H3Africa - Genomic and Environmental Risk Factors for Cardiometabolic Disease in Africans

The long-term vision of the AWI-Gen Collaborative Centre (CC) is to build sustainable capacity in Africa for research that leads to an understanding of the interplay between genetic, epigenetic and environmental risk factors for obesity and related cardiometabolic diseases (CMD) in sub-Saharan Africa. The CC will be consolidated under the auspices of the University of the Witwatersrand (Wits) and the International Network for the Demographic Evaluation of Populations and Their Health in Developing Countries (INDEPTH). It will capitalize on the unique strengths of existing longitudinal cohorts, including the urban Soweto and rural Agincourt studies in South Africa (Wits based), and the well established INDEPTH demographic health and surveillance centers in Kenya, Ghana, Burkina Faso and South Africa. The centers offer established infrastructure, trained fieldworkers, long-standing community engagement, and detailed longitudinal phenotypic data, focusing on obesity and cardiometabolic health. Key strengths are harmonized phenotyping across sites, building on strong existing cohorts, and representation of the geographic and social variability of African populations. We aim to: 1. Build sustainable infrastructure (biobanks and laboratories) and capabilities (well characterized population cohorts, genotyping and bioinformatics) for genomic research on the African continent; 2. Understand the genomic architecture of sub-Saharan populations from west, east and south Africa to guide genomic studies (genome sequencing and high throughput SNP and CNV arrays using unrelated individuals and family trios to improve the accuracy of haplotype analyses) and; 3. Investigate the independent and synergistic genomic contributions to body fat distribution (BMI, hip/waist circumference, subcutaneous and visceral fat) in these populations considering the relevant environmental and social contexts (rural/urban communities, quickly transitioning obesity prevalence, differential HIV, TB, and malaria infection histories). We will investigate the effect of obesity and fat distribution on the risk for CMD in the longitudinal cohorts.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

5 Datasets 29 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006418	These samples were sequenced at the Broad Institute on an Illumina HiSeqX at 30x -- PCR Free. The CRAMS and VCF are as produced by Broad. The VCFs produced were generated by the Broad using GATK.		100
EGAD00001006425	The phenotypic data for ~12500 samples of the AWI-Gen Phase 1 Population cross-sectional study of older adults (mostly between 40 and 60 years), men and women. Six study sites in four sub-Saharan African counties including Ghana, Burkina Faso, Kenya and South Africa. Some groups are missing data for specific variables. Data includes questionnaire data (demography, health history, family health history, behaviour and infection data); anthropometry; and laboratory assays on blood and urine.		12032
EGAD00001006581	This is human phenotype data for participants in a gut microbiome study. This data was collected at the same time as the stool samples used for the microbiome component. Participants were also part of the AWI-Gen Phase 1 main study. https://www.ebi.ac.uk/ena/data/view/PRJEB40733		171
EGAD00010001258	Pilot study on the interplay between genetic, epigenetic, and environmental risk factors for obesity and related cardiometabolic diseases with 973 samples from South Africa genotyped on Illumina Human MetaboChip array.	Human Cardio Metabochip	973
EGAD00010001996	The samples were genotyped on the H3Africa array (~2.3M SNPs) using the Illumina FastTrack Sequencing Service2. The default Illumina pipeline was used for the genotype calling (build GRCh37/hg19). The data was converted to PLINK using the h3abionet/h3agwas/call2plink pipeline and QC done using the h3abionet/h3agwas/qc pipeline		10776

Publications	Citations
