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1.  Association of matrix metalloproteinase -7 (-181A/G) promoter polymorphism in chronic pancreatitis 
Background & objectives:
Chronic pancreatitis is progressive and irreversible destruction of the pancreas. Matrix metalloproteinase-7 (MMP-7) is a secreted matrilysin, which contributes to angiogenesis and breakdown of basement membranes of pancreatic tissues. The present study was aimed to investigate the association of MMP-7 −181A/G (rs11568818) gene promoter polymorphism in patients with chronic pancreatitis.
Methods:
A total of 100 chronic pancreatitis patients and 150 unrelated healthy individuals were included in this case control study. The genotyping of the MMP-7 gene (− 181 A/G) (rs11568818) was carried out based on PCR-RFLP. The serum levels of MMP-7 were determined by ELISA. Association between genotypes and chronic pancreatitis was examined by odds ratio (OR) with 95% confidence interval (CI).
Results:
The frequencies of the genotypes in promoter of MMP-7 were AA 49 per cent, AG 25 per cent and GG 26 per cent in chronic pancreatitis patients and AA 53 per cent, AG 38 per cent and GG 9 per cent in control subjects. Frequency of MMP-7 −181GG genotype and − 181G allele was significantly associated with chronic pancreatitis compared to healthy subjects [OR = 1.58 (95% CI: 1.06 –2.36), P =0.019]. There was no significant difference in the serum MMP-7 levels in the patients compared to control subjects.
Interpretation &conclusions:
The present study revealed a significant association of MMP-7 -181A/G (rs11568818) GG genotype with chronic pancreatitis patients, indicating its possible association with the disease.
PMCID: PMC4311313  PMID: 25579141
Chronic pancreatitis; genetic susceptibility; genotypes; inflammation; matrix metalloproteinase; myofibroblasts
2.  Haplotype Analyses of DNA Repair Gene Polymorphisms and Their Role in Ulcerative Colitis 
PLoS ONE  2014;9(9):e108562.
Ulcerative colitis (UC) is a major clinical form of inflammatory bowel disease. UC is characterized by mucosal inflammation limited to the colon, always involving the rectum and a variable extent of the more proximal colon in a continuous manner. Genetic variations in DNA repair genes may influence the extent of repair functions, DNA damage, and thus the manifestations of UC. This study thus evaluated the role of polymorphisms of the genes involved in DNA repair mechanisms. A total of 171 patients and 213 controls were included. Genotyping was carried out by ARMS PCR and PCR-RFLP analyses for RAD51, XRCC3 and hMSH2 gene polymorphisms. Allelic and genotypic frequencies were computed in both control & patient groups and data was analyzed using appropriate statistical tests. The frequency of ‘A’ allele of hMSH2 in the UC group caused statistically significant increased risk for UC compared to controls (OR 1.64, 95% CI 1.16–2.31, p = 0.004). Similarly, the CT genotype of XRCC3 gene was predominant in the UC group and increased the risk for UC by 1.75 fold compared to controls (OR 1.75, 95% CI 1.15–2.67, p = 0.03), further confirming the risk of ‘T’ allele in UC. The GC genotype frequency of RAD51 gene was significantly increased (p = 0.02) in the UC group (50.3%) compared to controls (38%). The GC genotype significantly increased the risk for UC compared to GG genotype by 1.73 fold (OR 1.73, 95% CI 1.14–2.62, p = 0.02) confirming the strong association of ‘C’ allele with UC. Among the controls, the SNP loci combination of hMSH2:XRCC3 were in perfect linkage. The GTC and ACC haplotypes were found to be predominant in UC than controls with a 2.28 and 2.93 fold significant increase risk of UC.
doi:10.1371/journal.pone.0108562
PMCID: PMC4172686  PMID: 25247297
3.  Role of Interstitial Collagenase Gene Promoter Polymorphism in the Etiology of Gastric Cancer 
Background/Aims:
Gastric cancer (GC) is a multifactorial disorder mediated by genetic, epigenetic, and environmental risk factors. GC is the most common cancer in India and it is the third prominent cause of cancer death worldwide. A single nucleotide polymorphism (SNP) in the promoter region of interstitial collagenase (MMP-1) gene appears to have an impact on the transcriptional activity and regulation of its expression. Hence, the present study is aimed to evaluate the role of interstitial collagenase gene-1607 1G/2G (rs1799750) promoter polymorphism in the etiology of GC.
Patients and Methods:
The study included 166 GC patients and 202 control subjects. Genomic DNA was isolated from whole blood samples of the subjects, and the genotyping of interstitial collagenase promoter polymorphism was carried out by polymerase chain reaction-restriction fragment length polymorphism method followed by agarose gel electrophoresis. Appropriate statistical methods were applied to test the significance of the results.
