H3Africa Chip Design - Aim of designing a cost-effective GWAS chip with content appropriate for use in genomics studies of individuals from the African continent.

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
EGAD00001004220	41 samples from Zambia generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	41
EGAD00001004316	24 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	24
EGAD00001004334	50 samples from Mali generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	50
EGAD00001004393	26 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	26
EGAD00001004448	60 samples from Burkina Faso and Ghana generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	60
EGAD00001004505	49 samples from Nigeria generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	49
EGAD00001004533	48 samples from Botswana generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	48
EGAD00001004557	The dataset includes BAM, FASTQ and decompressed gVCF files for 50 samples from Benin generated for the H3Africa Chip Design Study.	Illumina HiSeq 2500	50
EGAD00001005310	Basic phenotypic data (country, ethnicity and sex) for 348 samples of the H3Africa Chip Design Study. Divided into 8 datasets of 41 samples from Zambia, 24 samples from Cameroon, 50 samples from Mali, 26 samples from Cameroon, 49 samples from Nigeria, 48 samples from Botswana, 50 samples from Benin, 60 samples from Burkina Faso and Ghana.		348

Publications	Citations
High-depth African genomes inform human migration and health. Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, Adebamowo SN, Chimusa ER, Muzny D, Metcalf G, Gibbs RA, TrypanoGEN Research Group, Rotimi C, Ramsay M, H3Africa Consortium, Adeyemo AA, Lombard Z, Hanchard NA. Nature 586: 2020 741-748	152
G6PD distribution in sub-Saharan Africa and potential risks of using chloroquine/hydroxychloroquine based treatments for COVID-19. da Rocha JEB, Othman H, Tiemessen CT, Botha G, Ramsay M, Masimirembwa C, Adebamowo C, Choudhury A, Brandenburg JT, Matshaba M, Simo G, Gamo FJ, Hazelhurst S, as members of the H3Africa Consortium. Pharmacogenomics J 21: 2021 649-656	10
The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations. da Rocha JEB, Othman H, Botha G, Cottino L, Twesigomwe D, Ahmed S, Drögemöller BI, Fadlelmola FM, Machanick P, Mbiyavanga M, Panji S, Wright GEB, Adebamowo C, Matshaba M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Baldwin S, Chiano M, Cox C, Gross AS, Thomas P, Gamo FJ, Hazelhurst S. Front Pharmacol 12: 2021 634016	14
A quality control portal for sequencing data deposited at the European genome-phenome archive. Fernández-Orth D, Rueda M, Singh B, Moldes M, Jene A, Ferri M, Vasallo C, Fromont LA, Navarro A, Rambla J. Brief Bioinform 23: 2022 bbac136	1
Characterization of CYP2D6 Pharmacogenetic Variation in Sub-Saharan African Populations. Twesigomwe D, Drögemöller BI, Wright GEB, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Clin Pharmacol Ther 113: 2023 643-659	7
Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans. Monnakgotla NR, Mahungu AC, Heckmann JM, Botha G, Mulder NJ, Wu G, Rampersaud E, Myers J, Van Blitterswijk M, Rademakers R, Taylor JP, Wuu J, Benatar M, Nel M. Neurol Genet 9: 2023 e200077	1
A deep population reference panel of tandem repeat variation. Ziaei Jam H, Li Y, DeVito R, Mousavi N, Ma N, Lujumba I, Adam Y, Maksimov M, Huang B, Dolzhenko E, Qiu Y, Kakembo FE, Joseph H, Onyido B, Adeyemi J, Bakhtiari M, Park J, Javadzadeh S, Jjingo D, Adebiyi E, Bafna V, Gymrek M. Nat Commun 14: 2023 6711	16
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	5
The genetic legacy of the expansion of Bantu-speaking peoples in Africa. Fortes-Lima CA, Burgarella C, Hammarén R, Eriksson A, Vicente M, Jolly C, Semo A, Gunnink H, Pacchiarotti S, Mundeke L, Matonda I, Muluwa JK, Coutros P, Nyambe TS, Cikomola JC, Coetzee V, de Castro M, Ebbesen P, Delanghe J, Stoneking M, Barham L, Lombard M, Meyer A, Steyn M, Malmström H, Rocha J, Soodyall H, Pakendorf B, Bostoen K, Schlebusch CM. Nature 625: 2024 540-547	8
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