Pradeep Kumar Ghosh

MTHFR C677T and factor V Leiden in recurrent pregnancy loss: a study among an endogamous group in North India.

AIM In our study an attempt has been made to find the prevalence of genetic thrombophilia in recurrent pregnancy loss (RPL). METHODS Methylene tetrahydrofolate reductase C677 (MTHFR C677T) and factor V Leiden (FVL) were investigated in 84 Rajput women with two or more pregnancy losses and in 80 age- and ethnicity-matched healthy controls. Restriction digestions of polymerase chain reaction product with HinfI and Mnl I were used for MTHFR C677T and FVL polymorphism detection, respectively. RESULTS MTHFR C677T mutation was found in 9/84 patients (10.71%) and 2/80 controls (2.5%), yielding an odds ratio (OR) for RPL related to MTHFR C677T of 4.68 (95% confidence interval [CI] = 0.98-22.37; p = 0.03). FVL was found in 4/84 patients (4.76%) and none among the controls, yielding a modified OR for RPL related to FVL of 9.00 (95% CI = 0.48-169.9; p = 0.05). Both, MTHFR C677T and FVL were not found to be significantly more prevalent in patients than controls as a whole. However, MTHFR C677T showed significant association with early pregnancy loss (OR = 6.3; 95% CI = 1.22-32.85; p-value = 0.03; Bonferroni-corrected p-value = 0.04). CONCLUSIONS Our study supports the association between MTHFR C677T and patients with early RPL among north Indian Rajputs and strengthens the notion that thrombophilia plays a role in this clinical entity.

Hypospadias Risk and Polymorphism in SRD5A2 and CYP17 Genes: Case-Control Study Among Indian Children

PURPOSE Hypospadias is a common congenital error of genital development, the frequency of which is increasing. As androgens have a significant role in the development of the male urethra, we sought to investigate the association between 2 functional polymorphisms, CYP17-A1/A2 and SRD5A2-V89L, which are involved in the biosynthesis of testosterone and dihydrotestosterone, respectively, in relation to hypospadias. MATERIALS AND METHODS We examined DNA samples of 80 cases and 100 controls for SRD5A2-V89L and CYP17-A1/A2 gene polymorphisms. Information pertaining to family history, preoperative position of the urethral meatus and parental occupations along with maternal reproductive profile were collected for cases and controls. RESULTS Genotyping of 80 cases and 100 controls revealed a significant association between V89L polymorphism and hypospadias (OR 2.4, 95% CI 1.2-4.6, p <0.05). When analyzing the risk of hypospadias based on grade, genotypic distribution of SRD5A2-LL genotype differed significantly between severe forms and controls, with an odds ratio of 3.6 (95% CI 1.2-10.0, p = 0.02). Of affected children 71.25% had parents from a rural background, with agriculture as the primary occupation. A statistically significant association was observed for the LL genotype (OR 4.6, 95% CI 1.7-12.29, p <0.05) between children with parents having an agricultural background (likely exposed to pesticides) and controls with no such exposure. CYP17-A1/A2 genotypes did not show any significant results. CONCLUSIONS V89L polymorphism of the SRD5A2 gene is a strong determinant of hypospadias risk among children of Indian origin. However, our results suggest that the presence of leucine allele, especially among agriculturalists, may increase the propensity of having a child with hypospadias.

MTHFR C677T polymorphism, folate, vitamin B12 and homocysteine in recurrent pregnancy losses: a case control study among north Indian women

Abstract Aim: The present study attempts to understand the role of methylenetetrahydrofolate reductase C677T (MTHFR C677T) in recurrent pregnancy losses in North Indian women because of hyperhomocysteinemia in light of serum folate and vitamin B12. Methods: One hundred and seven women with three or more consecutive unexplained recurrent pregnancy losses and 343 women with two or more successful and uncomplicated pregnancies were recruited. Plasma homocysteine, serum folate and vitamin B12 were analyzed using chemiluminescence. MTHFR C677T detection was completed in all subjects. Results: MTHFR genotypic distribution among cases and controls showed no significant difference (P=0.409). However, MTHFR C677T polymorphism was found to be significantly associated with increased homocysteine in the case group (P=0.031). Hyperhomocysteinemia and vitamin B12 deficiency were found to be significant risk factors for recurrent pregnancy loss (RPL) (OR=7.02 and 16.39, respectively). Folate deficiency was more common in controls (63.47%) as compared to the case group (2.56%). Conclusion: Low vitamin B12 increases homocysteine, specifically among T allele carrying case mothers, suggesting T allele is detrimental with B12 deficiency. The study emphasizes the importance of vitamin B12 in the prevention of RPL in North Indian women.

Spectrum of MTHFR gene SNPs C677T and A1298C: a study among 23 population groups of India.