Results:
The risk factor profile of the patients revealed that male gender, age above 50 years, addiction to alcohol and smoking were the most common risk factors (P < 0.05). There was a significant difference in the distribution of 2G/2G genotype (2G/2G vs. 1G/1G, P = 0.016) and 1G/2G genotype (2G/2G + 1G/2G vs. 1G/1G, P = 0.010) in patient group compared with that of the control subjects.
Conclusion:
The present study provides indirect evidence for the role of interstitial collagenase gene 1G/2G promoter polymorphism in the etiology of GC in South Indian population.
doi:10.4103/1319-3767.141693
PMCID: PMC4196347  PMID: 25253367
Gastric cancer; genotype; interstitial collagenase; Matrix metalloproteinases-1; polymorphism; polymerase chain reaction-restriction fragment length polymorphism
4.  A Novel Arginine to Tryptophan (R144W) Mutation in Troponin T (cTnT) Gene in an Indian Multigenerational Family with Dilated Cardiomyopathy (FDCM) 
PLoS ONE  2014;9(7):e101451.
Cardiomyopathy is a major cause of heart failure and sudden cardiac death; several mutations in sarcomeric protein genes have been associated with this disease. Our aim in the present study is to investigate the genetic variations in Troponin T (cTnT) gene and its association with dilated cardiomyopathy (DCM) in south-Indian patients. Analyses of all the exons and exon-intron boundaries of cTnT in 147 DCM and in 207 healthy controls had revealed a total of 15 SNPs and a 5 bp INDEL; of which, polymorphic SNPs were compared with the HapMap population data. Interestingly, a novel R144W mutation, that substitutes polar-neutral tryptophan for a highly conserved basic arginine in cTnT, altering the charge drastically, was identified in a DCM, with a family history of sudden-cardiac death (SCD). This mutation was found within the tropomyosin (TPM1) binding domain, and was evolutionarily conserved across species, therefore it is expected to have a significant impact on the structure and function of the protein. Family studies had revealed that the R144W is co-segregating with disease in the family as an autosomal dominant trait, but it was completely absent in 207 healthy controls and in 162 previously studied HCM patients. Further screening of the proband and three of his family members (positive for R144W mutant) with eight other genes β-MYH7, MYBPC3, TPM1, TNNI3, TTN, ACTC, MYL2 and MYL3, did not reveal any disease causing mutation, proposing the absence of compound heterozygosity. Therefore, we strongly suggest that the novel R144W unique/private mutant identified in this study is associated with FDCM. This is furthermore signifying the unique genetic architecture of Indian population.
doi:10.1371/journal.pone.0101451
PMCID: PMC4081629  PMID: 24992688
6.  Novel mutations of KCNQ1 in Long QT syndrome 
Indian Heart Journal  2013;65(5):552-560.
Background
Autosomal recessive Long QT syndrome is characterized by prolonged QTc along with congenital bilateral deafness depends on mutations in K+ channel genes. A family of a Long QT syndrome proband from India has been identified with novel indel variations.
Methods
The molecular study of the proband revealed 4 novel indel variations in KCNQ1. In-silico analysis revealed the intronic variations has led to a change in the secondary structure of mRNA and splice site variations. The exonic variations leads to frameshift mutations. DNA analysis of the available family members revealed a carrier status.
Results and Conclusion
It is thus predicted that the variations may lead to a change in the position of the splicing enhancer/inhibitor in KCNQ1 leading to the formation of a truncated S2–S3 fragment of KCNQ1 transmembrane protein in cardiac cells as well as epithelial cells of inner ear leading to deafness and aberrant repolarization causing prolonged QTc.
doi:10.1016/j.ihj.2013.08.025
PMCID: PMC3861163  PMID: 24206879
Long QT syndrome; JLN syndrome; 3D KCNQ1 structure; Novel mutations; Family study
7.  An In Silico Analysis of Troponin I Mutations in Hypertrophic Cardiomyopathy of Indian Origin 
PLoS ONE  2013;8(8):e70704.
Hypertrophic Cardiomyopathy (HCM) is an autosomal dominant disorder of the myocardium which is hypertrophied resulting in arrhythmias and heart failure leading to sudden cardiac death (SCD). Several sarcomeric proteins and modifier genes have been implicated in this disease. Troponin I, being a part of the Troponin complex (troponin I, troponin C, troponin T), is an important gene for sarcomeric function. Four mutations (1 novel) were identified in Indian HCM cases, namely, Pro82Ser, Arg98Gln, Arg141Gln and Arg162Gln in Troponin I protein, which are in functionally significant domains. In order to analyse the effect of the mutations on protein stability and protein-protein interactions within the Troponin complex, an in silico study was carried out. The freely available X-ray crystal structure (PDB ID: 1JIE) was used as the template to model the protein followed by loop generation and development of troponin complex for both the troponin I wild type and four mutants (NCBI ID: PRJNA194382). The structural study was carried out to determine the effect of mutation on the structural stability and protein-protein interactions between three subunits in the complex. These mutations, especially the arginine to glutamine substitutions were found to result in local perturbations within the troponin complex by creating/removing inter/intra molecular hydrogen bonds with troponin T and troponin C. This has led to a decrease in the protein stability and loss of important interactions between the three subunits. It could have a significant impact on the disease progression when coupled with allelic heterogeneity which was observed in the cases carrying these mutations. However, this can be further confirmed by functional studies on protein levels in the identified cases.
