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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.

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 100
EGAD00001006425 12032
EGAD00001006581 171
EGAD00010001258 Human Cardio Metabochip 973
EGAD00010001996 10776
Publications Citations
Candidate gene polymorphisms study between human African trypanosomiasis clinical phenotypes in Guinea.
PLoS Negl Trop Dis 11: 2017 e0005833
Candidate genes-based investigation of susceptibility to Human African Trypanosomiasis in Côte d'Ivoire.
PLoS Negl Trop Dis 11: 2017 e0005992
Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition.
BMC Microbiol 20: 2020 330
Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study.
Nat Commun 11: 2020 5754
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.
Front Genet 11: 2020 456661
Genetic substructure and complex demographic history of South African Bantu speakers.
Nat Commun 12: 2021 2080
Prevalence and socio-demographic correlates of tobacco and alcohol use in four sub-Saharan African countries: a cross-sectional study of middle-aged adults.
BMC Public Health 21: 2021 1126
G6PD distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19.
Pharmacogenomics J 21: 2021 649-656
The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations.
Front Pharmacol 12: 2021 634016
Genetic associations with carotid intima-media thickness link to atherosclerosis with sex-specific effects in sub-Saharan Africans.
Nat Commun 13: 2022 855
Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa.
Nat Commun 13: 2022 926
Meta-analysis of sub-Saharan African studies provides insights into genetic architecture of lipid traits.
Nat Commun 13: 2022 2578
Apolipoprotein L1 High-Risk Genotypes and Albuminuria in Sub-Saharan African Populations.
Clin J Am Soc Nephrol 17: 2022 798-808
Racial and Ethnic Differences in the Association Between Classical Cardiovascular Risk Factors and Common Carotid Intima-Media Thickness: An Individual Participant Data Meta-Analysis.
J Am Heart Assoc 11: 2022 e023704
Characterization of <i>POR</i> haplotype distribution in African populations and comparison with other global populations.
Pharmacogenomics 23: 2022 771-782
Frequent vegetable consumption is inversely associated with hypertension among indigenous Africans.
Eur J Prev Cardiol 29: 2022 2359-2371
Characterization of CYP2D6 Pharmacogenetic Variation in Sub-Saharan African Populations.
Clin Pharmacol Ther 113: 2023 643-659
Genetic insights into smoking behaviours in 10,558 men of African ancestry from continental Africa and the UK.
Sci Rep 12: 2022 18828
H3AGWAS: a portable workflow for genome wide association studies.
BMC Bioinformatics 23: 2022 498
Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community.
Commun Biol 6: 2023 328
Diabetes care cascade and associated factors in 10 700 middle-aged adults in four sub-Saharan African countries: a cross-sectional study.
BMJ Open 13: 2023 e069193
Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans.
Neurol Genet 9: 2023 e200077
Performance and accuracy evaluation of reference panels for genotype imputation in sub-Saharan African populations.
Cell Genom 3: 2023 100332
Genome-wide association study of esophageal squamous cell cancer identifies shared and distinct risk variants in African and Chinese populations.
Am J Hum Genet 110: 2023 1690-1703
Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study.
Nat Commun 14: 2023 8376