Elevated homocysteine is a risk factor for many complex disorders. The role of methylenetetrahydrofolate reductase (MTHFR) gene in methylation of homocysteine makes it one of the most important candidate genes for these disorders. Considering the heterogeneity in its distribution in world populations, we screened MTHFR C677T and A1298C single nucleotide polymorphisms in a total of 23 Indian caste, tribal and religious population groups from five geographical regions of India and belonging to four major linguistic groups. The frequencies of MTHFR 677T and 1298C alleles were found to be 10.08 and 20.66%, respectively. MTHFR homozygous genotype 677TT was absent in eight population groups and homozygous 1298CC was absent in two population groups. 677T allele was found to be highest among north Indian populations with Indo-European tongue and 1298C was high among Dravidian-speaking tribes of east India and south India. The less common mutant haplotype 677T-1298C was observed among seven population groups and overall the frequency of this haplotype was 0.008, which is similar to that of African populations. cis configuration of 677T and 1298C was 0.94%. However, we could not find any individual with four mutant alleles which supports the earlier observation that presence of more than two mutant alleles may decrease the viability of foetus and possibly be a selective disadvantage in the population.

DRD2 and ANKK1 Gene Polymorphisms and Alcohol Dependence: A Case–Control Study among a Mendelian Population of East Asian Ancestry

AIMS Dopamine receptors are extensively studied in association with alcohol dependence (AD), since they are thought to be the key neural substrate for alcohol and other drug-related reinforcement and reward behaviours. The present study aims to understand the role of dopamine receptors in susceptibility to AD with respect to three sites of DRD2 gene (-141C Ins/Del, TaqIB and TaqID) and TaqIA site of ANKK1 gene among Meiteis of Manipur, a Mendelian population of India. METHODS A total of 129 individuals who all met the DSM-IV criteria for AD and 286 controls were screened for four single-nucleotide polymorphisms (SNPs) -141C Ins/Del, TaqIB TaqID and TaqIA. Both AD cases and controls were unrelated up to first cousin. RESULTS Early age of onset of alcohol consumption and smoking status were significantly associated with AD. Improvement in education and occupation statuses showed decreased risk of AD. The heterozygous and mutant homozygous conditions of ANKK1 TaqIA polymorphism were found to be significantly associated with AD (odds ratio = 2.13, 95% confidential interval 1.04-4.39, P < 0.05), whereas a borderline significance of the -141C Del allele was observed (P = 0.059). Such a trend was not observed between AD and the other polymorphism, i.e., TaqIB and TaqID. CONCLUSIONS Individuals carrying the A1 allele of ANKK1 TaqIA polymorphism may be relatively more susceptible to AD. Interaction of both ANKK1 TaqIA and -141C Ins/Del polymorphism is likely to increase risk of AD phenotypes among Meiteis of Manipur, India.

Pro-inflammatory cytokine gene polymorphisms and threat for coronary heart disease in a North Indian Agrawal population

The association of IFN-γ (+874 A/T; rs2430561), TNF-α (-308 G/A; rs1800629) and TNF-β (+252 A/G; rs909253) with Coronary Heart Disease (CHD) has not been rigorously tested in Indian population. In the present study we sought to examine the role of these cytokines in the causation of CHD and their association with conventional CHD risk factors. A total of 138 case and 187 unrelated healthy controls aged 35 to 80years, matched on ethnicity and geography were collected from North Indian Agrawal population. Single nucleotide polymorphisms at the promoter TNF-α -308 G/A and the intronic IFN-γ +874 A/T were analyzed by allele-specific PCR, and the intronic TNF-β +252 A/G was analyzed by RFLP. Of the three selected polymorphisms, genotypic distribution of IFN-γ +874 A/T and TNF-β +252 A/G polymorphisms was significantly different between patients and controls in the present study. OR revealed statistically significant risk for CHD with respect to IFN-γ +874 T allele, whereas OR for TNF-β +252 A/G showed three fold risk in homozygous condition though not significant. No such trend could be observed for TNF-α -308 G/A polymorphism. Multivariate logistic regression after adjusting for all the confounders showed significant risk for CHD with the genotypes and genotypic combinations of all the three markers (albeit not significant with TNF-α). Increased risk for CHD was likely to be associated with interaction of IFN-γ with diastolic hypertension, TNF-α with diabetes and BMI, and TNF-β with serum triglyceride and very low density lipoprotein (VLDL) levels. The results suggest that these selected cytokine polymorphisms could possibly serve as potential bio-markers for CHD in conjunction with specific conventional risk factors.

Genomic and Linguistic Affinities: A Study of Allelic and Haplotype Diversity at DRD2 Locus Among the Tribes of Gujarat, Western India

Do genetic and linguistic affinities necessarily go hand in hand? An attempt has been made in the present work to explore this dimension of population structure using three evolutionarily important TaqI sites (TaqI A, TaqI B, and TaqI D) on the dopamine receptor D2 (DRD2) locus. For the first time, DNA samples from 612 unrelated individuals belonging to 11 Indo-European-speaking tribal population groups of Gujarat, western India, have been analyzed for these three sites. All the three sites are found to be polymorphic with greater interpopulation variation seen at the TaqI B site. The average heterozygosity for the haplotype system has been found to be high in the populations under study. Most of the populations share six of the eight haplotypes pointing toward underlying genetic uniformity, which is further reaffirmed by regression analysis of heterozygosity on genetic distance. The frequency of ancestral haplotype B2D2A1 is found to range between 1.9% and 15.9%. Linkage disequilibrium between TaqI B and TaqI D sites and between TaqI B and TaqI A sites is statistically significant in all but one population. Our findings reveal strong affinities between Indo-European-speaking tribal groups of Gujarat and Dravidian-speaking tribal groups of South India, suggesting that genetic affinities may not necessarily be dependent on linguistic similarities.

