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1.  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
2.  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
3.  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
4.  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
5.  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
6.  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
7.  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
8.  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
9.  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
10.  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
11.  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
12.  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
13.  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
14.  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
15.  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
16.  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
17.  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)
18.  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
19.  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
20.  Genetic variations of β-MYH7 in hypertrophic cardiomyopathy and dilated cardiomyopathy 
CONTEXT:
Hypertrophic cardiomyopathy (HCM) is known to be manifested by mutations in 12 sarcomeric genes and dilated cardiomyopathy (DCM) is known to manifest due to cytoskeletal mutations. Studies have revealed that sarcomeric mutations can also lead to DCM. Therefore, in the present study, we have made an attempt to compare and analyze the genetic variations of beta-myosin heavy chain gene (β-MYH7), which are interestingly found to be common in both HCM and DCM. The underlying pathophysiological mechanism leading to two different phenotypes has been discussed in this study. Till date, about 186 and 73 different mutations have been reported in HCM and DCM, respectively, with respect to this gene.
AIM:
The screening of β-MYH7 gene in both HCM and DCM has revealed some common genetic variations. The aim of the present study is to understand the pathophysiological mechanism underlying the manifestation of two different phenotypes.
MATERIALS AND METHODS:
100 controls, 95 HCM and 97 DCM samples were collected. Genomic DNA was extracted following rapid nonenzymatic method as described by Lahiri and Nurnberger (1991), and the extracted DNA was later subjected to polymerase chain reaction (PCR) based single stranded conformation polymorphism (SSCP) analysis to identify single nucleotide polymorphism (SNP)s/mutations associated with the diseased phenotypes.
RESULTS AND CONCLUSION:
Similar variations were observed in β-MYH7 exons 7, 12, 19 and 20 in both HCM and DCM. This could be attributed to impaired energy compromise, or to dose effect of the mutant protein, or to even environmental factors/modifier gene effects wherein an HCM could progress to a DCM phenotype affecting both right and left ventricles, leading to heart failure.
doi:10.4103/0971-6866.69348
PMCID: PMC2955954  PMID: 21031054
Diastolic dysfunction; dose effect; dilated cardiomyopathy; hypertrophic cardiomyopathy; single nucleotide polymorphism; systolic dysfunction
21.  Paternally derived translocation t(8;18)(q22.1;q22)pat associated in a patient with developmental delay: Case report and review 
The common cause of mental impairment and the wide range of physical abnormalities is balanced chromosome rearrangement. As such, it is difficult to interpret, posing as a diagnostic challenge in human development. We present a unique familial case report with the paternally inherited autosomal-balanced reciprocal translocation involving chromosomal regions 8q and 18q. The etiology of the translocation, i.e. 46,XX,t(8;18)(q22.1;q22) was detected by conventional high-resolution Giemsa–Trypsin–Giemsa-banding and fluorescence in situ hybridization techniques. The father was found to be the carrier of the chromosome defect and also the same was observed in the first female child referred with a history of delayed milestone development. However, the second female child showed normal 46, XX karyotype. This is the first report of reciprocal translocation involving 8q and 18q associated with the delayed milestone development. The reason likely may be due to the rearrangement of genetic material at these breakpoints having a crucial relationship and thus manifesting developmental delay in the progeny. Accordingly, this paper also shows genetic counseling discussion for the cause.
doi:10.4103/1817-1745.66686
PMCID: PMC2964802  PMID: 21042514
Balanced reciprocal translocation; chromosomes 8 and 18; delayed milestones; Giemsa–Trypsin–Giemsa banding and FISH; translocation carrier
22.  Linkage analysis of three families with arrythmogenic right ventricular cardiomyopathy in India 
BACKGROUND:
Arrythmogenic Right Ventricular Cardiomyopathy (ARVC) is a primary myocardial disorder morphologically characterized by subtle to severe replacement of the right ventricular myocardium by fatty and fibrous tissue. ARVC is known to be highly prevalent in European population with recent reports implicating it to be a major cause of sudden death in young individuals even from American and Asian population.
AIM:
To implicate or exclude TMEM43 (ARVC-5), DSP(ARVC-8) genes and the yet to be identified gene at ARVC-6 locus in the pathogenesis in three families affected with ARVC from India.
MATERIALS AND METHODS:
Three families comprising of 42 affected/unaffected members were included in the study. Three microsatellite markers, D3S3613 (ARVC5) D10S1664 (ARVC6), D6S309 (ARVC8) were genotyped by PCR-based native PAGE. Two-point Linkage analysis was performed using LINKAGE program version 5.2
RESULTS AND DISCUSSION:
LOD scores from linkage analysis for the microsatellite marker D10S1664 (ARVC-6) in families KS and REV have shown positive value hinting the involvement of this locus in the etiology of ARVC, while linkage analysis in the SB family ruled out involvement of DSP, TMEM43 and ARVC-6, as negative LOD scores were obtained with all three loci. Therefore, linkage analysis carried out in the present study indicates that ARVC-6 (cumulative LOD score is equal to plus 1.203376 at θ is equal to 0.05) could be the locus harboring the mutated gene in two out of three families.
doi:10.4103/0971-6866.55216
PMCID: PMC2910949  PMID: 20680152
Arrythmogenic right ventricular cardiomyopathy; linkage analysis; LOD; sudden death
23.  MYBPC3 gene variations in hypertrophic cardiomyopathy patients in India 
BACKGROUND
Hypertrophic cardiomyopathy (HCM) is a complex cardiac muscular disorder, inherited as an autosomal dominant disease with variable penetrance. Cardiac myosin-binding protein C (MyBPC) is the predominant myosin-binding protein isoform in the heart muscle. One hundred forty-seven mutations have been detected in MYBPC3, accounting for 15% of all HCM cases.
