Sickle Cell Institute Chhattisgarh

Raipur, India

Sickle Cell Institute Chhattisgarh

Raipur, India
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PubMed | Sickle Cell Institute Chhattisgarh, Madras Medical College and Government General Hospital, Indian Institute of Technology Madras and University of Madras
Type: | Journal: Meta gene | Year: 2015

The KIF6 719Arg allele is an interesting genomic variant widely screened in various populations and is reported to be associated with the risk of Coronary Artery Disease (CAD) and statin treatment outcome. Recent population based clinical studies and large-scale meta-analyses pondered over the role of 719Arg variant in CAD risk and treatment response. We screened the KIF6 Trp719Arg polymorphism (rs20455) in south Indian CAD patients in a case-control approach. A total of 1042 samples (510 CAD patients and 532 controls) were screened for the KIF6 Trp719Arg SNP by TaqMan SNP genotyping assay, followed by meta-analysis of the genotype data of non-Europeans reports. The 719Arg risk genotype (GG) was observed in 29.6% of CAD cases and in 30.1% of controls with an odds ratio (OR) of 1.07 (95% CI: 0.76-1.50), p value=0.709. No significant difference in the genotype frequency was observed between CAD and controls in both dominant model (AG+GG vs AA) and allelic model (719Arg vs 719Trp) with an OR of 1.11 (p=0.491) and 1.03 (p=0.767), respectively. The covariate analysis indicated that smoking & alcohol consumption increased the risk for MI among CAD patients. Meta-analysis showed that the KIF6 719Arg allele is not associated with CAD risk in both fixed effect (p=0.515, OR=1.023, 95% CI=0.956-1.094) and random effect (p=0.547, OR=1.022, 95% CI=0.953-1.096). The symmetrical shape of the Eggers funnel plots revealed that there is no publication bias. These results suggest that there is no association of KIF6 719Arg allele with CAD risk in South Indian population and the meta-analysis confirms the same among non-European population.

PubMed | Sickle Cell Institute Chhattisgarh, Sri Venkateswara University, Narayana Medical College, Estonian Biocentre and University of Madras
Type: | Journal: Human genome variation | Year: 2016

The N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes involved in the metabolism of drugs, environmental toxins and the aromatic amine carcinogens present in cigarette smoke. Genetic variations in NAT2 have long been recognized as the cause of variable enzymatic activity or stability, leading to slow or rapid acetylation. In the present study, we genotyped three single-nucleotide polymorphisms (SNPs) from the NAT2 gene (rs1799929, rs1799930 and rs1799931), using TaqMan allelic discrimination, among 212 individuals from six major South Indian populations and compared the results with other available Indian and worldwide data. All three of the markers followed Hardy-Weinberg equilibrium and were highly polymorphic in the studied populations. The constructed haplotypes showed a high level of heterozygosity. All of the populations in the present study commonly shared only four haplotypes out of the eight possible three-site haplotypes. The haplotypes exhibited fairly high frequencies across multiple populations, where three haplotypes were shared by all six populations with a cumulative frequency ranging from 88.2% (Madiga) to 97.0% (Balija). We also observed a tribal-specific haplotype. A strong linkage disequilibrium (LD) between rs1799929 and rs1799930 was consistent in all of the studied populations, with the exception of the Madiga. A comparison of the genomic regions 20-kb up- and downstream of rs1799930 in a large number of worldwide samples showed a strong LD of this SNP with another NAT2 SNP, rs1112005, among the majority of the populations. Moreover, our lifestyle test (hunter-gatherer versus agriculturist) in comparison with the NAT2 variant suggested that two of the studied populations (Balija and Madiga) have likely shifted their diet more recently.

