Frequency of fokI and taqI polymorphism of vitamin D receptor gene in Indian population and its association with 25-hydroxyvitamin D levels

Background: The VDR protein is at the centre of the vitamin D endocrine system, a complex physiological system with substantial feedback regulatory mechanisms involved in maintaining serum calcium and 1, 25 dihydroxy vitamin D3. Variations in VDR gene are shown to have implications in several diseases and have also been implicated as an important genetic factor affecting bone mass. Aim: To determine the frequency of Fok I and Taq I variants in healthy Indian individuals and its association with 25-OH-Vitamin D levels. Settings and Design: Blood samples were collected from 143 unrelated normal individuals (Male-84 and Female-59) and their genotypes determined. Materials and Methods: After amplification by polymerase chain reaction, each polymorphism was genotyped by restriction fragment length polymorphism. For 100 normal healthy individuals 25-hydroxyvitamin D estimation was done using DiaSorin kit method. Statistical Analysis: Graph pad software was used to calculate the P values from the Chi-square. Results: Out of 143 samples analyzed for FokI and TaqI polymorphisms the following genotypic frequency was obtained FF 59%, Ff 36%, ff 5% and TT 49%, Tt 43%, tt 8% respectively. Conclusions: Results indicate that the distribution of the polymorphic loci Fok I and Taq I vary considerably not only in different populations, but also within India. Furthermore, when the genotypes were analyzed with respect to 25-OH-Vitamin D levels, a significant association was seen for the Taq 1 SNP but not with the Fok I

The contribution of childhood adversity to cortisol measures of early life stress amongst infants in rural India: findings from the early life stress sub-study of the SPRING cluster randomised controlled trial (SPRING-ELS)

Background: The majority of the world’s children live in low- and middle-income countries and face multiple obstacles to optimal wellbeing. The mechanisms by which adversities – social, cultural, psychological, environmental, economic – get ‘under the skin’ in the early days of life and become biologically embedded remain an important line of enquiry. We therefore examined the contribution of childhood adversity through pregnancy and the first year of life to hair and salivary cortisol measures of early life stress in the India SPRING home visits cluster RCT which aims to improve early childhood development. Methods: We assessed 22 adversities across four domains: socioeconomic, maternal stress, family-child relationship, and child and summed them to make a cumulative adversity score & quintiles, and four subscale scores. We cut 3 cm of hair from the posterior vertex and took three saliva samples from morning till late afternoon on each of two days (total six samples). We analysed both for cortisol concentration using ELISA techniques. We used multiple linear regression techniques to assess the relationship between cumulative adversity and log hair cortisol concentration and saliva diurnal slope and area under the curve. Results: We assessed 712 children for hair, and 752 children for saliva cortisol at 12 months of age. We found a strong positive relationship between adversity and hair cortisol; each additional adversity factor was associated with hair cortisol increases of 6.1% (95% CI 2.8, 9.4, p < 0.001) and the increase from adversity quintile one to five was 59.4%. Socioeconomic, relationship and child scales were independent predictors of hair cortisol (socioeconomic 6.4% (95% CI -0.4, 13.6); relationship 11.8% (95% CI 1.4, 23.2); child 7.9% (95% CI -0.5, 16.9). We did not find any association between any measures of adversity and either of the saliva cortisol outcomes. Discussion: This is the largest study of hair cortisol in young children, and the first in a low- and middle-income country setting. Whilst the short-term diurnal measures of cortisol did not appear to be linked with adversity, chronic exposure over several months appears to be strongly associated with cumulative adversity. These findings should spur further work to understand the specific ways in which adversity becomes biologically embedded, and how this can be tackled. They also lend support to ongoing action to tackle childhood adversity in communities around the world

Promoter variants in interleukin-6 and tumor necrosis factor alpha and risk of coronary artery disease in a population from Western India

Introduction: A central component of the atherosclerotic process is inflammation. Single nucleotide polymorphisms (SNPs) present in the promoter region of various cytokines can lead to altered levels of the transcript and a state of low-grade inflammation exacerbating the risk of coronary artery disease (CAD). The present work tries to understand the role of permissive promoter variants in the interleukin-6 gene (IL-6-174G/C) and the tumor necrosis factor alpha (TNFα-308G/A) in the causation of CAD and also dyslipidemia. Materials and Methods: Genotyping was conducted on 100 cases of CAD and 150 controls by the allele termination assay SNaPshot. Biochemical parameters were determined by routine enzymatic endpoint methods. The results were analyzed by appropriate statistical methods. Results: No differences in the minor allele frequency IL-6-174G/C SNP were seen between cases and controls (0.13 vs. 0.12). The differences in the allele frequency of TNFα-308A between cases (6%) and controls (2%) have led to an odds ratio, 3.370; 95% confidence interval, 1.039-11.543; P=0.033 in the univariate analysis. In the final logistic regression analysis, however none of the variants were associated with an increased risk of CAD. Conclusions: In summary, no association of the permissive promoter variants in the IL-6 gene and the TNFα gene were seen with an increased CAD risk. These and other studies highlight the importance of doing population specific studies

Frequency and association of disabled homolog 2-interacting protein (DAB2IP) variant rs7025486 G>A with coronary artery disease risk in Indian population

Genome wide association study has identified rs7025486 G>A polymorphism within DAB2IP (Disabled homolog 2-interacting protein) gene with increased risk of coronary heart disease (CAD). In this study we have determined the frequency and association of rs7025486 with CAD in Indians. The study was performed on 214 patients with CAD and 125 controls. The ‘AA’ genotype was associated with an increased risk in the CAD age group 50 yrs (OR 3.149; P 0.034) and controls >50 yrs (OR 3.430; P 0.080). The risk allele (A) was significantly associated with premature CAD. Keywords: Coronary artery disease, Single nucleotide polymorphism, Association study, Indians, Genotypin

