Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterisation of African genetic diversity is needed. The African Genome Variation Project (AGVP) provides a resource to help design, implement and interpret genomic studies in sub-Saharan Africa (SSA) and worldwide. The AGVP represents dense genotypes from 1,481 and whole genome sequences (WGS) from 320 individuals across SSA. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across SSA. We identify new loci under selection, including for malaria and hypertension. We show that modern imputation panels can identify association signals at highly differentiated loci across populations in SSA. Using WGS, we show further improvement in imputation accuracy supporting efforts for large-scale sequencing of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa, showing for the first time that such designs are feasible.

Highlights d The Uganda Genome Resource comprises genetic and phenotypic data on 6,400 individuals d Ugandans show geographically correlated genetic substructure and complex admixture d The Uganda sequence panel substantially improves imputation in African populations d The Uganda Genome Resource enables novel discovery of loci associated with traits

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OBJECTIVETo determine the prevalence of metabolic syndrome and to define optimal ethnic-specific waist-circumference cutoff points in a rural South African black community.RESEARCH DESIGN AND METHODSThis was a cross-sectional survey conducted by random-cluster sampling of adults aged >15 years. Participants had demographic, anthropometric, and biochemical measurements taken, including a 75-g oral glucose tolerance test. Metabolic syndrome was defined using the 2009 Joint Interim Statement (JIS) definition.RESULTSOf 947 subjects (758 women) studied, the age-adjusted prevalence of metabolic syndrome was 22.1%, with a higher prevalence in women (25.0%) than in men (10.5%). Peak prevalence was in the oldest age-group (≥65 years) in women (44.2%) and in the 45- to 54-year age-group in men (25.0%). The optimal waist circumference cutoff point to predict the presence of at least two other components of the metabolic syndrome was 86 cm for men and 92 cm for women. The crude prevalence of metabolic syndrome was higher with the JIS definition (26.5%) than with the International Diabetes Federation (IDF) (23.3%) or the modified Third Report of the National Cholesterol Education Program Adult Treatment Panel (ATPIII) (18.5%) criteria; there was very good agreement with the IDF definition (κ = 0.90 [95% CI 0.87–0.94]) and good concordance with ATPIII criteria (0.77 [0.72–0.82]).CONCLUSIONSThere is a high prevalence of metabolic syndrome, especially in women, suggesting that this community, unlike other rural communities in Africa, already has entered the epidemic of metabolic syndrome. Waist circumference cutoff points differ from those currently recommended for Africans.

OBJECTIVE -The purpose of this study was to determine the prevalence of diabetes, impaired glucose tolerance (IGT), impaired fasting glycemia (IFG), and associated risk factors in a rural South African black community.RESEARCH DESIGN AND METHODS -This was a cross-sectional survey conducted by random cluster sampling of adults aged Ͼ15 years. Participants had a 75-g oral glucose tolerance test using the 1998 World Health Organization criteria for disorders of glycemia.RESULTS -Of 1,300 subjects selected, 1,025 subjects (815 women) participated (response rate 78.9%). The overall age-adjusted prevalence of diabetes was 3.9%, IGT 4.8%, and IFG 1.5%. The prevalence was similar in men and women for diabetes (men 3.5%; women 3.9%) and IGT (men 4.6%; women 4.7%) but higher in men for IFG (men 4.0%; women 0.8%). The prevalence of diabetes and IGT increased with age both in men and women, with peak prevalence in the 55-to 64-year age-group for diabetes and in the Ն65-year age-group for IGT. Of the cases of diabetes, 84.8% were discovered during the survey. In multivariate analysis, the significant independent risk factors associated with diabetes included family history (odds ratio 3.5), alcohol ingestion (2.8), waist circumference (1.1), systolic blood pressure (1.0), serum triglycerides (2.3), and total cholesterol (1.8); hip circumference was protective (0.9).CONCLUSIONS -There is a moderate prevalence of diabetes and a high prevalence of total disorders of glycemia, which suggests that this community, unlike other rural communities in Africa, is well into an epidemic of glucose intolerance. There is a low proportion of known diabetes and a significant association with potentially modifiable risk factors.