doi:10.1371/journal.pone.0070704
PMCID: PMC3742764  PMID: 23967088
8.  Haplotypes of NOS3 Gene Polymorphisms in Dilated Cardiomyopathy 
PLoS ONE  2013;8(7):e70523.
Dilated Cardiomyopathy (DCM) is characterized by systolic dysfunction, followed by heart failure necessitating cardiac transplantation. The genetic basis is well established by the identification of mutations in sarcomere and cytoskeleton gene/s. Modifier genes and environmental factors are also considered to play a significant role in the variable expression of the disease, hence various mechanisms are implicated and one such mechanism is oxidative stress. Nitric Oxide (NO), a primary physiological transmitter derived from endothelium seems to play a composite role with diverse anti-atherogenic effects as vasodilator. Three functional polymorphisms of endothelial nitric oxide synthase (NOS3) gene viz., T-786C of the 5′ flanking region, 27bp VNTR in intron4 and G894T of exon 7 were genotyped to identify their role in DCM. A total of 115 DCM samples and 454 controls were included. Genotyping was carried out by PCR -RFLP method. Allelic and genotypic frequencies were computed in both control & patient groups and appropriate statistical tests were employed. A significant association of TC genotype (T-786C) with an odds ratio of 1.74, (95% CI 1.14 - 2.67, p = 0.01) was observed in DCM. Likewise the GT genotypic frequency of G894T polymorphism was found to be statistically significant (OR 2.10, 95% CI 1.34–3.27, p = 0.0011), with the recessive allele T being significantly associated with DCM (OR 1.64, 95% CI 1.18 - 2.30, p = 0.003). The haplotype carrying the recessive alleles of G894T and T-786C, C4bT was found to exhibit 7 folds increased risk for DCM compared to the controls. Hence C4bT haplotype could be the risk haplotype for DCM. Our findings suggest the possible implication of NOS3 gene in the disease phenotype, wherein NOS3 may be synergistically functioning in DCM associated heart failure via the excessive production of NO in cardiomyocytes resulting in decreased myocardial contractility and systolic dysfunction, a common feature of DCM phenotype.
doi:10.1371/journal.pone.0070523
PMCID: PMC3726655  PMID: 23923002
9.  A novel chromosomal translocation and heteromorphism in a female with recurrent pregnancy loss—a case study 
Purpose
To evaluate the clinical, biochemical and cytogenetic analyses of a couple with reproductive failure.
Methods
A couple with a history of recurrent pregnancy loss was referred to the Institute of Genetics for cytogenetic evaluation. Chromosomal analysis of the phenotypically normal parents was done to ascertain the role of chromosomal abnormalities and offer appropriate genetic counseling. Further, advanced karyotype analysis by spectral karyotyping was also carried out in the couple and parents of the female partner.
Results
Clinical and hormonal profile of the couple revealed normal phenotypes. The ultrasound scan of the female showed normal uterus and ovaries. Chromosomal analysis of the couple revealed a normal 46, XY karyotype in the male spouse, and a unique balanced reciprocal translocation 46, XX, t(12;13) (q13;q33) + 15pstk+ chromosomal constitution in the female partner. Cytogenetic analysis of her parents revealed a similar translocation between chromosomes 12 and 13 in the father and 15pstk+ in the mother. Further, corroboration of the chromosome abnormalities was carried out by spectral karyotyping.
Conclusion
A unique and novel familial transmission of paternally derived balanced reciprocal translocation and maternally derived heteromorphism in a female with the history of recurrent pregnancy loss was reported as an original investigation.
doi:10.1007/s10815-012-9756-4
PMCID: PMC3401254  PMID: 22476504
Recurrent pregnancy loss; Balanced translocation; Heteromorphism; Spectral karyotype; Familial transmission; Hormonal profile; Chromosomal defect; Miscarriage
10.  Role of Tumor Necrosis Factor-α -308 G/A Promoter Polymorphism in Gastric Cancer 
Background/Aim:
Gastric cancer (GC) is the fourth most common cancer and the second most common cause of cancer death world-wide after lung cancer. It is a multifactorial disease with the involvement of both genetic and environmental risk factors. Genetic variation in genes encoding cytokines and their receptors, determine the intensity of the inflammatory response, which may contribute to individual differences in severity of outcome of the disease. Tumor necrosis factor alpha (TNF-α) is a potent pro-inflammatory cytokine and acid inhibitor. A bi allelic G to A polymorphism at -308 upstream from the transcription initiation site of the promoter is associated with elevated TNF levels. The present study is aimed at evaluating the role of TNF-α-308 (G → A) gene polymorphism and susceptibility to GC.