Murthy J.,Sri Ramachandra University | Venkatesh Babu G.Z.,Sri Ramachandra University | Bhaskar L.V.K.S.,Sri Ramachandra University | Bhaskar L.V.K.S.,Sickle Cell Institute Chhattisgarh
Malaysian Journal of Nutrition | Year: 2015

Introduction: Non-syndromic cleft lip with or without cleft palate (NSCLP) is a multifactorial threshold trait (MFT) involving both genetic and environmental factors. Choline, methionine and folate metabolism are interrelated in converting the homocysteine to methionine. Phosphatidylethanolamine N-methyltransferase (PEMT) is involved in biosynthesis of choline. Methods: We studied the PEMT rs4244593 SNP to assess its effect on NSCLP risk in the South Indian population. Blood samples of 142 cases with NSCLP and 141 controls were collected and genotyped using PCR-RFLP. Statistical analysis of the results was performed by calculating OR, and 95% CI via x2 test. Results: Proportions of genotypes were 16.9 % AA,64.8 % AC,16.9 % CCincasesand35.5 % AA,47.5 % AC,17.0 % CC in controls. The C allele frequency was 50.7% for cases and 40.8% for controls. An increased risk was found for co-dominant (AC vs. AA: OR =2.86, 95% CI =1.60 to 5.11, p<0.001; CC vs. AA: OR =2.26, 95% CI =1.08 to 4.72, p=0.029), dominant (AC+CC vs. AA: OR =2.70, 95% CI =1.55 to 4.72, p<0.001) and allelic models (C vs. A: OR =1.49,95% CI =1.07 to 2.08, p=0.018). Conclusions: Although our results indicate that the PEMT rs4244.593 polymorphism is one of the important genetic determinants of NSCLP risk in South Indian subjects, in the absence of mechanistic studies, this polymorphism cannot be considered as a determinant of NSCLP risk. Additional studies with fully validated functional SNPs and larger sample sizes are needed to confirm our findings.

Ramanathan G.,Sri Ramachandra University | Periyasamy S.,Sri Ramachandra University | Lakkakula B.V.,Sri Ramachandra University | Lakkakula B.V.,Sickle Cell Institute Chhattisgarh
Nephrology | Year: 2014

Aim Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary and progressive renal disorder. It is also recognised as the most frequent genetic cause of chronic kidney diseases (CKD). In the present study, four tagging SNPs and two more well studied polymorphisms (Intron 4 VNTR and Glu298Asp) the NOS3 gene were investigated to unravel the potential modifier effect of NOS3 gene on the progression of CKD in ADPKD. Methods A total of 102 ADPKD patients and 106 controls were selected for the study. The tagSNPs and Glu298Asp polymorphisms were genotyped using FRET-based KASPar method and intron-4 VNTR by polymerase chain reaction electrophoresis. The genotypes and haplotypes in the controls and ADPKD subjects were analysed by χ2 tests and haploview software. Mantel-Haenszel stratified and univariate analyses were performed to estimate the influence of different genotypes between different CKD stages and hypertension. Results The tagSNPs of NOS3 genotypes and haplotypes did not exhibit any significant differences between controls and ADPKD patients. The significant linkage disequilibrium was observed between the rs3918184 and rs2853796 by forming LD block. In univariate analysis, the age and family history of Diabetes mellitus (DM) showed significant association with advancement of CKD, but not with the eNOS polymorphisms. Conclusions Our data suggests that there is no evidence for the involvement of NOS3 tag SNPs in the progression to CKD in ADPKD patients. A systematic study using well validated functional SNPs is necessary to clarify the role of the NOS3 gene in the development of CKD in ADPKD. Summary at a Glance The variability in progression to kidney failure in autosomal dominant polycystic kidney disease (ADPKD) could be explained, in part, by single nucleotide polymorphisms (SNPs) in candidate modifier genes. However, the results of the present study provide further evidence that SNPs in the NOS3 gene are not involved in the progression of ADPKD patients. © 2014 Asian Pacific Society of Nephrology.

Murthy J.,Sri Ramachandra University | Gurramkonda V.-B.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sickle Cell Institute Chhattisgarh
Medicina Oral, Patologia Oral y Cirugia Bucal | Year: 2014

Objectives: Nonsyndromic cleft lip and palate (NSCLP) is genetically distinct from those with syndromic clefts, and accounts for ~70% of cases with Oral clefts. Folate, or vitamin B9, is an essential nutrient in our diet. Allelic variants in genes involved in the folate pathway might be expected to have an impact on risk of oral clefts. Given the key role of methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) in folate metabolism, it would be of significant interest to assess its role in NSCLP etiology.Study Design: The present study aims at examining the association between MTHFD1 1958G>A polymorphism and NSCLP risk by conducting a case-control study in south Indian population. Our sample comprised of 142 cases with nonsyndromic clefts and 141 controls without clefts or family history of clefting. The MTHFD1 1958G>A polymorphism was genotyped using PCR-RFLP.Results: An increased risk was found for the heterozygous 1958GA (OR=2.44; P=0.020) and homozygous 1958AA (OR=2.45; P=0.012) genotypes in the children. When the dominant model (AG+AA vs GG) was applied the risk remained the same as co-dominant model, but the level of significance increased (OR=2.44; P=0.002).Conclusions: The results indicated the MTHFD1 1958G>A polymorphism to be one of the important genetic determinants of NSCLP risk in South Indian subjects. © Medicina Oral S. L.

