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The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide.

The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa.

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Studying these populations in the context of Eurasian and African HG populations suggest extensive Eurasian and HG admixture across Africa.

0.019) (Supplementary Methods and Supplementary Table 1).

Understanding this variation can provide insights into evolutionary processes that shape both human adaptation and variation in disease susceptibility have greatly enhanced our understanding of genetic variation globally, the characterization of African populations remains limited.

Other efforts examining African genetic diversity have been limited by variant density and sample sizes in individual populations, limiting relevance to more widespread populations across Africa.

ADMIXTURE analysis suggests substructure between North, East, West and South Africa.

We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa.

Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes.

The African Genome Variation Project (AGVP) is an international collaboration that expands on these efforts by systematically assessing genetic diversity among 1,481 individuals from 18 ethno-linguistic groups from sub-Saharan Africa (SSA) (Fig.

1 and Supplementary Methods Tables 1 and 2) with the Human Omni2.5M genotyping array and whole-genome sequences (WGS) from 320 individuals (Supplementary Methods Table 2).

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Importantly, the AGVP has evolved to help develop local resources for public health and genomic research, including strengthening research capacity, training, and collaboration across the region.

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