Subjects and Methods:
A case-control study was carried out in 114 GC patients and 229 healthy control subjects. TNF-α genotyping at position-308 (G → A) was carried out by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method followed by agarose gel electrophoresis.
Results:
The distribution of TNF-α genotypes at -308 (G → A) were GG 28.07%, GA 66.67% and AA 5.26% in GC patients and GG 33.19%, GA 55.89% and AA 10.92% in control subjects. The frequencies of alleles G and A were 0.614 and 0.386 in GC patients and 0.611 and 0.389 in control subjects respectively.
Conclusion:
The study showed no significant difference in the distribution of genotype and allelic frequencies between GC patients and control subject.
doi:10.4103/1319-3767.114513
PMCID: PMC3745661  PMID: 23828749
Gastric cancer; Helicobacter pylori; promoter polymorphism; tumor necrosis factor alpha
11.  Hidden magicians of genome evolution 
The Indian Journal of Medical Research  2013;137(6):1052-1060.
Transposable elements (TEs) represent genome's dynamic component, causing mutations and genetic variations. Transposable elements can invade eukaryotic genomes in a short span; these are silenced by homology-dependent gene silencing and some functional parts of silenced elements are utilized to perform novel cellular functions. However, during the past two decades, major interest has been focused on the positive contribution of these elements in the evolution of genomes. The interaction between mobile DNAs and their host genomes are quite diverse, ranging from modifications of gene structure to alterations in general genome architecture and can be regarded as hidden magicians in shaping evolution of genomes. Some of the prominent examples that impressively demonstrate the beneficial impact of TEs on host biology over evolutionary time include their role in structure and functions of eukaryotic genomes.
PMCID: PMC3734710  PMID: 23852286
Dynamic component; evolution; homology-dependent gene silencing; horizontal transfer; structural & functional roles; transposable elements
12.  Plasma TGF-β1, MMP-1 and MMP-3 Levels in Chronic Pancreatitis 
Chronic pancreatitis (CP) presenting clinically with upper abdominal pain, as well as exocrine and endocrine insufficiencies, is characterized by irreversible morphological and functional alterations in the pancreas. The objective of the present study is to investigate the plasma levels of transforming growth factor-β 1 (TGF-β1), matrix metalloproteinases MMP-1 (collagenase) and MMP-3 (stromelysin) in CP. A total of 71 CP patients and 100 control subjects were considered for the study. Plasma levels of TGF-β1, MMP-1 and MMP-3 were determined by enzyme-linked immunosorbent assay in patients and control subjects. The plasma levels of TGF-β1 and MMP-1 were significantly elevated in patients compared to control group (*P = 0.0301, **P < 0.0001). However, there was no significant difference in the plasma levels of MMP-3 between patients and controls (P = 0.3756). The elevated levels of TGF-β1 and MMP-1 may influence the inflammatory reactions by enhancing the pancreatic stellate cell activation and deposition of extracellular matrix resulting in pancreatic fibrosis. Thus, the present study highlights the role of fibrogenic cytokine marker TGF-β1 and matrix metalloproteinases in the pathogenesis of CP.
doi:10.1007/s12291-011-0167-6
PMCID: PMC3358373  PMID: 23542130
Transforming growth factor-β1; Matrix metalloproteinases; Chronic pancreatitis; Fibrosis; Pancreatic stellate cells
13.  Evaluation of Interleukin-10 (G-1082A) Promoter Polymorphism in Preeclampsia 
Background
Preeclampsia is a pregnancy-specific syndrome that may be life-threatening, especially to the fetus. Several causes have been reported that may have a possible role in the development of the disorder. Interleukin-10 affect maternal intravascular inflammation, as well as endothelial dysfunction. The aim of this study was to investigate the association between IL-10 G-1082A polymorphism and preeclampsia.
Methods
A total of eighty−eight pregnant women with preeclampsia and 100 women with normal pregnancy attending the Gynecological unit of Government Maternity Hospital, Petlaburz, Hyderabad, India, were considered for the study. A standard amplification refractory mutation system (ARMS) PCR was carried out for genotyping IL-10 G-1082A promoter polymorphism in all the participants. Genotypic distribution of the control and patient groups were compared with values predicted by Hardy-Weinberg equilibrium using χ2 test. Odd ratios (OR) and their respective 95% confidence intervals were used to measure the strength of association between IL-10 gene polymorphism and preeclampsia.
Results
The frequencies of IL-10 G-1082A genotypes, GG, GA and AA, were 17.8%, 41.09% and 41.09% in women with preeclampsia and 25%, 28% and 47% in the controls respectively. There was no significant difference in the distribution of genotypes and alleles of IL-10 G-1082A between the two groups (Test power=0.66).
