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.

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

1 Dataset 15 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
EGAD00010000965	Array data from 4778 individuals from general population of rural Uganda		4778

Publications	Citations
Linear mixed model for heritability estimation that explicitly addresses environmental variation. Heckerman D, Gurdasani D, Kadie C, Pomilla C, Carstensen T, Martin H, Ekoru K, Nsubuga RN, Ssenyomo G, Kamali A, Kaleebu P, Widmer C, Sandhu MS. Proc Natl Acad Sci U S A 113: 2016 7377-7382	47
The transferability of lipid loci across African, Asian and European cohorts. Kuchenbaecker K, Telkar N, Reiker T, Walters RG, Lin K, Eriksson A, Gurdasani D, Gilly A, Southam L, Tsafantakis E, Karaleftheri M, Seeley J, Kamali A, Asiki G, Millwood IY, Holmes M, Du H, Guo Y, Kumari M, Dedoussis G, Li L, Chen Z, Sandhu MS, Zeggini E, Understanding Society Scientific Group. Nat Commun 10: 2019 4330	61
Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa. Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS. Cell 179: 2019 984-1002.e36	131
Unpaired data empowers association tests. Gong M, Liu P, Sciurba FC, Stojanov P, Tao D, Tseng GC, Zhang K, Batmanghelich K. Bioinformatics 37: 2021 785-792	0
Discovery and fine-mapping of kidney function loci in first genome-wide association study in Africans. Fatumo S, Chikowore T, Kalyesubula R, Nsubuga RN, Asiki G, Nashiru O, Seeley J, Crampin AC, Nitsch D, Smeeth L, Kaleebu P, Burgess S, Nyirenda M, Franceschini N, Morris AP, Tomlinson L, Newton R. Hum Mol Genet 30: 2021 1559-1568	17
The flashfm approach for fine-mapping multiple quantitative traits. Hernández N, Soenksen J, Newcombe P, Sandhu M, Barroso I, Wallace C, Asimit JL. Nat Commun 12: 2021 6147	12
Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores. Weissbrod O, Kanai M, Shi H, Gazal S, Peyrot WJ, Khera AV, Okada Y, Biobank Japan Project, Martin AR, Finucane HK, Price AL. Nat Genet 54: 2022 450-458	157
Transferability of genetic risk scores in African populations. Kamiza AB, Toure SM, Vujkovic M, Machipisa T, Soremekun OS, Kintu C, Corpas M, Pirie F, Young E, Gill D, Sandhu MS, Kaleebu P, Nyirenda M, Motala AA, Chikowore T, Fatumo S. Nat Med 28: 2022 1163-1166	52
Uganda Genome Resource: A rich research database for genomic studies of communicable and non-communicable diseases in Africa. Fatumo S, Mugisha J, Soremekun OS, Kalungi A, Mayanja R, Kintu C, Makanga R, Kakande A, Abaasa A, Asiki G, Kalyesubula R, Newton R, Nyirenda M, Sandhu MS, Kaleebu P. Cell Genom 2: 2022 None	15
Multivariate GWAS analysis reveals loci associated with liver functions in continental African populations. Soremekun C, Machipisa T, Soremekun O, Pirie F, Oyekanmi N, Motala AA, Chikowore T, Fatumo S. PLoS One 18: 2023 e0280344	0
Low and differential polygenic score generalizability among African populations due largely to genetic diversity. Majara L, Kalungi A, Koen N, Tsuo K, Wang Y, Gupta R, Nkambule LL, Zar H, Stein DJ, Kinyanda E, Atkinson EG, Martin AR. HGG Adv 4: 2023 100184	28
Polygenic risk scores for disease risk prediction in Africa: current challenges and future directions. Fatumo S, Sathan D, Samtal C, Isewon I, Tamuhla T, Soremekun C, Jafali J, Panji S, Tiffin N, Fakim YJ. Genome Med 15: 2023 87	14
Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations. Tallman S, Sungo MDD, Saranga S, Beleza S. Nat Commun 14: 2023 7967	0
Prevalence and correlates of common mental disorders among participants of the Uganda Genome Resource: Opportunities for psychiatric genetics research. Kalungi A, Kinyanda E, Akena DH, Gelaye B, Ssembajjwe W, Mpango RS, Ongaria T, Mugisha J, Makanga R, Kakande A, Kimono B, Amanyire P, Kirumira F, Lewis CM, McIntosh AM, Kuchenbaecker K, Nyirenda M, Kaleebu P, Fatumo S. Mol Psychiatry 30: 2025 122-130	0
Accounting for heterogeneity due to environmental sources in meta-analysis of genome-wide association studies. Wang S, Ojewunmi OO, Kamiza A, Ramsay M, Morris AP, Chikowore T, Fatumo S, Asimit JL. Commun Biol 7: 2024 1512	1