Screening for the presence of single nucleotide polymorphisms associated with type 2 diabetes in a black South African population
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Date
2018-01
Authors
Diseko, Lerato Gloria
Journal Title
Journal ISSN
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Publisher
University of the Free State
Abstract
Introduction: The number of people suffering from type 2 diabetes (T2D) is expected to rise to 642 million by 2040. It is estimated that the highest proportion of undiagnosed individuals are African. The increasing prevalence of T2D has become a leading public health challenge throughout the world and has led to an intense search for genetic risk factors to this disease. The large increase in the prevalence of T2D coincides with a higher prevalence of obesity and insulin resistance. The aetiology of T2D is not fully understood, as a result, impairing the development of curative interventions to relieve the burden of T2D.
Objective: The present study was conducted to screen for the association of SNPs in candidate genes identified through genome wide association studies, with T2D in a black South African population. The identification of T2D risk associated alleles could aid in preventing the clinical onset of the diabetes by intervention of a modified lifestyle.
Methods: A descriptive case control study was performed on a cohort of 188 South African participants (T2D patients: n=96 and non T2D controls: n=92) of mostly Sotho descent, living in the central Free State area of Mangaung. The two groups were individually matched according to gender, age (20-60 years) and Body Mass Index (BMI) conferring to WHO categories. HbA1c levels were recorded for both groups. Non-T2D controls were included only if their HbA1c<6.5%.
Genotyping was determined using Real time PCR on a Quant Studio 5 qPCR system (Applied Biosystems) using hydrolysis probe technology. Genotype of the following six SNPs were determined: TCF7L2 (rs7903146, rs12255372), IRS1 (rs2943641), CDKAL1 (rs7754840), KCNJ11 (rs5219) and RND3-RBM43 (rs7560163). Each qPCR run was performed with a technical homozygous control for each genotype as well as a non-template control. All the reactions were set up in duplicate. Control samples were sequenced using Sanger sequencing to confirm genotype, and for the rare allele control, synthetic oligomers (gBlocks® Gene Fragments; IDT) were purchased and applied.
Differences in allele and genotype frequencies between patients and controls were calculated with Chi-squared and 2x2 contingency tables (VassarStats). Odds ratios and 95% confidence intervals were determined. A p<0.05 indicated statistical significance.
Results: TCF7L2 rs12255372 showed a significantly higher allele frequency in the T2D patient group than in non-T2D control group with value of p= 0.0000708. Increased homozygosity for the mutant TT genotype at TCF7L2 rs12255372 was observed in 23% of T2D patients vs 3% in non-T2D controls (odds ratio 8.82, 95% confidence interval: 2.54-30.63 p= 0.0000599). The same trend was observed for the rare C allele of IRS1 rs2943641, but without significance (p= 0.559). An increase in heterozygosity was observed for the CDKAL1 rs7755840 in T2D patients, also without statistical significance p=1.89. No mutant homozygyotes for KCNJ11 rs5219 were found in both cohorts. The rare/mutant allele of both IRS1 and RND3-RBM43 were higher in both patients and controls than the ancestral allele.
Conclusion: The TCF7L2 rs12255372 is the only SNP that is significantly associated with T2D. Differences in ethnic background or environmental factors can possibly be attributable to differences in the results found in this study of black South African population compared to other ethnic groups. Results from this study emphasizes the need to investigate genetic variants associated with complex diseases such as T2D in the black South African population.
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Keywords
T2D, SNP, Genetics, TCF7L2, KCNJ11, IRS1, CDKAL1, RND3-RBM43, GWAS, South African population, Dissertation (M.Sc. (Genetics))--University of the Free State, 2018