kerrin S. Small
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Dominic P. Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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30
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Teo YY, Fry AE, Bhattacharya K, Small KS, Kwiatkowski DP, Clark TG. Genome-wide comparisons of variation in linkage disequilibrium. Genome Res 2009; 19:1849-60. [PMID: 19541915 DOI: 10.1101/gr.092189.109] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Current genome-wide surveys of common diseases and complex traits fundamentally aim to detect indirect associations where the single nucleotide polymorphisms (SNPs) carrying the association signals are not biologically active but are in linkage disequilibrium (LD) with some unknown functional polymorphisms. Reproducing any novel discoveries from these genome-wide scans in independent studies is now a prerequisite for the putative findings to be accepted. Significant differences in patterns of LD between populations can affect the portability of phenotypic associations when the replication effort or meta-analyses are attempted in populations that are distinct from the original population in which the genome-wide study is performed. Here, we introduce a novel method for genome-wide analyses of LD variations between populations that allow the identification of candidate regions with different patterns of LD. The evidence of LD variation provided by the introduced method correlated with the degree of differences in the frequencies of the most common haplotype across the populations. Identified regions also resulted in greater variation in the success of replication attempts compared with random regions in the genome. A separate permutation strategy introduced for assessing LD variation in the absence of genome-wide data also correctly identified the expected variation in LD patterns in two well-established regions undergoing strong population-specific evolutionary pressure. Importantly, this method addresses whether a failure to reproduce a disease association in a disparate population is due to underlying differences in LD structure with an unknown functional polymorphism, which is vital in the current climate of replicating and fine-mapping established findings from genome-wide association studies.
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Affiliation(s)
- Yik Y Teo
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom.
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31
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Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M, Sirugo G, Sisay-Joof F, Usen S, Auburn S, Bumpstead SJ, Campino S, Coffey A, Dunham A, Fry AE, Green A, Gwilliam R, Hunt SE, Inouye M, Jeffreys AE, Mendy A, Palotie A, Potter S, Ragoussis J, Rogers J, Rowlands K, Somaskantharajah E, Whittaker P, Widden C, Donnelly P, Howie B, Marchini J, Morris A, SanJoaquin M, Achidi EA, Agbenyega T, Allen A, Amodu O, Corran P, Djimde A, Dolo A, Doumbo OK, Drakeley C, Dunstan S, Evans J, Farrar J, Fernando D, Hien TT, Horstmann RD, Ibrahim M, Karunaweera N, Kokwaro G, Koram KA, Lemnge M, Makani J, Marsh K, Michon P, Modiano D, Molyneux ME, Mueller I, Parker M, Peshu N, Plowe CV, Puijalon O, Reeder J, Reyburn H, Riley EM, Sakuntabhai A, Singhasivanon P, Sirima S, Tall A, Taylor TE, Thera M, Troye-Blomberg M, Williams TN, Wilson M, Kwiatkowski DP. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet 2009; 41:657-65. [PMID: 19465909 PMCID: PMC2889040 DOI: 10.1038/ng.388] [Citation(s) in RCA: 277] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 04/27/2009] [Indexed: 11/08/2022]
Abstract
We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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32
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Teo YY, Small KS, Fry AE, Wu Y, Kwiatkowski DP, Clark TG. Power consequences of linkage disequilibrium variation between populations. Genet Epidemiol 2009; 33:128-35. [PMID: 18814308 DOI: 10.1002/gepi.20366] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We quantify the degree to which LD differences exist in the human genome and investigates the consequences that variations in patterns of LD between populations can have on the power of case-control or family-trio association studies. Although only a small proportion of SNPs show significant LD differences (0.8-5%), these can introduce artificial signals of associations and reduce the power to detect true associations in case-control designs, even when meta-analytic approaches are used to account for stratification. We show that combining trios from different populations in the presence of significant LD differences can adversely affect power even though the number of trios has increased. Our results have implications on genetic studies conducted in populations with substantial population structure and show that the use of meta-analytic approaches or family-based designs to protect Type 1 error does not prevent loss of power due to differences in LD across populations.
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Affiliation(s)
- Yik Y Teo
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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33
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Hofer T, Ray N, Wegmann D, Excoffier L. Large Allele Frequency Differences between Human Continental Groups are more Likely to have Occurred by Drift During range Expansions than by Selection. Ann Hum Genet 2009; 73:95-108. [PMID: 19040659 DOI: 10.1111/j.1469-1809.2008.00489.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- T Hofer
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
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34
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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: 508] [Impact Index Per Article: 31.8] [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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35
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Liu L, Muralidhar S, Singh M, Sylvan C, Kalra IS, Quinn CT, Onyekwere OC, Pace BS. High-density SNP genotyping to define beta-globin locus haplotypes. Blood Cells Mol Dis 2008; 42:16-24. [PMID: 18829352 DOI: 10.1016/j.bcmd.2008.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 07/24/2008] [Indexed: 10/21/2022]
Abstract
Five major beta-globin locus haplotypes have been established in individuals with sickle cell disease (SCD) from the Benin, Bantu, Senegal, Cameroon, and Arab-Indian populations. Historically, beta-haplotypes were established using restriction fragment length polymorphism (RFLP) analysis across the beta-locus, which consists of five functional beta-like globin genes located on chromosome 11. Previous attempts to correlate these haplotypes as robust predictors of clinical phenotypes observed in SCD have not been successful. We speculate that the coverage and distribution of the RFLP sites located proximal to or within the globin genes are not sufficiently dense to accurately reflect the complexity of this region. To test our hypothesis, we performed RFLP analysis and high-density single nucleotide polymorphism (SNP) genotyping across the beta-locus using DNA samples from healthy African Americans with either normal hemoglobin A (HbAA) or individuals with homozygous SS (HbSS) disease. Using the genotyping data from 88 SNPs and Haploview analysis, we generated a greater number of haplotypes than that observed with RFLP analysis alone. Furthermore, a unique pattern of long-range linkage disequilibrium between the locus control region and the beta-like globin genes was observed in the HbSS group. Interestingly, we observed multiple SNPs within the HindIII restriction site located in the Ggamma-globin intervening sequence II which produced the same RFLP pattern. These findings illustrated the inability of RFLP analysis to decipher the complexity of sequence variations that impacts genomic structure in this region. Our data suggest that high-density SNP mapping may be required to accurately define beta-haplotypes that correlate with the different clinical phenotypes observed in SCD.
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Affiliation(s)
- Li Liu
- Department of Molecular and Cell Biology, Sickle Cell Disease Research Center, University of Texas at Dallas, Richardson, TX 75083, USA
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