Candidate gene polymorphisms study between human African trypanosomiasis clinical phenotypes in Guinea. Kaboré JW, Ilboudo H, Noyes H, Camara O, Kaboré J, Camara M, Koffi M, Lejon V, Jamonneau V, MacLeod A, Hertz-Fowler C, Belem AMG, Matovu E, Bucheton B, Sidibe I, TrypanoGEN Research Group as members of The H3Africa Consortium. PLoS Negl Trop Dis 11: 2017 e0005833	15
Candidate genes-based investigation of susceptibility to Human African Trypanosomiasis in Côte d'Ivoire. Ahouty B, Koffi M, Ilboudo H, Simo G, Matovu E, Mulindwa J, Hertz-Fowler C, Bucheton B, Sidibé I, Jamonneau V, MacLeod A, Noyes H, N'Guetta SP, TrypanoGEN Research Group as members of The H3Africa Consortium. PLoS Negl Trop Dis 11: 2017 e0005992	10
Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS, Hazelhurst S. BMC Microbiol 20: 2020 330	18
Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study. Ceballos FC, Hazelhurst S, Clark DW, Agongo G, Asiki G, Boua PR, Xavier Gómez-Olivé F, Mashinya F, Norris S, Wilson JF, Ramsay M. Nat Commun 11: 2020 5754	9
Candidate Gene Analysis Reveals Strong Association of <i>CETP</i> Variants With High Density Lipoprotein Cholesterol and <i>PCSK9</i> Variants With Low Density Lipoprotein Cholesterol in Ghanaian Adults: An AWI-Gen Sub-Study. Agongo G, Amenga-Etego L, Nonterah EA, Debpuur C, Choudhury A, Bentley AR, Oduro AR, Rotimi CN, Crowther NJ, Ramsay M, AWI-Gen and H3Africa, H Africa. Front Genet 11: 2020 456661	3
Genetic substructure and complex demographic history of South African Bantu speakers. Sengupta D, Choudhury A, Fortes-Lima C, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K, Gunnink H, Chousou-Polydouri N, Delius P, Tollman S, Gómez-Olivé FX, Norris S, Mashinya F, Alberts M, AWI-Gen Study, H3Africa Consortium, Hazelhurst S, Schlebusch CM, Ramsay M. Nat Commun 12: 2021 2080	31
Prevalence and socio-demographic correlates of tobacco and alcohol use in four sub-Saharan African countries: a cross-sectional study of middle-aged adults. Boua PR, Soo CC, Debpuur C, Maposa I, Nkoana S, Mohamed SF, Choma S, Oduro A, Asiki G, Micklesfield LK, Gómez-Olivé FX, Sorgho H, Mall S, Ramsay M, as members of AWI-Gen and the H3Africa Consortium. BMC Public Health 21: 2021 1126	14
G6PD distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19. da Rocha JEB, Othman H, Tiemessen CT, Botha G, Ramsay M, Masimirembwa C, Adebamowo C, Choudhury A, Brandenburg JT, Matshaba M, Simo G, Gamo FJ, Hazelhurst S, as members of the H3Africa Consortium. Pharmacogenomics J 21: 2021 649-656	10
The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations. da Rocha JEB, Othman H, Botha G, Cottino L, Twesigomwe D, Ahmed S, Drögemöller BI, Fadlelmola FM, Machanick P, Mbiyavanga M, Panji S, Wright GEB, Adebamowo C, Matshaba M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Baldwin S, Chiano M, Cox C, Gross AS, Thomas P, Gamo FJ, Hazelhurst S. Front Pharmacol 12: 2021 634016	14
Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans. Boua PR, Brandenburg JT, Choudhury A, Sorgho H, Nonterah EA, Agongo G, Asiki G, Micklesfield L, Choma S, Gómez-Olivé FX, Hazelhurst S, Tinto H, Crowther NJ, Mathew CG, Ramsay M, AWI-Gen Study, H3Africa Consortium. Nat Commun 13: 2022 855	3
Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Tamburini FB, Maghini D, Oduaran OH, Brewster R, Hulley MR, Sahibdeen V, Norris SA, Tollman S, Kahn K, Wagner RG, Wade AN, Wafawanaka F, Gómez-Olivé FX, Twine R, Lombard Z, H3Africa AWI-Gen Collaborative Centre, Hazelhurst S, Bhatt AS. Nat Commun 13: 2022 926	27
Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits. Choudhury A, Brandenburg JT, Chikowore T, Sengupta D, Boua PR, Crowther NJ, Agongo G, Asiki G, Gómez-Olivé FX, Kisiangani I, Maimela E, Masemola-Maphutha M, Micklesfield LK, Nonterah EA, Norris SA, Sorgho H, Tinto H, Tollman S, Graham SE, Willer CJ, AWI-Gen study, H3Africa Consortium, Hazelhurst S, Ramsay M. Nat Commun 13: 2022 2578	18
Apolipoprotein L1 High-Risk Genotypes and Albuminuria in Sub-Saharan African Populations. Brandenburg JT, Govender MA, Winkler CA, Boua PR, Agongo G, Fabian J, Ramsay M. Clin J Am Soc Nephrol 17: 2022 798-808	6
