RESEARCH HIGHLIGHTS Nature Reviews Genetics | AOP, published online 16 December 2014; doi:10.1038/nrg3886

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The African Genome Variation Project

insights into population migrations and admixture, as well as providing a resource that can be used to design and interpret genomic studies PhotoDisc/Getty Images

Africa is the most genetically diverse continent in the world, although few studies have focused on characterizing the genome-wide genetic diversity of African populations. Now, the collaborative efforts of the African Genome Variation Project (AGVP) are published in Nature, leading to insights into population migrations and admixture, as well as providing a resource that can be used to design and interpret genomic studies in the future. Migration, selection and drift have contributed to genetically structured human populations, and dissecting the patterns of this variation can lead to clues regarding disease. In this study, the AGVP first used the HumanOmni2.5M genotyping array to examine genetic diversity of 1,481 individuals from 18 ethno-linguistic groups from sub-Saharan Africa. Genetic differentiation was found

to be fairly modest, with a low level of differentiation between the Niger-Congo language-speaking populations, which reflects the Bantu expansion — a population migration that occurred 3,000–5,000 years ago. Whole-genome sequencing of 320 Ethiopian (including Oromo, Amhara and Somali ethno-linguistic groups), Zulu and Bagandan individuals identified 29.8 million single-nucleotide polymorphisms (SNPs). Notably, a substantial proportion of these SNPs were unshared (11–23%) and novel (16–24%), emphasizing the need for large-scale sequencing of divergent sub-Saharan African populations to uncover all constituent genetic diversity. Quantification of admixture revealed a substantial European ancestry in several populations (0–50%), with the highest proportions in East Africa. Hunter-gatherer admixture (0–26%)

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was highest in the Zulu and Sotho populations in South Africa. The researchers note complex and regionally distinct admixture with multiple Eurasian and hunter-gatherer populations across sub-Saharan Africa over time. To identify SNPs that might have undergone selection, the team examined SNPs that were highly differentiated either between African and European populations, or between the African populations. They found several new gene regions that are highly differentiated, including genes linked to malaria susceptibility and hypertension. In addition, by comparing populations that live in endemic and non-endemic infectious diseases regions, several genes that associate with infectious disease susceptibility were identified. Finally, the team demonstrate the feasibility of developing a pan-African genotype array, which will be important for future research. Bryony Jones ORIGINAL RESEARCH PAPER Gurdasani, D et al. The African Genome Variation Project shapes medical genetics in Africa. Nature http://dx.doi. org/10.1038/nature13997 (2014)

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Population genetics: the African Genome Variation Project.

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