APCDR AGV Project: Whole genome sequencing of 3 African populations (curated data)

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
EGAD00001001663	Low coverage (4x-8x) Illumina HiSeq curated sequence data from 3 African populations from the AGV project; 100 Baganda from Uganda (4x), 100 Zulu from South Africa (4x), and 120 Gumuz, Wolayta, Oromo, Somali and Amhara from Ethiopia (8x). Pre-processed, jointly called and filtered with GATK, refined with Beagle3, phased with SHAPEIT2.		1

Publications	Citations
The African Genome Variation Project shapes medical genetics in Africa. Gurdasani D, Carstensen T, Tekola-Ayele F, Pagani L, Tachmazidou I, Hatzikotoulas K, Karthikeyan S, Iles L, Pollard MO, Choudhury A, Ritchie GR, Xue Y, Asimit J, Nsubuga RN, Young EH, Pomilla C, Kivinen K, Rockett K, Kamali A, Doumatey AP, Asiki G, Seeley J, Sisay-Joof F, Jallow M, Tollman S, Mekonnen E, Ekong R, Oljira T, Bradman N, Bojang K, Ramsay M, Adeyemo A, Bekele E, Motala A, Norris SA, Pirie F, Kaleebu P, Kwiatkowski D, Tyler-Smith C, Rotimi C, Zeggini E, Sandhu MS. Nature 517: 2015 327-332	317
Whole-Exome Sequencing Reveals Uncaptured Variation and Distinct Ancestry in the Southern African Population of Botswana. Retshabile G, Mlotshwa BC, Williams L, Mwesigwa S, Mboowa G, Huang Z, Rustagi N, Swaminathan S, Katagirya E, Kyobe S, Wayengera M, Kisitu GP, Kateete DP, Wampande EM, Maplanka K, Kasvosve I, Pettitt ED, Matshaba M, Nsangi B, Marape M, Tsimako-Johnstone M, Brown CW, Yu F, Kekitiinwa A, Joloba M, Mpoloka SW, Mardon G, Anabwani G, Hanchard NA, Collaborative African Genomics Network (CAfGEN) of the H3Africa Consortium. Am J Hum Genet 102: 2018 731-743	30
Importance of Genetic Studies of Cardiometabolic Disease in Diverse Populations. Fernández-Rhodes L, Young KL, Lilly AG, Raffield LM, Highland HM, Wojcik GL, Agler C, Love SM, Okello S, Petty LE, Graff M, Below JE, Divaris K, North KE. Circ Res 126: 2020 1816-1840	14
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	29
A weakly structured stem for human origins in Africa. Ragsdale AP, Weaver TD, Atkinson EG, Hoal EG, Möller M, Henn BM, Gravel S. Nature 617: 2023 755-763	11
Increased homozygosity due to endogamy results in fitness consequences in a human population. Swinford NA, Prall SP, Gopalan S, Williams CM, Sheehama J, Scelza BA, Henn BM. Proc Natl Acad Sci U S A 120: 2023 e2309552120	2
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