Ramanathan G.,Sri Ramachandra University | Elumalai R.,Sri Ramachandra University | Periyasamy S.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sickle Cell Institute Chhattisgarh
Iranian Journal of Kidney Diseases | Year: 2014

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited disease of the kidneys and is marked by progressive cyst growth and decline in kidney function, resulting in end-stage renal disease (ESRD). Hypertension is thought to be a significant modifying factor in the progression of renal failure in ADPKD. A number of genetic variations involved in reninangiotensin-aldosterone system (RAAS) pathway genes have clinical or physiological impacts on pathogenesis of hypertensioninduced ESRD in ADPKD. Information on RAAS pathway gene polymorphisms and their association with ESRD and ADPKD, published till March 2013, was collected using MEDLINE search. The present review deals with RAAS gene polymorphisms focused on hypertension-induced ESRD in ADPKD in different populations. The results were inconclusive and limited by heterogeneity in the study designs and the population stratification. In lieu of applying next generation sequencing technologies to study complex diseases, it is also possible to apply the same to unravel the complexity of ESRD in ADPKD.

Lavu V.,Sri Ramachandra University | Venkatesan V.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sickle Cell Institute Chhattisgarh | Venugopal P.,Sri Ramachandra University | And 2 more authors.
Genetic Testing and Molecular Biomarkers | Year: 2015

Objective: The objectives of this study were to determine the association between single nucleotide polymorphisms (SNPs) in IL1B (-511, +3954), IL1A (-889, +4845), and the variable number of tandem repeats (VNTRs) polymorphism in the IL-1RN gene with chronic periodontitis susceptibility and to analyze gene-gene interactions in a hospital-based sample population from South India. Subjects and Methods: A total of 400 individuals were recruited for this study; 200 individuals with healthy gingiva and 200 chronic periodontitis patients. Genomic DNA was isolated from peripheral blood samples and genotyping was performed for the above-mentioned single nucleotide and VNTR polymorphisms by polymerase chain reaction, DNA sequencing, and agarose gel electrophoresis. Results: A higher proportion of the variant alleles were observed in the chronic periodontitis group for all the SNPs examined. The SNP at +3954 (C>T) in the IL1B gene was found to be significantly associated with chronic periodontitis (p=0.007). VNTR genotypes (χ2 value: 5.163, df=1, p=0.023) and alleles (χ2 value: 6.818, df=1, p=0.009) were found to have a significant association with chronic periodontitis susceptibility. Conclusion: In the study population examined, the SNP in the IL1B gene (+3954) and VNTR polymorphisms in the IL1RN gene were found to have a significant association with chronic periodontitis susceptibility. © 2015, Mary Ann Liebert, Inc.

Hussain H.,Sri Ramachandra University | Ramachandran V.,Sri Ramachandra University | Ravi S.,Sri Ramachandra University | Sajan T.,Sri Ramachandra University | And 5 more authors.
Endokrynologia Polska | Year: 2014

Diabetic nephropathy (DN) is a chronic microangiopathic complication of both type 1 (T1DM) and type 2 diabetes mellitus (T2DM). The TCF7L2 gene has been reported to be associated with type 2 diabetes risk. We aimed to investigate the impact of TCF7L2 gene on the susceptibility of T2DM and DN in a south Indian population. Plus to evaluate the association of rs7903146 in the TCF7L2 gene with T2DM in the Indian population. The subjects recruited for this included 55 diabetic cases with diabetic nephropathy, 68 diabetic cases without nephropathy, and 82 non-diabetic healthy controls. Genomic DNA was isolated from blood and genotyping of TCF7L2 rs7903146 was performed by PCR-RFLP analysis. A literature survey was carried out into the effect of rs7903146 on genetic susceptibility to T2DM in Indian populations and we then performed a meta-analysis in order to evaluate its association with T2DM. Analysis of TCF7L2 rs7903146 in normal controls and diabetics with or without nephropathy demonstrated that the 'T' allele is associated with both diabetes (p = 0.049) and DN (p = 0.024), but this association is not independent of T2DM. Meta-analysis showed that the mutant allele and genotypes are associated with T2DM in Indian populations. In summary, a significant association exists between the 'T' allele and DN, but this association is not independent of T2DM. Pooled meta-analysis of studies on rs7903146 and T2DM confirmed that rs7903146 is significantly associated with susceptibility to T2DM in Indian populations.

