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Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.

ABSTRACT: Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.

SUBMITTER: Gurdasani D

PROVIDER: S-EPMC7202134 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.

Gurdasani Deepti D Carstensen Tommy T Fatumo Segun S Chen Guanjie G Franklin Chris S CS Prado-Martinez Javier J Bouman Heleen H Abascal Federico F Haber Marc M Tachmazidou Ioanna I Mathieson Iain I Ekoru Kenneth K DeGorter Marianne K MK Nsubuga Rebecca N RN Finan Chris C Wheeler Eleanor E Chen Li L Cooper David N DN Schiffels Stephan S Chen Yuan Y Ritchie Graham R S GRS Pollard Martin O MO Fortune Mary D MD Mentzer Alex J AJ Garrison Erik E Bergström Anders A Hatzikotoulas Konstantinos K Adeyemo Adebowale A Doumatey Ayo A Elding Heather H Wain Louise V LV Ehret Georg G Auer Paul L PL Kooperberg Charles L CL Reiner Alexander P AP Franceschini Nora N Maher Dermot D Montgomery Stephen B SB Kadie Carl C Widmer Chris C Xue Yali Y Seeley Janet J Asiki Gershim G Kamali Anatoli A Young Elizabeth H EH Pomilla Cristina C Soranzo Nicole N Zeggini Eleftheria E Pirie Fraser F Morris Andrew P AP Heckerman David D Tyler-Smith Chris C Motala Ayesha A AA Rotimi Charles C Kaleebu Pontiano P Barroso Inês I Sandhu Manj S MS

Cell 20191001 4

Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We de ...[more]

PMID: 31675503

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Project description:Hmong-Mien (HM) -speaking populations, widely distributed in South China, the north of Thailand, Laos, and Vietnam, have experienced different settlement environments, dietary habits, and pathogenic exposure. However, their specific biological adaptation remained largely uncharacterized, which is important in the population evolutionary genetics and Trans-Omics for regional Precision Medicine. Besides, the origin and genetic diversity of HM people and their phylogenetic relationship with surrounding modern and ancient populations are also unknown. Here, we reported genome-wide SNPs in 52 representative Miao people and combined them with 144 HM people from 13 geographically representative populations to characterize the full genetic admixture and adaptive landscape of HM speakers. We found that obvious genetic substructures existed in geographically different HM populations; one localized in the HM clines, and others possessed affinity with Han Chinese. We also identified one new ancestral lineage specifically existed in HM people, which spatially distributed from Sichuan and Guizhou in the north to Thailand in the south. The sharing patterns of the newly identified homogenous ancestry component combined the estimated admixture times via the decay of linkage disequilibrium and haplotype sharing in GLOBETROTTER suggested that the modern HM-speaking populations originated from Southwest China and migrated southward in the historic period, which is consistent with the reconstructed phenomena of linguistic and archeological documents. Additionally, we identified specific adaptive signatures associated with several important human nervous system biological functions. Our pilot work emphasized the importance of anthropologically informed sampling and deeply genetic structure reconstruction via whole-genome sequencing in the next step in the deep Chinese Population Genomic Diversity Project (CPGDP), especially in the regions with rich ethnolinguistic diversity.

Dataset Information

Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.

Publications

Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa.

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