Racial and Ethnic Differences in the Association Between Classical Cardiovascular Risk Factors and Common Carotid Intima-Media Thickness: An Individual Participant Data Meta-Analysis. Nonterah EA, Crowther NJ, Klipstein-Grobusch K, Oduro AR, Kavousi M, Agongo G, Anderson TJ, Asiki G, Boua PR, Choma SSR, Couper DJ, Engström G, de Graaf J, Kauhanen J, Lonn EM, Mathiesen EB, Micklesfield LK, Okazaki S, Polak JF, Rundek T, Salonen JT, Tollman SM, Tuomainen TP, Grobbee DE, Ramsay M, Bots ML, H3Africa AWI‐Gen, USE‐IMT collaborative study group. J Am Heart Assoc 11: 2022 e023704	7
Characterization of <i>POR</i> haplotype distribution in African populations and comparison with other global populations. Booyse RP, Twesigomwe D, Hazelhurst S. Pharmacogenomics 23: 2022 771-782	1
Frequent vegetable consumption is inversely associated with hypertension among indigenous Africans. Akpa OM, Okekunle AP, Asowata OJ, Chikowore T, Mohamed SF, Sarfo F, Akinyemi R, Akpalu A, Wahab K, Obiako R, Komolafe M, Owolabi L, Osaigbovo GO, Ogbole G, Tiwari HK, Akinyemi J, Fakunle A, Uvere E, Adeoye AM, Lackland D, Arnett DK, Ovbiagele B, Ramsay M, Owolabi M. Eur J Prev Cardiol 29: 2022 2359-2371	6
Characterization of CYP2D6 Pharmacogenetic Variation in Sub-Saharan African Populations. Twesigomwe D, Drögemöller BI, Wright GEB, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Clin Pharmacol Ther 113: 2023 643-659	7
Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK. Piga NN, Boua PR, Soremekun C, Shrine N, Coley K, Brandenburg JT, Tobin MD, Ramsay M, Fatumo S, Choudhury A, Batini C. Sci Rep 12: 2022 18828	1
H3AGWAS: a portable workflow for genome wide association studies. Brandenburg JT, Clark L, Botha G, Panji S, Baichoo S, Fields C, Hazelhurst S. BMC Bioinformatics 23: 2022 498	5
Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community. Soo CC, Brandenburg JT, Nebel A, Tollman S, Berkman L, Ramsay M, Choudhury A. Commun Biol 6: 2023 328	1
Diabetes care cascade and associated factors in 10 700 middle-aged adults in four sub-Saharan African countries: a cross-sectional study. Wade AN, Maposa I, Agongo G, Asiki G, Boua P, Choma SSR, Gómez-Olivé FX, Maimela E, Micklesfield LK, Mohamed SF, Nonterah EA, Norris SA, Sorgho H, Ramsay M, Crowther NJ, AWIGen and the H3Africa Consortium. BMJ Open 13: 2023 e069193	6
Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans. Monnakgotla NR, Mahungu AC, Heckmann JM, Botha G, Mulder NJ, Wu G, Rampersaud E, Myers J, Van Blitterswijk M, Rademakers R, Taylor JP, Wuu J, Benatar M, Nel M. Neurol Genet 9: 2023 e200077	1
Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations. Sengupta D, Botha G, Meintjes A, Mbiyavanga M, AWI-Gen Study, H3Africa Consortium, Hazelhurst S, Mulder N, Ramsay M, Choudhury A. Cell Genom 3: 2023 100332	8
Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations. Chen WC, Brandenburg JT, Choudhury A, Hayat M, Sengupta D, Swiel Y, Babb de Villiers C, Ferndale L, Aldous C, Soo CC, Lee S, Curtis C, Newton R, Waterboer T, Sitas F, Bradshaw D, Abnet CC, Ramsay M, Parker MI, Singh E, Lewis CM, Mathew CG. Am J Hum Genet 110: 2023 1690-1703	2
Characterization of <i>CYP2C19</i> pharmacogenetic variation in African populations and comparison with other global populations. Booyse RP, Twesigomwe D, Hazelhurst S. Pharmacogenomics 24: 2023 845-857	0
Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study. Singh S, Choudhury A, Hazelhurst S, Crowther NJ, Boua PR, Sorgho H, Agongo G, Nonterah EA, Micklesfield LK, Norris SA, Kisiangani I, Mohamed S, Gómez-Olivé FX, Tollman SM, Choma S, Brandenburg JT, Ramsay M. Nat Commun 14: 2023 8376	2
Genetic association and transferability for urinary albumin-creatinine ratio as a marker of kidney disease in four Sub-Saharan African populations and non-continental individuals of African ancestry. Brandenburg JT, Chen WC, Boua PR, Govender MA, Agongo G, Micklesfield LK, Sorgho H, Tollman S, Asiki G, Mashinya F, Hazelhurst S, Morris AP, Fabian J, Ramsay M. Front Genet 15: 2024 1372042	0
Variability of polygenic prediction for body mass index in Africa. Chikowore T, Läll K, Micklesfield LK, Lombard Z, Goedecke JH, Fatumo S, Norris SA, Magi R, Ramsay M, Franks PW, Pare G, Morris AP. Genome Med 16: 2024 74	0
Ancestry-aligned polygenic scores combined with conventional risk factors improve prediction of cardiometabolic outcomes in African populations. Kamp M, Pain O, Lewis CM, Ramsay M. Genome Med 16: 2024 106	0