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APCDR AGV Project: The African Genome Variation Project(dense array genotyping data)

The African Genome Variation Project (AGVP) aims to provide a global resource to understand population diversity and help design, implement and interpret genomic studies in sub-Saharan Africa (SSA), and worldwide. The AGVP represents dense genotyping data on 1,481 individuals from 18 ethno-linguistic groups and low coverage whole genome sequencing data on 320 individuals from 7 ethno-linguistic groups in SSA.

Type: Other
Archive: European Genome-phenome Archive (EGA)

13 Datasets 10 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
EGAD00010001045	APCDR AGV Project: Array data from 99 Igbo. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2.5-4v1_B	-
EGAD00010001046	APCDR AGV Project: Array data from 86 Sotho. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2-5_8v1_A	-
EGAD00010001047	APCDR AGV Project: Array data from 107 Ethiopians (Amhara, Oromo, Somali; subset of Ethiopian Genome Project Genotyping). Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2-5_8v1_A	-
EGAD00010001048	APCDR AGV Project: Array data from 79 Jola. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2-5_8v1_A	-
EGAD00010001049	APCDR AGV Project: Array data from 99 Kikuyu. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2.5-4v1_B	-
EGAD00010001050	APCDR AGV Project: Array data from 78 Wolof. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2-5_8v1_A	-
EGAD00010001051	APCDR AGV Project: Array data from 97 Barundi. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2-5_8v1_A	-
EGAD00010001052	APCDR AGV Project: Array data from 100 Kalenjin. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2.5-4v1_B	-
EGAD00010001053	APCDR AGV Project: Array data from 100 Banyarwanda. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2.5-4v1_B and HumanOmni2-5_8v1_A	-
EGAD00010001054	APCDR AGV Project: Array data from 74 Fula	Illumina HumanOmni2-5_8v1_A	-
EGAD00010001055	APCDR AGV Project: Array data from 100 Baganda. Raw data, intensity files and post-QC Plink files.		-
EGAD00010001056	APCDR AGV Project: Array data from 100 Zulu. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2.5-4v1_B and HumanOmni2-5_8v1_A	-
EGAD00010001057	APCDR AGV Project: Array data from 88 Mandinka. Raw data, intensity files and post-QC Plink files.	Illumina HumanOmni2-5_8v1_A	-

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	478
Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans. McManus KF, Taravella AM, Henn BM, Bustamante CD, Sikora M, Cornejo OE. PLoS Genet 13: 2017 e1006560	81
Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase. Shriner D, Rotimi CN. Am J Hum Genet 102: 2018 547-556	72
Genetic differentiation in East African ethnicities and its relationship with endurance running success. Zani ALS, Gouveia MH, Aquino MM, Quevedo R, Menezes RL, Rotimi C, Lwande GO, Ouma C, Mekonnen E, Fagundes NJR. PLoS One 17: 2022 e0265625	6
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	42
BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups. Breton G, Barham L, Mudenda G, Soodyall H, Schlebusch CM, Jakobsson M. Nat Commun 15: 2024 7307	1
Population history and admixture of the Fulani people from the Sahel. Fortes-Lima CA, Diallo MY, Janoušek V, Černý V, Schlebusch CM. Am J Hum Genet 112: 2025 261-275	3
Nested Admixture During and After the Trans-Atlantic Slave Trade on the Island of São Tomé. Ciccarella M, Laurent R, Szpiech ZA, Patin E, Dessarps-Freichey F, Utgé J, Lémée L, Semo A, Rocha J, Verdu P. Mol Biol Evol 42: 2025 msaf156	0
Exome sequencing identifies known and candidate genes in hearing impairment in Cameroon. Wonkam A, Wonkam-Tingang E, Yalcouyé A, Noubiap JJ, Nguefack S, Ngo Bitoungui VJ, Xhakaza L, Popel K, Bharadwaj T, Latanich R, Fortes-Lima CA, de Kock C, Esoh K, Zhang H, Schrauwen I, Mueller U, Leal SM. Commun Med (Lond) 6: 2026 331	0
Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period. Rodríguez-Varela R, Pochon Z, Mas-Sandoval A, Yaka R, Fortes-Lima CA, García Rubio A, Márquez-Grant N, Marí J, Graziani G, Ferrer Abárzuza A, Vicente M, Lorca-Francisco L, Linderholm A, Lagerholm VK, Arauna LR, Pérez-Ramallo P, Krzewińska M, Schlebusch CM, Götherström A. Nat Commun 17: 2026 2703	0