Tamilian Population Research Articles

Apolipoprotein AI and Apolipoprotein B gene polymorphisms and lipid profile in Tamilian population

Apolipoprotein (ApoAI) is the major protein constituent of high density lipoproteins (HDL). Apolipoprotein (apo) B-100, a component of low density lipoprotein (LDL), serves as a ligand for the removal of LDL from the circulation by the LDL receptor. Genotyping of ApoAI and ApoB polymorphisms was carried out in 185 healthy Tamilian volunteers of south India after clinical examination. Lipid profile was estimated and polymorphisms were detected by the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method. The frequency of the rare M1−, M2− and R− alleles were 21%, 4.3% and 5.4%, respectively. An increase of 9.1 mg dL−1 (0.23 mmol L−1) in HDL-cholesterol (HDL-C) levels was observed with M1−/− genotype when compared to M1+/+ genotype, which was not found after adjustments were made for confounding risk factors. A paradoxical increase in levels of total cholesterol and LDL-cholesterol (LDL-C) was observed with M2+/− genotype when compared to M2+/+ genotype. Analysis of combination of genotypes of ApoAI revealed no influence on the lipid parameters. ApoB EcoRI in contrast to ApoAI polymorphisms had no significant effect on lipid profile.

Gender specific association of endothelial nitric oxide synthase gene (Glu298Asp) polymorphism with essential hypertension in a south Indian population

Background Endothelial derived nitric oxide (NO) plays a major role in blood pressure regulation. The role of missense variant eNOS-Glu298Asp has been demonstrated by many studies with conflicting results. Our objective was to investigate the association of eNOS gene polymorphism with essential hypertension in a south Indian population. Methods We carried out a case control study in 438 hypertensive patients and 444 healthy control subjects in a homogenous population. Genotyping was done by PCR-RFLP method. Multiple logistic regression analysis was used to detect the association between genotype and hypertension. Results The homozygous variant genotype Asp298Asp was significantly associated with hypertension (odds ratio 2.4; 95% CI, 1.23–5.0, p < 0.01). Gender specific analysis showed both the heterozygous (odds ratio, 2.0; 95% CI, 1.3–2.9, p < 0.01) and homozygous variants (odds ratio, 7.9; 95% CI, 2.0–4.1, p < 0.001) were positively associated with hypertension in females. The variant allele Asp was higher in female hypertensives when compared to male hypertensive cases (22% vs. 16%). Conclusion The eNOS gene polymorphism is a candidate gene for hypertension and the association to be gender specific with respect to females in a south Indian Tamilian population.

ABCB1 genetic polymorphism and risk of upper aerodigestive tract cancers among smokers, tobacco chewers and alcoholics in an Indian population

Upper aerodigestive tract (UADT) cancers are associated with the tobacco use and alcohol consumption. Certain toxins and carcinogens causing UADT cancers are found to be substrates of polymorphic ABCB1 gene encoded P-glycoprotein efflux pump. This study investigates the association between ABCB1 gene polymorphism at exon 26 (3435C>T) and risk to UADT cancers in Tamilians, a population of south India. The study included 219 unrelated histopathologically confirmed cases and 210 population-based controls. Genomic DNA was extracted from peripheral leukocytes and genotyped for ABCB1 3435C>T polymorphism by PCR-restriction fragment length polymorphism method. The multivariate logistic regression analyses demonstrated that the homozygous ABCB1 TT genotype was significantly associated with an overall increased risk for developing UADT cancers [odds ratio (OR): 2.53; 95% confidence interval (CI): 1.28-5.02]. Further, the determination of gene-environment interaction by stratified analyses have revealed a significant interaction between the smoking and homozygous TT genotype [(OR: 7.52; CI: 1.50-37.70) and (OR: 16.89; CI: 3.87-73.79) for 11-20 and >20 pack-years, respectively]. The strongest interaction was observed among the regular tobacco chewers (OR: 45.29; CI: 8.94-130.56) homozygous for TT genotype. No suggestion, however, of an interaction between the genotypes and the alcohol consumption on the multiplicative scale was made. The ABCB1 gene polymorphism at exon 26 (3435C>T) may be one of the risk factors for susceptibility to UADT cancers. Furthermore, the significant interaction among habitual smokers and tobacco chewers, homozygous for TT genotype modulates the risk to UADT cancers in the Tamilian population of south India.

