Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

Podoconiosis is a tropical lymphedema resulting from long-term barefoot exposure to red-clay soil derived from volcanic rock. The World Health Organization recently designated it as a neglected tropical disease. Podoconiosis develops in only a subgroup of exposed people, and studies have shown familial clustering with high heritability (63%). We conducted a genomewide association study of 194 case patients and 203 controls from southern Ethiopia. Findings were validated by means of family-based association testing in 202 family trios and HLA typing in 94 case patients and 94 controls. We found a genomewide significant association of podoconiosis with the single-nucleotide polymorphism (SNP) rs17612858, located 5.8 kb from the HLA-DQA1 locus (in the allelic model: odds ratio, 2.44; 95% confidence interval [CI], 1.82 to 3.26; P=1.42×10⁻⁹; and in the additive model: odds ratio, 2.19; 95% CI, 1.66 to 2.90; P=3.44×10⁻⁸), and suggestive associations (P<1.0×10⁻⁵) with seven other SNPs in or near HLA-DQB1, HLA-DQA1, and HLA-DRB1. We confirmed these associations using family-based association testing. HLA typing showed the alleles HLA-DRB1*0701 (odds ratio, 2.00), DQA1*0201 (odds ratio, 1.91), and DQB1*0202 (odds ratio, 1.79) and the HLA-DRB1*0701–DQB1*0202 haplotype (odds ratio, 1.92) were risk variants for podoconiosis. Association between variants in HLA class II loci with podoconiosis (a noncommunicable disease) suggests that the condition may be a T-cell–mediated inflammatory disease and is a model for gene–environment interactions that may be relevant to other complex genetic disorders. (Funded by the Wellcome Trust and others.)

This article reviews peer-reviewed publications and book chapters on the history, epidemiology, genetics, ecology, pathogenesis, pathology and management of podoconiosis (endemic non-filarial elephantiasis). Podoconiosis is a non-infectious geochemical elephantiasis caused by exposure of bare feet to irritant alkalic clay soils. It is found in at least 10 countries in tropical Africa, Central America and northwest India, where such soils coexist with high altitude, high seasonal rainfall and low income. Podoconiosis develops in men and women working barefoot on irritant soils, with signs becoming apparent in most patients by the third decade of life. Colloid-sized silicate particles appear to enter through the skin, are taken up into macrophages in the lower limb lymphatics and cause endolymphangitis and obliteration of the lymphatic lumen. Genetic studies provide evidence for high heritability of susceptibility to podoconiosis. The economic burden is significant in affected areas dependent on subsistence farming. Podoconiosis is unique in being an entirely preventable non-communicable disease. Primary prevention entails promoting use of footwear in areas of irritant soil; early stages are reversible given good foot hygiene, but late stages result in considerable economic and social difficulties, and require extended periods of elevation and occasionally nodulectomy.

Summary: Background Endemic non‐filarial elephantiasis or podoconiosis is a chronic and debilitating geochemical disease occurring in individuals exposed to red clay soil derived from alkalic volcanic rock. It is a major public health problem in countries in tropical Africa, Central America and North India.Objective To estimate the direct and the average productivity cost attributable to podoconiosis, and to compare the average productivity time of podoconiosis patients with non‐patients.Methods Matched comparative cross sectional survey involving 702 study subjects (patients and non‐patients) supplemented by interviews with key informants in Wolaita Zone, southern Ethiopia.Results Total direct costs of podoconiosis amounted to the equivalent of US$ 143 per patient per year. The total productivity loss for a patient amounted to 45% of the total working days per year, causing a monetary loss equivalent to US$ 63. In Wolaita zone, the overall cost of podoconiosis exceeds US$ 16 million per year.Conclusions Podoconiosis has enormous economic impact in affected areas. Simple preventive measures (such as use of robust footwear) must be promoted by health policy makers.

Persistent organic pollutants (POPs) are linked with insulin resistance and type-2 diabetes (T2D) in the general population. However, their associations with gestational diabetes (GDM) are inconsistent. We prospectively evaluated the associations of POPs measured in early pregnancy with GDM risk. We also assessed whether pre-pregnancy BMI (ppBMI) and family history of T2D modify this risk. In NICHD Fetal Growth Study, Singletons, we measured plasma concentration of 76 POPs, including 11 organochlorine pesticides (OCPs), 9 polybrominated diphenylethers (PBDEs), 44 polychlorinated biphenyls (PCBs), and 11 per-and polyfluoroalkyl substances (PFAS) among 2334 healthy non-obese women at 8-13 weeks of gestation. GDM was diagnosed by Carpenter and Coustan criteria. We constructed chemical networks using a weighted-correlation algorithm and examined the associations of individual chemical and chemical networks with GDM using multivariate Poisson regression with robust variance. Higher concentrations of PCBs with six or more chlorine atoms were associated with increased risk of GDM in the overall cohort (risk ratios [RRs] range: 1.08-1.13 per 1-standard deviation [SD] increment) and among women with a family history of T2D (RRs range: 1.08-1.48 per 1-SD increment) or normal ppBMI (RRs range: 1.08-1.22 per 1-SD increment). Similar associations were observed for the chemical network comprised of PCBs with ≥6 chlorine atoms and the summary measure of total PCBs and non-dioxin like PCBs (138, 153, 170, 180). Furthermore, four PFAS congeners - perfluorononanoic acid (PFNA), perfluorooctanoic acid (PFOA), perfluoroheptanoic acid (PFHpA), and perfluorododecanoic acid (PFDoDA) - showed significant positive associations with GDM among women with a family history of T2D (RRs range:1.22-3.18 per 1-SD increment), whereas BDE47 and BDE153 showed significant positive associations among women without a family history of T2D. Environmentally relevant levels of heavily chlorinated PCBs and some PFAS and PBDEs were positively associated with GDM with suggestive effect modifications by family history of T2D and body adiposity status.