Brief communication: Allelic and haplotypic structure at the DRD2 locus among five North Indian caste populations

The dopamine D2 receptor (DRD2) gene, with its known human-specific derived alleles that can facilitate haplotype reconstruction, presents an important locus for anthropological studies. The three sites (TaqIA, TaqIB, and TaqID) of the DRD2 gene are widely studied in various world populations. However, no work has been previously published on DRD2 gene polymorphisms among North Indian populations. Thus, the present study attempts to understand the genetic structure of North Indian upper caste populations using the allele and haplotype frequencies and distribution patterns of the three TaqI sites of the DRD2 gene. Two hundred forty-six blood samples were collected from five upper caste populations of Himachal Pradesh (Brahmin, Rajput and Jat) and Delhi (Aggarwal and Sindhi), and analysis was performed using standard protocols. All three sites were found to be polymorphic in all five of the studied populations. Uniform allele frequency distribution patterns, low heterozygosity values, the sharing of five common haplotypes, and the absence of two of the eight possible haplotypes observed in this study suggest a genetic proximity among the selected populations. The results also indicate a major genetic contribution from Eurasia to North Indian upper castes, apart from the common genetic unity of Indian populations. The study also demonstrates a greater genetic inflow among North Indian caste populations than is observed among South Indian caste and tribal populations.

MTHFR C677T polymorphism and its homocysteine-driven effect on blood pressure

High blood pressure (hypertension) is the single most important modifiable risk factor for ischemic stroke (1) and is defined as systolic blood pressure ≥140 mmHg and/or as diastolic blood pressure ≥90 mmHg. Data suggest that elevated homocysteine is an independent risk factor for hypertension (2). Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism has been found to be associated with increased homocysteine (>15 μmol/L) and hypertension (3), although associations are conflicting (4). Interrelationship among MTHFR C677T, homocysteine, and blood pressure is less understood. We examined the effect of MTHFR C677T polymorphism and hyperhomocysteinemia on blood pressure in a North Eastern population with East Asian ancestry. A total of 1142 individuals aged 35–75 years (unrelated up to first cousin) were recruited and fasting lipids and glucose, height, weight, waist and hip circumferences, blood pressure, and homocysteine (n = 200) were measured, and MTHFR C677T was genotyped after taking their written informed consent. Two hundred forty-eight individuals were identified with hypertension, and a crosssectional design was formulated with their 248 age and gender-matched controls (normotensives). Individuals having TT genotype of MTHFR C677T had significantly higher blood pressure than those having CC genotype. TT genotype and elevated homocysteine levels between 10 to 15 μmol/L and above showed significant eightfold and threefold increased risks, respectively, for hypertension. Hyperhomocysteinemia and MTHFR C677T showed significant increased risk even after controlling for probable confounders. We, therefore, conclude that MTHFR 677TT genotype and elevated homocysteine levels (even in the upper limits of the normal range of 5–15 μmol/L) are significantly associated with hypertension particularly in the present population, regardless of age and gender. Although the study did not assess the association of MTHFR C677T and increased homocysteine levels directly with stroke, the study highlights a homocysteine-driven effect of MTHFR C677T on blood pressure that is an important risk factor for stroke and various stroke-related anomalies.

A49T, R227Q and TA repeat polymorphism of steroid 5 alpha-reductase type II gene and Hypospadias risk in North Indian children

Background/Aims Hypospadias is a common congenital error of genital development, the frequency of which is increasing. As androgens have a significant role in the development of the male urethra, we sought to investigate the association between functional polymorphisms of SRD5A2 gene in relation to hypospadias. Methods We examined DNA samples of 96 cases and 105 controls for SRD5A2-A49T, R227Q and TA repeat gene polymorphisms. Result Absence of 49T locus and 227Q locus was observed in the present study. At the (TA) n repeat site, TA (0) allele was observed to be the most common allele in both cases (91.7%) and controls (90%). TA (9/9) genotype exhibited an odds ratio of 3.03 (95% C.I. = 0.18–50.14, p = 0) with respect to only middle phenotypes. Analysis of the demographic data depicted the agricultural background aspect of the parents of the cases. 72.27% of the cases (affected with Hypospadias) have parents having agriculture as a primary occupation. Conclusion As longer TA repeats are associated with lower enzymatic activity and lower DHT levels as reported among Caucasians, this polymorphism may have an effect (rather small) in predisposing the population of the present study to the risk of Hypospadias of lesser severity. Due to small sample size, the 3.03 O.R. is not significant and a larger sample is needed to validate the results. Large scale screening of Hypospadias and other 46 X,Y disorders of sexual development is needed especially in India, where the majority of the population is from agricultural background. The results of the present study are likely to assist the health planners to initiate screening of Hypospadias among the farmer community to combat the risk of Hypospadias.