Genetic polymorphisms of glutathione- S-transferase genes ( GSTM1, GSTT1 and GSTP1) and upper aerodigestive tract cancer risk among smokers, tobacco chewers and alcoholics in an Indian population

The glutathione- S-transferase (GST) genes are involved in the detoxification of various carcinogens that increase the risk to upper aerodigestive tract (UADT) cancers. In the present study, 408 unrelated histopathologically confirmed cases and 220 population based controls, matched by age and gender, which belonged to the Tamilian population of south India were genotyped for polymorphisms in GSTM1, GSTT1 and GSTP1 using polymerase chain reaction (PCR) based methods. The multivariate logistic regression analyses demonstrated that GSTT1 null genotype was significantly associated with increased risk for UADT cancers (odds ratio (OR) 2.5; 95% confidence intervals (CIs) 1.3–4.7). The combined effects of GST genes have shown that concurrent lack of GSTM1 and GSTT1 had a significantly increased risk (OR 4.6; 95% CI 1.3–15.6), while GSTT1 null genotype along with GSTP1 polymorphic variants further increased the cancer risk (OR 5.3; 95% CI 2.0–13.6). The most remarkable risk was seen among individuals carrying GSTM1 null, GSTT1 null genotypes and GSTP1 polymorphic variants (OR 7.8; 95% CI 1.0–61.0). Tobacco chewers carrying GSTM1 null genotype had an enhanced risk for UADT cancers. An enhanced risk among tobacco chewers and alcoholics (regular) was noted in individuals with GSTT1 null genotype. Similarly, a significant interaction was observed among smokers (>40 pack-year (PY)) and tobacco chewers carrying GSTP1 mutant genotypes. Although the null genotype of GSTT1 is a strong predisposing risk factor for UADT cancers, we conclude that the significant gene–gene and gene–environment interactions of GST genes may confer a substantial risk to UADT cancers in the Tamilian population of south India.

Common variants of Cholesteryl ester transfer protein gene and their association with lipid parameters in healthy volunteers of Tamilian population

Background Cholesteryl ester transfer protein (CETP) is involved in a key pathway of reverse cholesterol transport implicated in atherosclerosis and coronary heart disease. CETP gene is known to have many single nucleotide polymorphisms which have been associated with CETP activity and plasma high density lipoprotein cholesterol (HDL-C) concentrations. No data on the prevalence of these polymorphisms and their phenotypic association is available in South Indian population. Methods Three CETP polymorphisms: TaqIB, −629C/A and I405V were studied in 171 healthy volunteers from Tamilnadu, a major population of South India. Subjects were clinically examined and lipid profile was estimated. Genotyping was performed by PCR-RFLP and genotype frequencies estimated. Results The allele frequencies of TaqIB: B1 allele was 0.51; −629C/A: C allele was 0.36; and that of I405V: I allele was 0.47. Study of association between these three polymorphisms and plasma lipid concentrations revealed no significant differences in lipid parameters between genotypes. A gender based subgroup analysis revealed a significant increase in HDL-C in men with B2B2 genotype and decrease in TG in B1B2 genotype. Analysis of the combined effect of multiple mutant genotypes revealed that as the number of mutant genotypes increased, the concentrations of low density lipoprotein-cholesterol (LDL-C), HDL-C and total cholesterol (TC) increased whereas that of triglyceride (TG) decreased in the group of three mutant genotypes significantly. Conclusion The frequency of B2 and A alleles of TaqIB and −629C/A polymorphisms were highest in Tamilian population when compared to other major ethnic groups while that of V allele of I405V polymorphism is between Caucasians and African Americans. Taq1B polymorphism was associated with HDL-C and TG concentrations only in men. Combination of these three polymorphisms was significantly associated with lipid profile than the individual polymorphisms.

Allele and Genotype Frequency of MDR1 C3435T in Tamilian Population

The allele and genotype frequencies of MDR1 C3435T polymorphism were determined in 185 unrelated healthy Tamilians. The genomic DNA was extracted from peripheral leucocytes using phenol chloroform method and genotyped by PCR-RFLP method. The frequencies of MDR1 C3435 and T3435 alleles in Tamilian population were 0.46 and 0.54 respectively. The distribution of T3435 in this population was found to be greater than Africans and almost similar to Caucasians and Orientals. The distribution of CC, CT and TT genotypes was 0.18, 0.56 and 0.26 respectively. The frequency distribution of the CC genotype was lower in them when compared with Chinese and Africans whereas CT genotype was higher in comparison with all the major ethnic groups.

