Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans

Choudhury, Ananyo ; Ramsay, Michele ; Hazelhurst, Scott ; Aron, Shaun ; Bardien, Soraya ; Botha, Gerrit ; Chimusa, Emile R. ; Christoffels, Alan ; Gamieldien, Junaid ; Sefid-Dashti, Mahjoubeh J. ; Joubert, Fourie ; Meintjes, Ayton ; Mulder, Nicola ; Ramesar, Raj ; Rees, Jasper ; Scholtz, Kathrine ; Sengupta, Dhriti ; Soodyall, Himla ; Venter, Philip ; Warnich, Louise ; Pepper, Michael S. (2017)

CITATION: Choudhury, A., et al. 2017. Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nature Communications, 8, Article number: 2062, doi:10.1038/s41467-017-00663-9.

The original publication is available at https://www.nature.com


ENGLISH ABSTRACT: The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10−6) differentiation, and FST analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease.

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