OBJECTIVE
To screen exons 16, 18, 19, 22, 24, 28, 30, 31 and 34 in the MYBPC3 gene in Indian HCM patients.
METHODS
Sixty control and 95 HCM samples were collected from cardiology units of the CARE Hospital (Nampally, Banjara Hills, Secunderabad, India) for genomic DNA isolation followed by polymerase chain reaction and single-stranded conformational polymorphism analysis.
RESULTS
Screening of the exons revealed two variations – one novel frame shift mutation in exon 19 at the nucleotide position 11577^11578 and one novel single nucleotide polymorphism (SNP) in codon 1093 of exon 31, coding for glycine with a C>T transition (GGC/GGT), in addition to the seven known SNPs mainly in the intronic region and one known missense mutation D770N in this population.
CONCLUSION
The novel frame shift mutation identified in exon 19, D570fs, with the insertion of an adenine residue in codon 570 coding for aspartate, results in a premature termination codon that produces a truncated protein lacking myosin- and titin-binding sites, explaining the role of the nonsense-mediated decay pathway. A novel SNP identified in codon 1093 of exon 31 was found to be a synonymous codon, which may have a regulatory effect at the translational level, attributing to affinity differences between codon-anticodon interactions. The screening of this gene may be relevant in the Indian context.
PMCID: PMC2644567  PMID: 18273486
Hypertrophic cardiomyopathy; MYBPC3; Nonsense-mediated decay pathway; Novel mutation
24.  Clinical Picture Of Arrhythmogenic Right Ventricular Dysplasia / Cardiomyopathy Patients From Indian Origin 
Objective
Among the inherited cardiomyopathies, Arrhythmogenic right ventricular dysplasia/cardiomyopathy is unique with a peculiar pathology of fibro-fatty replacement. Studies have been carried out all over the world and several groups have reported clinical heterogeneity in manifestation of ARVD/C related symptoms. Present study is an attempt to identify the clinical profile of ARVD/C patients from Asian Indian origin.
Methods
31 patients in the span of three years were diagnosed with ARVD/C. Diagnosis was based on proposed task force criteria.
Results
The mean age at diagnosis was 32.9 ± 16.4 years with slight tilt in male to female ratio (1.46). About 80% cases had palpitations, syncope in 45.16% and dyspnea in 22.5%, whereas 16% of patients were asymptomatic. About 50% of patients revealed a family history of confirmed ARVD/C or sudden death of a family member without any known cause. ECG showed T-wave inversion in about 60% cases, prolongation of QRS was observed in 20% cases. RV dilatation was observed in 80% of patients and 66.7% showed systolic dysfunction. RV free wall motion abnormalities were found in 33% patients. Most of the early onset cases with less than 30 years of age showed family history indicative of ARVD/C. Familial study in three patients indicated early onset of condition in younger generations in two families.
Conclusions
ARVD/C in India shows relatively early age at onset when compared with other Asian populations with more than half of patients showing the disease below the age of 30 years. History in most of the early onset cases revealed family history indicating strong genetic influence.
PMCID: PMC2615057  PMID: 19165354
Cardiomyopathies; ARVD/C; Clinical heterogeneity
25.  t-plasminogen activator inhibitor-1 polymorphism in idiopathic pulmonary arterial hypertension 
AIM:
The aim of the present study was to identify the possible genotypic association of 3’UTR Hind III polymorphism of Plasminogen activator Inhibitor-1 (PAI-1) gene with idiopathic pulmonary arterial hypertension (IPAH).
BACKGROUND:
IPAH is a disorder with abnormally raised mean pulmonary arterial pressure and increase in the resistance to blood flow in pulmonary artery. One of the pathological features seen is development of intraluminal thrombin deposition leading to thrombosis. Plasminogen activator inhibitor-1 is an important inhibitor of the fibrinolytic system; its up-regulation may suppress fibrinolysis and result in an increased risk of thrombosis.
METHOD:
Blood samples from 54 IPAH patients and 100 healthy voluntary donors were analyzed by PCR-RFLP method for 3’UTR Hind III polymorphism.
RESULTS AND DISSCUSSION:
A significant association of Hd2 allele with the disease was observed. Raised mean level of right ventricular systolic pressure was observed in the Hd2/Hd2 genotypic patients, strengthening the role of Hd2 allele in the disease progression. Our data suggests an association of Hd2/Hd2 genotype, which may lead to the up-regulation of PAI-1 gene leading to increased levels of PAI-1, which is seen in IPAH. PAI-1 competes with plasminogen activators and hinders the normal mechanism of plasminogen activation system and leads to thrombosis and formation of plexiform lesions in the lung tissue, further strengthening its role in tissue remodeling and disease progression.
doi:10.4103/0971-6866.44103
PMCID: PMC2840792  PMID: 20300292
Fibrinolytic pathway; idiopathic pulmonary arterial hypertension; plasminogen activator inhibitor-1; thrombosis; tissue remodelingIntroduction

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