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

dc.contributor.authorChoudhury, Ananyo
dc.contributor.authorRamsay, Michele
dc.contributor.authorHazelhurst, Scott
dc.contributor.authorAron, Shaun
dc.contributor.authorBardien, Soraya
dc.contributor.authorBotha, Gerrit
dc.contributor.authorChimusa, Emile R.
dc.contributor.authorChristoffels, Alan
dc.contributor.authorGamieldien, Junaid
dc.contributor.authorSefid-Dashti, Mahjoubeh J.
dc.contributor.authorJoubert, Fourie
dc.contributor.authorMeintjes, Ayton
dc.contributor.authorMulder, Nicola
dc.contributor.authorRamesar, Raj
dc.contributor.authorRees, Jasper
dc.contributor.authorScholtz, Kathrine
dc.contributor.authorSengupta, Dhriti
dc.contributor.authorSoodyall, Himla
dc.contributor.authorVenter, Philip
dc.contributor.authorWarnich, Louise
dc.contributor.authorPepper, Michael Sean
dc.contributor.emailmichael.pepper@up.ac.zaen_ZA
dc.date.accessioned2018-08-16T08:35:15Z
dc.date.available2018-08-16T08:35:15Z
dc.date.issued2017-12-12
dc.descriptionM.R. and M.S.P. co-lead the SAHGP initiative, and the project was designed and coordinated by the core working group including M.R., M.S.P., S.B., H.S., R.R., J.R., K.S., P.V., N.M., F.J., S.H., and L.V. M.R. and H.S. obtained ethics approval for the study. The data analysis team was led by S.H. (PCA; STRUCTURE and Y chromosome analysis) and included A.C. (novel SNV characterization, LOF variant, f2, FST, SFS, and ROH analysis), N.M. (functional analysis), F.J. (variant calling), S.A. (variant calling), G.B. (functional annotation and data curation), E.R.C. (admixture), J.G. (functional annotation), M.J.S.D. (functional annotation), A.M. (functional annotation, SNV characterization, data curation, and mtDNA analysis), and D.S. (regional FST analysis, data visualization). All authors wrote the Methods section and notes on their analyses. M.R. and A.C. drafted the manuscript, and A.C. was responsible for coordinating Tables and Figures (including the Supplement).en_ZA
dc.description.abstractThe 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.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.departmentImmunologyen_ZA
dc.description.librarianam2018en_ZA
dc.description.sponsorshipThe South African National Department of Science and Technology for funding this initiative under the umbrella of the Southern African Human Genome Programme (SAHGP). A.C. was supported by the AWI-Gen Collaborative Centre funded by the NIH (1U54HG006938) as part of the H3Africa Consortium. M.R. is a South African Research Chair in Genomics and Bioinformatics of African populations hosted by the University of the Witwatersrand, funded by the Department of Science and Technology and administered by National Research Foundation of South Africa (N.R.F.). M.S.P. was funded by the South African Medical Research Council (Flagship and Stem Cell Extramural Unit awards) and the Institute for Cellular and Molecular Medicine (University of Pretoria). N.M. and S.A. were supported by the H3ABioNet NIH grant (U41HG006941).en_ZA
dc.description.urihttp://www.nature.com/ncommsen_ZA
dc.identifier.citationChoudhury, A., Ramsay, M., Hazelhurst, S. et al. 2017, 'Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans', Nature Communications, vol. 8, pp. 1-12.en_ZA
dc.identifier.issn2041-1723 (online)
dc.identifier.other10.1038/s41467-017-00663-9
dc.identifier.urihttp://hdl.handle.net/2263/66169
dc.language.isoenen_ZA
dc.publisherNature Publishing Groupen_ZA
dc.rights© 2017 [Choudhury et al.] This is an open-access article distributed under the terms of the Creative Commons Attribution License 4.0.en_ZA
dc.subjectWhole-genome sequencing (WGS)en_ZA
dc.subjectGenetic variationen_ZA
dc.subjectHuman genetic diversityen_ZA
dc.subjectSouthern African populationen_ZA
dc.titleWhole-genome sequencing for an enhanced understanding of genetic variation among South Africansen_ZA
dc.typeArticleen_ZA

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