Conclusion
The present study suggests that the IL-10 G-1082A gene promoter polymorphism is not a major genetic regulator in the etiology of preeclampsia.
PMCID: PMC3719316  PMID: 23926566
ARMS PCR; Cytokines; Interleukin-10; Polymorphism; Preeclampsia
14.  Role of Proteases and Antiprotease in the Etiology of Chronic Pancreatitis 
Background/Aim:
Chronic pancreatitis (CP) is the progressive and irreversible destruction of the pancreas characterized by the permanent loss of endocrine and exocrine function. Trypsin, the most important digestive enzyme plays a central role in the regulation of all other digestive enzymes. Chymotrypsin, an endopeptidase hydrolyzes peptides at amino acids with aromatic side chains. Alpha-1-antitrypsin is a principal antiprotease which protects the mucosal tissue from the proteolytic effects of trypsin and chymotrypsin by the formation of molar complexes. The present study is aimed at examining the role of proteases (trypsin and chymotrypsin) and anti-protease (α1-anti-trypsin) in the etiopathogenesis of chronic pancreatitis.
Patients and Methods:
A total of 90 CP patients and 110 age and sex matched controls were considered for the study. Serum trypsin, chymotrypsin and α1-anti-trypsin levels were determined prospectively in CP patients and compared to healthy controls as described previously.
Results:
The mean activity of trypsin were found to be increased in CP patients (X ± SD = 0.82 ± 0.838) in comparison to normal control group (X ± SD = 0.55 ± 0.328), (P = 0.001). Chymotrypsin activity were also found to be elevated in CP patients (X ± SD = 0.63 ± 0.278) in comparison to control group (X ± SD = 0.39 ± 0.295), (P = 0.0001). The mean α-1-anti-trypsin activity were found to be lowered in CP patients (X ± SD = 0.42 ± 0.494) in comparison to control group (X ± SD = 0.67 ± 0.465), with the variation being significant (P = 0.0003).
Conclusion:
The findings suggest an imbalance in the synthesis and degradation of proteolytic enzymes and antiprotease indicating an altered aggressive and defensive role in the pathogenesis of chronic pancreatitis.
doi:10.4103/1319-3767.103427
PMCID: PMC3530990  PMID: 23150021
Alpha 1 anti-trypsin; chronic pancreatitis; chymotrypsin; trypsin
15.  High prevalence of Arginine to Glutamine Substitution at 98, 141 and 162 positions in Troponin I (TNNI3) associated with hypertrophic cardiomyopathy among Indians 
BMC Medical Genetics  2012;13:69.
Background
Troponin I (TNNI3) is the inhibitory subunit of the thin filament regulatory complex Troponin, which confers calcium-sensitivity to striated muscle actomyosin ATPase activity. Mutations (2-7%) in this gene had been reported in hypertrophic cardiomyopathy patients (HCM). However, the frequencies of mutations and associated clinical presentation have not been established in cardiomyopathy patients of Indian origin, hence we have undertaken this study.
Methods
We have sequenced all the exons, including the exon-intron boundaries of TNNI3 gene in 101 hypertrophic cardiomyopathy patients (HCM), along with 160 healthy controls, inhabited in the same geographical region of southern India.
Results
Our study revealed a total of 16 mutations. Interestingly, we have observed Arginine to Glutamine (R to Q) mutation at 3 positions 98, 141 and 162, exclusively in HCM patients with family history of sudden cardiac death. The novel R98Q was observed in a severe hypertrophic obstructive cardiomyopathy patient (HOCM). The R141Q mutation was observed in two familial cases of severe asymmetric septal hypertrophy (ASH++). The R162Q mutation was observed in a ASH++ patient with mean septal thickness of 29 mm, and have also consists of allelic heterogeneity by means of having one more synonymous (E179E) mutation at g.4797: G → A: in the same exon 7, which replaces a very frequent codon (GAG: 85%) with a rare codon (GAA: 14%). Screening for R162Q mutation in all the available family members revealed its presence in 9 individuals, including 7 with allelic heterogeneity (R162Q and E179E) of which 4 were severely affected. We also found 2 novel SNPs, (g.2653; G → A and g.4003 C → T) exclusively in HCM, and in silico analysis of these SNPs have predicted to cause defect in recognition/binding sites for proteins responsible for proper splicing.
