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Wonkam A, Munung NS, Guindo A, Nnodu O. Priorities for sickle cell disease global research and implementation. Lancet 2024:S0140-6736(24)01400-4. [PMID: 39002545 DOI: 10.1016/s0140-6736(24)01400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024]
Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa; McKusick-Nathans Institute, Baltimore and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Nchangwi Syntia Munung
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Aldiouma Guindo
- Centre de Recherche et de Lutte contre la Drépanocytose (CRLD), Bamako, Mali
| | - Obiageli Nnodu
- Department of Haematology and Blood Transfusion and the Centre of Excellence for Sickle Cell Disease Research and Training (CESRTA), University of Abuja, Abuja, Nigeria
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2
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Mano RM, Kuona P, Misihairabgwi JM. Determination of birth prevalence of sickle cell disease using point of care test HemotypeSC™ at Rundu Hospital, Namibia. BMC Pediatr 2024; 24:323. [PMID: 38730340 PMCID: PMC11084002 DOI: 10.1186/s12887-024-04805-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Sickle cell disease (SCD), a noncommunicable disease, has the greatest burden in sub-Saharan Africa. The majority of children (50-90%) with SCD die before their 5th birthday, with approximately 150,000-300,000 annual SCD child deaths in Africa. In developed countries, newborn screening (NBS) has been shown to improve the survival of children with sickle cell disease, with under5 childhood mortality reduced tenfold due to interventions performed before the development of complications. Point -of-care tests have been developed for resource limited settings to expand NBS. The aim of this study was to determine the birth prevalence of sickle cell disease in Namibia using the HemoTypeSC™ point-of-care test. METHODS A cross-sectional descriptive study was carried out at Rundu Intermediate Hospital in the Kavango East Region. Two hundred and two (202) well newborns within 72 h of birth were recruited for the study from 22 February to the 23th March 2023. Descriptive statistics were used to compute the haemoglobin types of the study participants. RESULTS The majority of the participants (n = 105, 52%) were females, and (n = 97,48%) were males. The median age of the participants was 23 h (Q1, Q3; 11; 33),) with an age range of 2-98 h. Sickle cell trait was present in 9.4% of the screened newborns, no homozygous disease was detected, and 90.6% had Hb AA. CONCLUSIONS This study is the first to measure HbS gene carriage at birth using HemotypeSC point-of-care testing in Namibia. There was a moderate prevalence of sickle cell traits but no SCD. This baseline study may provide the foundation for larger epidemiological surveys to map HbS gene carriage in Namibia to provide evidence for policy makers to fashion appropriate SCD newborn screening services.
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Affiliation(s)
- Runyararo Mashingaidze Mano
- Department of Maternal & Child Health, Division of Paediatrics, School of Medicine, Faculty of Health Sciences and Veterinary Medicine, University of Namibia Hage Geingob Campus, Bach Street, Windhoek, Namibia.
| | - Patience Kuona
- Department of Child, Adolescent and Women's Health, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Jane Masiiwa Misihairabgwi
- Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia Faculty of Health Sciences & Veterinary Medicine, Windhoek, Namibia
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Sun KY, Bai X, Chen S, Bao S, Kapoor M, Zhang C, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Gioia AD, Rajagopal V, Lopez A, Varela JR, Alegre J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton J, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalog of protein-coding variation in 985,830 individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539329. [PMID: 37214792 PMCID: PMC10197621 DOI: 10.1101/2023.05.09.539329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Locke
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | - Jesus Alegre
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Roberto Tapia-Conyer
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Pablo Kuri-Morales
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jason Torres
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria. Int J Mol Sci 2022; 23:ijms23094849. [PMID: 35563239 PMCID: PMC9101746 DOI: 10.3390/ijms23094849] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/04/2022] Open
Abstract
Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.