Homozygous hemoglobin Monroe (codon 30 G>C) in a child of Goan (Indian) origin: A case report and family study

India has a huge burden of β-thalassemia with an estimated 100,000 patients and a prevalence of 3%–4% carriers. The five common mutations reported in the India are IVS 1–5 (G->C), IVS 1-1 (G->T), codon 41/42 (-TCTT), codon 8/9, and 619 bp deletion. We report this rare case of IVS 1-1 G>C variant (hemoglobin [Hb] Monroe) in homozygous form in a child of Goan origin. The propositus presented at 3 months with pallor, hepatosplenomegaly, and lymphadenopathy. Diagnostic workup of the child was suggestive of β-thalassemia major, the parents Hb electrophoresis revealed β-thalassemia trait in the mother, whereas the father had elevated HbF levels. Initial polymerase chain reaction by ARMS (amplification-refractory mutation specific) was negative for the common five mutations. β-globin full gene sequencing revealed the presence of IVS-1-1G>C (Hb Monroe) in the homozygous form and also c.-92 C>G in the homozygous form, the mother was heterozygous for both the mutations, whereas the father was negative. STR marker studies did not indicate uniparental disomy to be the reason for IVS-1-1 G>T homozygosity in the child in the absence of the same mutation in the father. The father showed a possibility of δβ deletional mutation. This report highlights the importance of molecular studies in participants with borderline HbA2 levels, including spouse of a typical β-thalassemia carrier. Assaying for only the common five mutations may not yield complete answers. Full gene sequencing should be performed in those individuals with a strong phenotype of β-thalassemia. The prenatal diagnosis should be offered to couples at risk

Reference ranges for lymphocyte subsets in adults from western India: Influence of sex, age and method of enumeration

Background: The enumeration of absolute CD4 counts is of primary importance, since therapeutic protocols for HIV1 patients are based on these. Aims: To establish reference ranges for the CD4 and CD8 T-lymphocytes in the Indian population. Settings and Design: Enumeration of absolute numbers and percentages of lymphocyte subsets was performed in 252 healthy adult Indians. Methods and Materials: The assays for SPT were carried out using the Beckman EPICS XL-MCL flow cytometer and the cytostat tetraCHROME reagent containing CD45/CD8/CD4/CD3 monoclonal antibodies. For comparison with DPT the absolute lymphocyte count was obtained using the Coulter STK-S fully automated hematology analyzer. Statistical Analysis: Regression analysis and Students t test were used for data analysis. Results: Median values were as follows; absolute CD3 counts 1446 cells/mm3 (total), 1361 cells/mm3 (males) and 1511 cells/mm3 (females); absolute CD4 counts are 771 cells/mm3 (total), 705 cells/mm3 (males) and 839 cells/mm3 (females); absolute CD8 counts are 555 cells/mm3 (total), 552 cells/mm3 (males) and 561 cells/mm3 (females). The median CD4/CD8 ratio for the total samples was 1.34, for males 1.22 and for females 1.49. Conclusions: In this study we have established reference ranges for normal Indian adults using the fully automated Single Platform Technology. The lymphocyte subsets values of our population are closer to those of the population from Botswana and China rather than the Western population. The absolute CD3 and CD4 counts and the CD4:CD8 ratio are higher in females than in males. Consistently higher values are obtained by the DPT as compared to the SPT

Status of TMPRSS2–ERG fusion in prostate cancer patients from India: correlation with clinico-pathological details and TMPRSS2 Met160Val polymorphism

Background: Prostate cancer (PCa) shows considerable clinical heterogeneity that has been primarily attributed to variable molecular alterations. TMPRSS2–ERG fusion is one such molecular subtype that has been associated with predominantly poor prognosis. More recently, a single nucleotide polymorphism (SNP) in the TMPRSS2 gene rs12329760 C>T (Met160Val) has been shown to positively correlate with the fusion status and also to be associated with increased risk for PCa. The aim of the present study is to determine the frequency of TMPRSS2–ERG fusion and association of rs12329760 in Indian PCa patients with fusion status. Methods: TMPRSS2–ERG fusion by fluorescence in situ hybridization was determined in 102 of 150 PCa biopsy-proven cases. Genotyping for rs12329760 was performed on the entire cohort of 150 cases by Sanger sequencing. Results: TMPRSS2–ERG fusion was seen in 27 of 102 (26%) cases. Fusion-positive patterns in this study showed fusion by translocation in nine of 27 cases (33.5%), by deletion in six of 27 (22%) cases, and by insertion in 12 of 27 cases (44.5%). No association of the fusion status with Gleason Score, pattern, or perineural invasion was seen. The TMPRSS2 SNP rs12329760 ‘T’ allele was prevalent with a frequency of 0.27 in the PCa patients. The SNP was significantly associated with fusion [odds ratio (OR) = 2.176, 95% confidence interval (CI) = 1.012–4.684, P = 0.04], more specifically fusion by deletion (P = 0.04). Conclusion: The results provided here determine the frequency of TMPRSS2–ERG fusions (26%) in a fairly large cohort of Indian PCa cases and also the association of rs12329760 SNP with TMPRSS2–ERG fusion. No association with other clinico-pathological features was observed. Future studies with clinical outcomes are warranted in this population. Keywords: Fluorescence in situ hybridization, Indians, Prostate cancer, rs12329760, Single nucleotide polymorphism, TMPRSS2–ER