Gurramkonda V.B.,Sri Ramachandra University | Hussain Syed A.,Sri Ramachandra University | Murthy J.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sri Ramachandra University | Lakkakula B.V.K.S.,Sickle Cell Institute Chhattisgarh
International Journal of Pediatric Otorhinolaryngology | Year: 2015

Objective: Non-syndromic cleft lip, with or without cleft palate (NSCL/P) is a common craniofacial birth defect, characterised by an incomplete separation between nasal and oral cavities without any other congenital anomaly in humans. Several genes which play a role in cell differentiation, migration, growth and apoptosis, have been associated with clefting. The purpose of this study was to investigate the association between single-nucleotide polymorphisms (SNPs) near MSX1 gene and NSCL/P among South Indian population. Methods: A case-control analysis of five single nucleotide polymorphisms near MSX1 gene (rs11726039, rs868257, rs6446693, rs1907998 and rs6832405) was carried out in 173 patients with NSCL/P and 176 unaffected controls to determine their association with NSCL/P. Results: All SNPs were polymorphic in the study population. Comparisons of allele and genotype frequencies revealed that the C variant allele and the TC/CC genotypes of rs11726039 was significantly higher in controls than in the NSCL/P group (OR: 0.63; 95% CI: 0.41. - 0.097; p= 0.037). However, neither of these findings remained significant after Bonferroni correction for multiple comparisons. The frequencies of rs868257, rs6446693, rs1907998 and rs6832405 minor alleles and genotypes were similar between the control and NSCL/P groups. No significant linkage disequilibrium (LD) was observed. Genotype-genotype interaction and the haplotype analysis did not reveal any significant association with NSCL/P. Conclusions: The study results were suggestive of a positive association between MSX1 rs11726039 and NSCL/P in the South Indian population. © 2015 Elsevier Ireland Ltd.

PubMed | Sickle Cell Institute Chhattisgarh and Sri Ramachandra University
Type: Journal Article | Journal: American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics | Year: 2016

Mandibular retrognathism may be the result of a developmental abnormality or the unfavorable positional relationship of developing jaws. Several lines of evidence suggest that muscles are known to have extensive mutual effects on bones. Studies with immunohistochemical staining and gene expression have shown unique combinations of myosin heavy chain isoforms in the masseter muscles. In this study, we aimed to evaluate MYO1H gene polymorphisms and haplotypes as risk factors for mandibular retrognathism.Twenty-five subjects with mandibular retrognathism and 25 control subjects of both sexes having an orthognathic maxilla (SNA, 822) between the ages of 12 and 30years of age were selected for this study. Based on the cephalometric values, subjects with SNB angles smaller than 78 were considered to have mandibular retrognathism. Orthognathic subjects (SNB, 80) without jaw deformations were used as the comparison group. Three polymorphisms of MYO1H gene (rs10850110, rs11611277, and rs3825393) were genotyped using polymerase chain reaction and restriction fragment length polymorphism. Associations were tested with the Pearson chi-square test and haplotype analyses.The single nucleotide polymorphism rs3825393 showed a statistically significant association with mandibular retrognathism. The cephalometric variables SNB and ANB angles showed significant differences among the various genotypes of rs3825393. Linkage disequilibrium was not strong and significant between the single nucleotide polymorphisms; hence, the haplotypes of the MYO1H gene are not associated with mandibular retrognathism.These results suggest that the rs3825393 polymorphism of the MYO1H gene is associated with an increased risk for mandibular retrognathism. The relatively small sample size used in the study resulted in modest statistical power. A parallel investigation on another population with larger samples to increase the power could further clarify the role of the MYO1H gene in causing mandibular retrognathism.

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