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Gusareva ES, Lorenzini PA, Ramli NAB, Ghosh AG, Kim HL. Population-specific adaptation in malaria-endemic regions of asia. J Bioinform Comput Biol 2021; 19:2140006. [PMID: 34753405 DOI: 10.1142/s0219720021400060] [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] [Indexed: 11/18/2022]
Abstract
Evolutionary mechanisms of adaptation to malaria are understudied in Asian endemic regions despite a high prevalence of malaria in the region. In our research, we performed a genome-wide screening for footprints of natural selection against malaria by comparing eight Asian population groups from malaria-endemic regions with two non-endemic population groups from Europe and Mongolia. We identified 285 adaptive genes showing robust selection signals across three statistical methods, iHS, XP-EHH, and PBS. Interestingly, most of the identified genes (82%) were found to be under selection in a single population group, while adaptive genes shared across populations were rare. This is likely due to the independent adaptation history in different endemic populations. The gene ontology (GO) analysis for the 285 adaptive genes highlighted their functional processes linked to neuronal organizations or nervous system development. These genes could be related to cerebral malaria and may reduce the inflammatory response and the severity of malaria symptoms. Remarkably, our novel population genomic approach identified population-specific adaptive genes potentially against malaria infection without the need for patient samples or individual medical records.
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Affiliation(s)
- Elena S Gusareva
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Paolo Alberto Lorenzini
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore
| | - Nurul Adilah Binte Ramli
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Amit Gourav Ghosh
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore
| | - Hie Lim Kim
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
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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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Abstract
Ancestral and geographical issues underlie the need to develop Africa-specific guidelines for the return of genomic research results in Africa. In this Commentary, we outline the challenges that will inform policies and practices moving forward.
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Affiliation(s)
- Ambroise Wonkam
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
| | - Jantina de Vries
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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8
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Gouveia MH, Bergen AW, Borda V, Nunes K, Leal TP, Ogwang MD, Yeboah ED, Mensah JE, Kinyera T, Otim I, Nabalende H, Legason ID, Mpoloka SW, Mokone GG, Kerchan P, Bhatia K, Reynolds SJ, Birtwum RB, Adjei AA, Tettey Y, Tay E, Hoover R, Pfeiffer RM, Biggar RJ, Goedert JJ, Prokunina-Olsson L, Dean M, Yeager M, Lima-Costa MF, Hsing AW, Tishkoff SA, Chanock SJ, Tarazona-Santos E, Mbulaiteye SM. Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt". PLoS Genet 2019; 15:e1008027. [PMID: 30849090 PMCID: PMC6426263 DOI: 10.1371/journal.pgen.1008027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 03/20/2019] [Accepted: 02/17/2019] [Indexed: 12/13/2022] Open
Abstract
Populations in sub-Saharan Africa have historically been exposed to intense selection from chronic infection with falciparum malaria. Interestingly, populations with the highest malaria intensity can be identified by the increased occurrence of endemic Burkitt Lymphoma (eBL), a pediatric cancer that affects populations with intense malaria exposure, in the so called "eBL belt" in sub-Saharan Africa. However, the effects of intense malaria exposure and sub-Saharan populations' genetic histories remain poorly explored. To determine if historical migrations and intense malaria exposure have shaped the genetic composition of the eBL belt populations, we genotyped ~4.3 million SNPs in 1,708 individuals from Ghana and Northern Uganda, located on opposite sides of eBL belt and with ≥ 7 months/year of intense malaria exposure and published evidence of high incidence of BL. Among 35 Ghanaian tribes, we showed a predominantly West-Central African ancestry and genomic footprints of gene flow from Gambian and East African populations. In Uganda, the North West population showed a predominantly Nilotic ancestry, and the North Central population was a mixture of Nilotic and Southern Bantu ancestry, while the Southwest Ugandan population showed a predominant Southern Bantu ancestry. Our results support the hypothesis of diverse ancestral origins of the Ugandan, Kenyan and Tanzanian Great Lakes African populations, reflecting a confluence of Nilotic, Cushitic and Bantu migrations in the last 3000 years. Natural selection analyses suggest, for the first time, a strong positive selection signal in the ATP2B4 gene (rs10900588) in Northern Ugandan populations. These findings provide important baseline genomic data to facilitate disease association studies, including of eBL, in eBL belt populations.
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Affiliation(s)
- Mateus H. Gouveia
- Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center for Research on Genomics & Global Health, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Andrew W. Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Victor Borda
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Thiago P. Leal
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Statistics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Martin D. Ogwang
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | | | - Tobias Kinyera
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | | | | | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone, Botswana
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | | | | | - Yao Tettey
- University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- University of Ghana Medical School, Accra, Ghana
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Robert J. Biggar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - James J. Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, US Department of Health and Human Services, Frederick, Maryland, United States of America
| | - M. Fernanda Lima-Costa
- Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ann W. Hsing
- Stanford Cancer Institute, Stanford University, Stanford, California, United States of America
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, University of Pennsylvania, Philadelphia, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
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