Conclusion
Our study has provided valuable information regarding the prevalence of TNNI3 mutations in Indian HCM patients and its risk assessment, these will help in genetic counseling and to adopt appropriate treatment strategies.
doi:10.1186/1471-2350-13-69
PMCID: PMC3495047  PMID: 22876777
TNNI3-Troponin I; Cardiomyopathy; SNPs; HCM; Indians; Mutations
16.  Association of Interleukin-10 Promoter Polymorphism (-1082 G/A) and Gastric Cancer in Andhra Pradesh Population of South India 
Background
Gastric Cancer (GC) is one of the most commonly diagnosed malignancies. Genetic variation in genes encoding cytokines and their receptors, determine the intensity of the inflammatory response, which may contribute to individual differences in the outcome and severity of the disease. Interleukin-10 (IL-10) is a multifunctional cytokine with both immunosuppressive and antiangiogenic functions. Polymorphisms in the IL-10 gene promoter genetically determine inter-individual differences in IL-10 production. In the present study, we investigated the association between the IL-10 -1082 G/A polymorphism and the susceptibility to gastric cancer in a South Indian population from Andhra Pradesh.
Methods
We genotyped 100 patients diagnosed with gastric cancer and 132 healthy control subjects for -1082G/A single nucleotide polymorphism by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR) method followed by agarose gel electrophoresis.
Results
The distribution of IL-10 genotypes at -1082 G/A were GG 18 %, GA 35% and AA 47 % in gastric cancer patients and GG 31.82 %, GA 37.88 % and AA 30.3% in control subjects. The allelic frequencies of G and A were 0.355 and 0.645 in GC patients and 0.508 and 0.492 in control subjects respectively. The IL-10 -1082 A allele was associated with risk of gastric cancer (OR=1.873, 95%CI-1.285-2.73and P= 0.001048**).
Conclusion
Our study indicates that allele A of IL-10-1082 G/A polymorphism may be considered as one of the important risk factor in the etiology of gastric cancer.
PMCID: PMC4294533  PMID: 25628830
Cytokines; Interleukin-10; Gastric cancer; Polymorphism
17.  Mosaic triple X syndrome in a female with primary amenorrhea 
Indian Journal of Human Genetics  2012;18(2):246-249.
BACKGROUND:
Turner's syndrome is the most common chromosomal abnormality in females, affecting 1 in 2,500 live female births. It is a result of absence of an X chromosome or the presence of a structurally abnormal X chromosome. Its most consistent clinical features are short stature and ovarian failure.
AIM:
The aim of the study was to report a rare case of mosaic triple X syndrome in a female with primary amenorrhea.
MATERIALS AND METHODS:
The chromosomal analysis using GTG banding was carried out, which revealed a mosaicism with 45,XO/47,XXX chromosomal constitution. Fluorescent in situ hybridization was also carried out to further confirm the observation made in the study.
CONCLUSION:
The physical features presented by the female could be due to the 45,XO/47,XXX mosaicism and the karyotype analysis was consistent with the diagnosis and clinical symptoms. Triple X mosaicism was confirmed with conventional and molecular cytogenetic analysis.
doi:10.4103/0971-6866.100790
PMCID: PMC3491304  PMID: 23162306
Fluorescent in situ hybridization; karyotype; primary amenorrhea; Turner's syndrome
18.  Unique Case Reports Associated with Ovarian Failure: Necessity of Two Intact X Chromosomes 
Case Reports in Genetics  2012;2012:640563.
Premature ovarian failure is defined as the loss of functional follicles below the age of 40 years and the incidence of this abnormality is 0.1% among the 30–40 years age group. Unexplained POF is clinically recognized as amenorrhoea (>6 months) with low level of oestrogen and raised level of Luteinizing Hormone (LH) and Follicle Stimulating Hormone (FSH > 20 IU/l) occurring before the age of 40. It has been studied earlier that chromosomal defects can impair ovarian development and its function. Since there is paucity of data on chromosomal defects in Indian women, an attempt is made to carry out cytogenetic evaluation in patients with ovarian failure. Cytogenetic analysis of women with ovarian defects revealed the chromosome abnormalities to be associated with 14% of the cases analyzed. Interestingly, majority of the abnormalities involved the X-chromosome and we report two unique abnormalities, (46,XXdel(Xq21-22) and q28) and (mos,45XO/46,X+ringX) involving X chromosome in association with ovarian failure. This study revealed novel X chromosome abnormalities associated with ovarian defects and these observations would be helpful in genetic counseling and apart from, infertility clinics using the information to decide suitable strategies to help such patients.
doi:10.1155/2012/640563
PMCID: PMC3447217  PMID: 23074690
19.  Role of Plasma MMP 9 levels in the Pathogenesis of Chronic Pancreatitis 
Pancreatic fibrosis is a key pathological feature in the etiology of chronic pancreatitis that leads to obliteration of exocrine and endocrine pancreatic tissues and its replacement by fibrous tissue resulting in clinical manifestations. Matrix metalloproteinase 9 is a member of the MMP family that is also known as gelatinase B, degrades type IV collagen of extracellular matrix and basal membrane. The present study is aimed at evaluating the clinical significance of plasma concentration of MMP-9 in chronic pancreatitis. The samples were obtained from 112 chronic pancreatitis patients and an equal number of age and sex matched healthy controls. MMP-9 levels were quantitatively measured by ELISA assay. Statistical analysis was applied to test the significance of results. The present study revealed a significant increase of plasma MMP 9 levels in chronic pancreatitis patients compared to control subjects. Elevated levels were also observed in all the patient groups compared to control subjects with regard to sex, age, addictions etc. MMP-9 degrades the type IV collagens in normal basement membrane, which in turn activates the pancreatic stellate cells which promote the development of pancreatitic fibrosis. Thus, elevated plasma levels of MMP-9 may act as a susceptibility factor for the development of chronic pancreatitis.
