Association of HLA-B Gene Polymorphisms with Type 2 Diabetes in Pashtun Ethnic Population of Khyber Pakhtunkhwa, Pakistan

Abstract

Human leukocyte antigen (HLA) system is the most polymorphic and gene dense region of human DNA that has shown many disease associations. It has been further divided into HLA classes I, II, and III. Polymorphism in HLA class II genes has been reported to play an important role in the pathogenesis of type 1 diabetes (T1D). It also showed association with T2D in different ethnic populations. However, a little is known about the relationship of HLA class I gene polymorphism and T2D. This study has evaluated the association of HLA-B (class I gene) variants with T2D in Pashtun ethnic population of Khyber Pakhtunkhwa. In the first phase of the study, whole exome sequencing (WES) of 2 pooled DNA samples was carried out, and DNA pools used were constructed from 100 diabetic cases and 100 control subjects. WES results identified a total of n = 17 SNPs in HLA-B gene. In the next phase, first 5 out of n = 17 reported SNPs were genotyped using MassARRAY® system in order to validate WES results and to confirm association of selected SNPs with T2D. Minor allele frequencies (MAFs) and selected SNPs×T2D association were determined using chi-square test and logistic regression analysis. The frequency of minor C allele was significantly higher in the T2D group as compared to control group (45.0% vs. 13.0%) ( p = 0.006 ) for rs2308655 in HLA-B gene. No significant difference in MAF distribution between cases and controls was observed for rs1051488, rs1131500, rs1050341, and rs1131285 ( p > 0.05 ). Binary logistic regression analyses showed significant results for SNP rs2308655 ( OR = 2.233 , CI 95 % = 1.223 ‐ 4.077 , and p = 0.009 ), while no considerable association was observed for the other 4 SNPs. However, when adjusted for these variants, the association of rs2308655 further strengthened significantly ( adjusted OR = 7.485 , CI 95 % = 2.353 ‐ 23.812 , and p = 0.001 ), except for rs1131500, which has no additive effect. In conclusion, the finding of this study suggests rs2308655 variant in HLA-B gene as risk variant for T2D susceptibility in Pashtun population.

Association of APOE (rs429358 and rs7412) and PON1 (Q192R and L55M) Variants with Myocardial Infarction in the Pashtun Ethnic Population of Khyber Pakhtunkhwa, Pakistan

“…According to the DNA-pooling techniques previously described [ 37 ], DNA pools were created from 200 MI patients and 100 control participants in order to cut costs and streamline the sequencing procedure. Each pool contains an equal quantity of genomic DNA (10 ng) from each subject.…”

Validation of Genome-Wide Association Studies (GWAS)-Identified Type 2 Diabetes Mellitus Risk Variants in Pakistani Pashtun Population

“…The prevalence ratios of the study participants’ demographics, general characteristics, and co-morbidities are described in Tables 2 and 3 . 33 A greater ratio of comorbid conditions like hypertension, renal failure, ischemic heart disease, hypercholesterolemia, nephropathy and retinopathy were observed in diabetic cases compared to controls. The majority of patients were obese and physically inactive.…”

Association between Aldosterone Synthase (CYP11B2) Gene Polymorphism and Hypertension in Pashtun Ethnic Population of Khyber Pakhtunkwha, Pakistan

“…Aldosterone gene CYP11B2 polymorphisms are associated with many diseases, such as Type 2 Diabetes Mellitus (T2DM) [50][51][52], myocardial infarction (MI) [53], left ventricular mass [54,55], hyperaldosteronism [56], arterial stiffness [57] and hypertension [58][59][60][61].…”

“…Whole exome sequencing (WES) was performed at the Centre of Genomics, Rehman Medical institute (RMI), Hayatabad, Peshawar. In order to minimize costs and time and simplify sequencing process, DNA pools were constructed from 200 HTN patients and 200 control subjects according to the previously described protocols [42,43]. Each pool contained an equimolar quantity of DNA (100 ng) from each individual.…”