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APCDR Uganda GWAS: Genome-wide sequence variation and susceptibility loci for cardiometabolic traits in a sub-Saharan African population (UGWAS component)

Genomic studies in African populations provide unique opportunities to understand disease aetiology, human genetic diversity and population history in a regional and a global context. To leverage the relative benefits of different strategies, we undertook a combined approach of genotyping and whole-genome sequencing (WGS) in a population-based study of 6,400 individuals from a geographically defined rural community in South-West Uganda. We present data from 4,778 individuals with genotypes for ~2.2 million SNPs from the Uganda GWAS resource (UGWAS), and sequence data on up to 1,978 individuals spanning 41.5M SNPs and 4.5M indels (UG2G); 343 individuals overlap between the two datasets. We highlight the value of the largest sequence panel from Africa to date as a global resource for variant discovery, imputation and understanding the mutational spectrum and its clinical relevance in African populations. Alongside phenotype data, we provide a rich new genomic resource for researchers in Africa and globally.

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
EGAD00010000965 4778
Publications Citations
Linear mixed model for heritability estimation that explicitly addresses environmental variation.
Proc Natl Acad Sci U S A 113: 2016 7377-7382
The transferability of lipid loci across African, Asian and European cohorts.
Nat Commun 10: 2019 4330
Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.
Cell 179: 2019 984-1002.e36
Unpaired data empowers association tests.
Bioinformatics 37: 2021 785-792
Discovery and fine-mapping of kidney function loci in first genome-wide association study in Africans.
Hum Mol Genet 30: 2021 1559-1568
The flashfm approach for fine-mapping multiple quantitative traits.
Nat Commun 12: 2021 6147
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores.
Nat Genet 54: 2022 450-458
Transferability of genetic risk scores in African populations.
Nat Med 28: 2022 1163-1166
Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa.
Cell Genom 2: 2022 None
Multivariate GWAS analysis reveals loci associated with liver functions in continental African populations.
PLoS One 18: 2023 e0280344
Low and differential polygenic score generalizability among African populations due largely to genetic diversity.
HGG Adv 4: 2023 100184
Polygenic risk scores for disease risk prediction in Africa: current challenges and future directions.
Genome Med 15: 2023 87
Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations.
Nat Commun 14: 2023 7967