doi:10.1007/s12291-010-0103-1
PMCID: PMC3107412  PMID: 22468039
Chronic pancreatitis; Pancreatic stellate cells; Extracellular matrix
20.  Genetic variations of α-cardiac actin and cardiac muscle LIM protein in hypertrophic cardiomyopathy in South India 
BACKGROUND:
Hypertrophic cardiomyopathy (HCM) is a disease of the heart muscle, with an autosomal dominant mode of inheritance. It is also known as the ‘disease of the sarcomere’, and is a major cause of morbidity and mortality worldwide. Mutations in the sarcomeric genes have been largely implicated in the manifestation of HCM. Modifier genes and environmental factors, along with causative mutation, add to the cumulative effect of the disease.
METHODS:
In the present study, the role of the cardiac actin gene and the cardiac muscle LIM protein as contributors to HCM – through genetic variation – has been elucidated by screening the entire coding region in 100 control and 100 HCM subjects through polymerase chain reaction-based single-strand conformation polymorphism analysis and direct sequencing.
RESULTS:
The authors could not find any novel or reported exonic variations in any of the genes in the studied population; however, intronic variations were revealed in the cardiac actin gene through direct sequencing. A case of compound heterozygosity was observed in a patient with a variation in intron 1, along with a novel heterozygous mutation in exon 7 (S215L) of α-tropomyosin.
CONCLUSIONS:
The particular genes are highly conserved, and account for only 1.5% of HCM cases. They do not seem to play a major role in the genesis of HCM in the present population, thus confirming earlier reports of conserved sequences and ethnicity.
PMCID: PMC3383364  PMID: 23204897
Alpha-tropomyosin; Cardiac actin; Cardiac muscle LIM protein; Hypertrophic cardiomyopathy
21.  A Dysmorphic Child with a Pericentric Inversion of Chromosome 8 
Case Reports in Pediatrics  2012;2012:813963.
An 8-year-old boy was referred to our institute with dysmorphic features such as mild lupus, micrognathia, low hair line, hypoplasia, hemi atrophy of left side of the face, abnormal size of ears, hypothenar, hypoplasia of chin, and tongue tie. MRI scan was found to be normal and EEG suggestive of generalized seizure disorder. Cytogenetic evaluation of the proband revealed a pericentric inversion of chromosome 8 with 46, XY, and inv 8 (p11.2; q21.2) karyotype.
doi:10.1155/2012/813963
PMCID: PMC3350233  PMID: 22606536
22.  Epistatic interactions in idiopathic pulmonary arterial hypertension 
BACKGROUND:
Idiopathic pulmonary arterial hypertension (IPAH) is a poorly understood complex disorder, which results in progressive remodeling of the pulmonary artery that ultimately leads to right ventricular failure. A two-hit hypothesis has been implicated in pathogenesis of IPAH, according to which the vascular abnormalities characteristic of PAH are triggered by the accumulation of genetic and/or environmental insults in an already existing genetic background. The multifactor dimensionality reduction (MDR) analysis is a statistical method used to identify gene–gene interaction or epistasis and gene–environment interactions that are associated with a particular disease. The MDR method collapses high-dimensional genetic data into a single dimension, thus permitting interactions to be detected in relatively small sample sizes.
AIM:
To identify and characterize polymorphisms/genes that increases the susceptibility to IPAH using MDR analysis.
MATERIALS AND METHODS:
A total of 77 IPAH patients and 100 controls were genotyped for eight polymorphisms of five genes (5HTT, EDN1, NOS3, ALK-1, and PPAR-γ2). MDR method was adopted to determine gene–gene interactions that increase the risk of IPAH.
RESULTS:
With MDR method, the single-locus model of 5HTT (L/S) polymorphism and the combination of 5HTT(L/S), EDN1(K198N), and NOS3(G894T) polymorphisms in the three-locus model were attributed to be the best models for predicting susceptibility to IPAH, with a P value of 0.05.