Prevalence of the Factor V G1691A and the Factor II/prothrombin G20210A gene polymorphisms among Tamilians

We have investigated the prevalence of the Factor II G20210A and Factor V G1691A single nucleotide polymorphisms (SNPs) in a South Indian-Tamil Nadu population. The SNP genotyping was performed using a polymerase chain reaction (PCR)/restriction fragment length polymorphism analysis and by a recently FDA-approved LightCycler real-time PCR assay. Of 72 samples that were genotyped, 4 (5.5%) patients were heterozygous for the Factor V SNP and no homozygous mutant patients were identified. None of the patients were shown to be either heterozygous or homozygous mutant for the Factor II SNP. All samples showed 100% concordance between the PCR/RFLP assay and the LightCycler assay. While this study identified the prevalence of the Factor V SNP to be similar to that of other reported populations, the absence of the Factor II allele is consistent with reports in more isolated populations. In addition, the results of this study do not support a role for these SNPs in acute myocardial infarction in the Tamilian population.

Allele and genotype frequency of CYP2C9 in Tamilnadu population

To identify the frequency of CYP2C9*1, *2 and *3 alleles and the genotype of CYP2C9 gene in the Tamilian population. The study was conducted on 135 unrelated healthy human volunteers. DNA was extracted from the peripheral leukocytes samples and was analyzed using the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) protocol. The PCR products were digested with AvaII, KpnI or NsiI restriction enzymes. The digested products were separated using 8% polyacrylamide gel and stained by ethidium bromide. Genotyping of the subjects was done based on DNA fragment size. The frequencies of CYP2C9*1, *2 and *3 alleles in the Tamilian population were 0.907, 0.026 and 0.067, respectively. The distribution of CYP2C9*1/*1, *1/*2, *1/*3 and *2/*3 genotypes were 0.823, 0.044, 0.126 and 0.007, respectively. CYP2C9*3 is the most frequent mutant allele found in the Tamilian population. The distribution of this mutant allele in the Tamilian population was found to be lesser than in Caucasians but higher than in Chinese.

Genotype and allele frequency of CYP2D6 in Tamilian population.

To assess the frequency of CYP2D6 *3, *4, *5 and *10 allelic variants in a South Indian population and compare the frequencies with other major populations. Polymerase chain reaction (PCR) or PCR-restriction fragment length polymorphism (RFLP)-based methods were used to identify the CYP2D6 genotypes of 106 healthy unrelated male and female volunteers of Tamilian origin. The allele and genotype frequencies observed were compared with other major populations. The *10 allele was the most frequent mutant allele in Tamilians (20.3%). The *5 allele occurred at 0.9% and the *3 allele was not detected. The most frequent allele causing enzyme inactivation was *4 allele in Tamilians (6.6%), which is significantly higher than that reported in Japanese (0%). The *10 allele is the most common mutant allele in Tamilians. The CYP2D6*4 and CYP2D6*5 alleles are distributed in a significantly different way in the Tamil population relative to Oriental populations.

Allele and genotype frequency of CYP2C19 in a Tamilian population.

To investigate the frequencies of CYP2C19*1, CYP2C19*2 and CYP2C19*3 alleles and CYP2C19 genotypes in a Tamilian population. The study was conducted in 112 unrelated healthy human volunteers. DNA was extracted from leucocytes and analyzed by the PCR-RFLP protocol. The PCR product was digested with restriction enzymes (SmaI and BamH1) and then separated electrophoretically using polyacrylamide gel. The frequencies of the CYP2C19*1, *2 and *3 alleles were 0.598 [95% confidence interval (CI) 0.507, 0.689], 0.379 (95% CI, 0.350,0.407) and 0.022 (95% CI -0.005, 0.049), respectively. The distribution of CYP2C19*1/*1,*1/*2, *1/*3, *2/*2 and *2/*3 genotypes were 0.295 (95% CI, 0.210, 0.379), 0.580 (95% CI, 0.488, 0.671), 0.027 (95% CI -0.003, 0.057), 0.080 (95% CI 0.030, 0.130) and 0.018 (95% CI -0.006, 0.042), respectively. The distribution of CYP2C19*1/*1 in the Tamilian population is lower than that in Caucasians, Africans and the North Indian population. The CYP2C19*1/*2 is significantly higher in Tamilians when compared with other populations. The CYP2C19*1/*3 allele, which was not reported in the North Indian and Caucasian populations has been identified in 2.7% of the Tamilian population.