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Genome wide association studies (GWAS) for type 2 diabetes (T2D) undertaken in European and Asian ancestry populations have yielded dozens of robustly associated loci. Sub-Saharan Africa (SSA) is one of the regions with the fastest growth in type 2 diabetes (T2D) worldwide (Wild et al., 2004).
Ethical approval for the study was obtained from the Institutional Review Board (IRB) of each participating institution.
The initial study sample consisted of 1822 unrelated subjects from the Africa America Diabetes Mellitus (AADM) study (Rotimi et al., 2001, 2004), a genetic epidemiology study of T2D in SSA. The initial set of 2,217,748 SNPs was filtered for missingness, Hardy-Weinberg equilibrium (HWE) and allele frequency as described in Supplementary Table 1.
Association analysis was done with mach2dat using the imputed SNP dosage data within a logistic regression framework.
We looked for evidence of transferability of established T2D susceptibility loci reported in the literature from GWAS and meta-analysis of GWAS (n = 106 loci—Supplementary Table 2). From our association tests, we looked for evidence of transferability of 106 established T2D SNPs.
Two of the 106 loci, INS-IGF2 rs3842770, and HLA-B rs2244020, were reported by the only meta-analysis GWAS in an African ancestry population [the MEta-analysis of T2D in African Americans (MEDIA) Consortium, Ng et al., 2014]. This means that you will not need to remember your user name and password in the future and you will be able to login with the account you choose to sync, with the click of a button.
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However, the genomics of T2D remains largely understudied in sub-Saharan Africa (SSA), where rates of T2D are increasing dramatically and where the environmental background is quite different than in these previous studies. All subjects provided written informed consent for the collection of samples and subsequent analysis.

All subjects were SSA, enrolled from university medical centers in Nigeria, Ghana, and Kenya.
Use of the allelic dosages is preferable to using the best guess genotypes because it accounts for the uncertainty in imputation. The cardiac myxomas may lead to SUDDEN CARDIAC death and other complications in carney complex patients. This study was conducted in accordance with the principles expressed in the Declaration of Helsinki.
Patients attending medical clinics at these medical centers or patients referred for clinical suspicion of diabetes were evaluated for potential inclusion in the study as described below. The allele frequency spectrum of the SNPs that passed QC is shown in Supplementary Figure 1. Participants with T2D had a mean waist circumference that was ~4 cm larger than that of controls (Table 1). Bentley1, Guanjie Chen1, Hanxia Huang1, Jie Zhou1, Daniel Shriner1, Olufemi Fasanmade2, Godfrey Okafor3, Benjamin Eghan Jr.4, Kofi Agyenim-Boateng4, Jokotade Adeleye5, Williams Balogun5, Abdel Elkahloun6, Settara Chandrasekharappa6, Samuel Owusu7, Albert Amoah7, Joseph Acheampong4, Thomas Johnson2, Johnnie Oli3, Clement Adebamowo8, Francis Collins9, Georgia Dunston10 and Charles N.
We tested each of these SNPs, and SNPs in linkage disequilibrium (LD) with these index SNPs, for an association with T2D in order to assess transferability and to fine map the loci leveraging the generally reduced LD of African genomes. However, most of these success stories have come from European and Asian ancestry populations. After providing informed consent, all participants underwent a clinical examination that included a medical history, clinical anthropometry, blood pressure measurements and blood sampling.
Next, we examined all the SNPs in the LD block (as determined by the method of Gabriel et al., 2002) containing the index SNP in the 1000 Genomes EUR or CHB population reference (as appropriate for the discovery hit) for evidence of local transferability.
Using a local replication strategy in which we examined SNPs in LD with the reported index SNP, we found an additional 30 SNPs showing significant association with T2D in this dataset (Table 3). A few GWAS for T2D have been done in African Americans, including a meta-analysis (Ng et al., 2014), but there is currently no similar study of indigenous Africans.
The remaining 1775 subjects (1035 T2D cases, 740 controls) formed the basis of this analysis.

The samples clustered as expected (Supplementary Figure 2) based on principal components (PCs) of the genotypes computed using an LD-pruned subset of 140,000 autosomal SNPs.
In sum, we found significant association with T2D for 41 of the 103 GWAS established T2D loci we examined in this study. To date, only one genome-wide linkage study of T2D in an African population has been published (Rotimi et al., 2004) and a GWAS of T2D in a SSA population has not yet been done. Body mass index (BMI) was computed as weight in kg divided by the square of the height in meters. The 1775 subjects included 1598 (90%) West Africans enrolled from Nigeria and Ghana (Rotimi et al., 2001, 2004) and 177 (10%) East Africans enrolled from Kenya. Given the relatively modest sample size and limited power for novel discovery, we focus on evaluation of previously reported T2D GWAS loci in this study of indigenous Africans, including looking for evidence of replication or transferability and conducting fine mapping studies to test whether the relatively weaker linkage disequilibrium (LD) and smaller haplotypes in this African sample could improve the resolution of previously reported loci. It should be noted that this SNP shows the strongest evidence of association with T2D in most GWAS and remains the most consistently associated locus in most populations studied so far. Alternatively, a diagnosis of T2D was accepted if an individual was on pharmacological treatment for T2D and review of clinical records indicated adequate justification for that therapy. The findings indicate that the genetic architecture of T2D in SSA is characterized by several risk loci shared with non-African ancestral populations and that data from African populations may facilitate fine mapping of risk loci. The study provides an important resource for meta-analysis of African ancestry populations and transferability of novel loci. Using data from our study sample and from the 1000 Genomes YRI, haplotype blocks were constructed around each locus that showed transferability to determine if African ancestry samples helped to fine-map the locus.

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