CONCLUSION:
MDR method can be useful in understanding the role of epistatic and gene–environmental interactions in pathogenesis of IPAH.
doi:10.4103/0971-6866.96652
PMCID: PMC3385180  PMID: 22754222
Gene–gene interactions; Idiopathic pulmonary arterial hypertension; multifactor dimensionality reduction; multilocus genotypes; polymorphisms
23.  The Genetic Bases of Uterine Fibroids; A Review 
Uterine leiomyomas/fibroids are the most common pelvic tumors of the female genital tract. The initiators remaining unknown, estrogens and progesterone are considered as promoters of fibroid growth. Fibroids are monoclonal tumors showing 40-50% karyo-typically detectable chromosomal abnormalities. Cytogenetic aberrations involving chromosomes 6, 7, 12 and 14 constitute the major chromosome abnormalities seen in leiomyomata. This has led to the discovery that disruptions or dysregulations of HMGIC and HMGIY genes contribute to the development of these tumors. Genes such as RAD51L1 act as translocation partners to HMGIC and lead to disruption of gene structure leading to the pathogenesis of uterine fibroids. The mechanism underlying this disease is yet to be identified. The occurrence of PCOLCE amid a cluster of at least eight Alu sequences is potentially relevant to the possible involvement of PCOLCE in the 7q22 rearrangements that occur in many leiomyomata. PCOLCE is implicated in cell growth processes. Involvement of Alu sequences in rearrangements can lead to the disruption of this gene and, hence, loss of control for gene expression leading to uncontrolled cell growth. This can also lead to the formation of fibroids. Though, cytogenetics provides a broad perspective on uterine fibroid formation, further molecular analysis is required to understand the etiopathogenesis of uterine fibroids.
PMCID: PMC3719293  PMID: 23926501
Chromosomal translocation; Chromosomal; Estrogen; Gene rearrangement; Progesterone; Uterine fibroids; Uterine Leiomyomas (UL)
24.  Novel mutations in arrhythmogenic right ventricular cardiomyopathy from Indian population 
BACKGROUND:
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a progressive condition with right ventricular myocardium being replaced by fibro-fatty tissue. The spectrum of the expression may range from benign palpitations to the most malignant sudden death. Most of the mutations identified for the condition are localized in desmosomal proteins although three other nondesmosomal genes (cardiac ryanodine receptor-2, TGF-β3, and TMEM43) have also been implicated in ARVC. Both desmosomal and nondesmosomal genes were screened in a set of patients from local population.
MATERIALS AND METHODS:
A set of 34 patients from local population were included in this study. Diagnosis was based on the criteria proposed by task force of European Society of Cardiology/International Society and Federation of Cardiology. Polymerase chain reaction-based single-strand conformation polymorphism analysis was carried out, and samples with abnormal band pattern were commercially sequenced.
RESULTS:
Screening of cardiac ryanodine receptor revealed an insertion of a base in the intronic region of exon-28 in a patient, leading to a creation of a cryptic splice site. Screening of plakohilin-2 for mutations revealed an abnormal band pattern in three patients. Two of them had similar abnormal band pattern for exon-3.1. Sequencing revealed a novel 2 base pair deletion (433_434 delCT), which would lead to premature truncation of the protein (L145EfsX8). Another patient showed abnormal band pattern for exon-3.2 and sequencing revealed a missense mutation C792T leading to amino acid change P244L, in N-terminal, and this substitution may cause disturbances in the various protein–protein interactions.
CONCLUSION:
This study reports novel cardiac ryanodine receptor (RyR-2) mutations and Pkp-2 for the first time from Indian population.
doi:10.4103/0971-6866.86182
PMCID: PMC3214321  PMID: 22090716
Arrhythmogenic right ventricular cardiomyopathy; fibro-fatty tissue; palpitations; sudden death
25.  Endothelin-1 and endothelial nitric oxide polymorphisms in idiopathic pulmonary arterial hypertension 
Idiopathic Pulmonary arterial hypertension (IPAH) is a debilitating disease associated with very poor prognosis. The disease is characterised by endothelial dysfunction, smooth muscle proliferation and insitu thrombosis in the pulmonary artery, eventually leading to right ventricular failure. Two of the key endothelial mediators implicated in the pathogenesis of IPAH are endothelin-1 (EDN1) and nitric oxide (NO). EDN1 is a potent endogenous vasoconstrictor whereas NO is a vasodilator. In the present study screening of the EDN1 gene (EDN1) and NOS3 polymorphisms was taken up, to evaluate their association with IPAH. A significant association of EDN1 3A/4A polymorphism (+138 A; rs10478694) (OR-3.485; CI-1.254, 9.999; p=0.013) and EDN1 Lys198Asn polymorphism (G/T, rs5370) (OR-3.378, CI-1.104, 10.582; p=0.03) with IPAH was observed. Our results indicate that EDN1 polymorphisms in interaction with other genetic markers may play a significant role in individual's susceptibility to the disease and its clinical progression.
PMCID: PMC3076769  PMID: 21537392
IPAH; endothelial dysfunction; EDN1; NOS3; polymorphism; Linkage Disequilibrium

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