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Kunal Ray

Publications and source records attributed to Kunal Ray.

24 records · Page 2Linked to original sources
PubMed2003

DNA linkage based diagnosis of Wilson disease in asymptomatic siblings.

BACKGROUND & OBJECTIVES: Wilson disease (WD) is an autosomal recessive disorder caused by defects in ATP7B gene located in chromosome 13q14, and manifested as hepatolenticular degeneration as a result of accumulation of copper. No information on the mutation in the ATP7B gene and haplotypes using linked markers is available for WD patients in India. Hence, the present study was undertaken to identify, by a PCR-based molecular diagnostic test, presymptomatic siblings of WD affected individuals in families with multiple offspring. METHODS: Genomic DNA was prepared from the peripheral blood of the patients, siblings and his/her first degree relatives. The repeat-markers flanking WD locus were amplified by PCR using fluorescent labeled primers. Amplified DNA fragments were analyzed by polyacrylamide gel electrophoresis in ABI 377 DNA sequencing system. Genotypes of the samples were determined using Genescan software. Haplotypes were determined based on segregation of the alleles in the families under study. RESULTS: Among 15 WD affected families with multiple children, 4 cases were identified where younger siblings shared same genotype as the patient at all three markers analyzed. Further, eight different haplotypes were detected in the four patients. INTERPRETATION & CONCLUSION: The siblings of the WD patients carrying the same genotype at the markers linked to WD locus were presymptomatically diagnosed individuals. Presence of eight different haplotypes in the four patients suggested mutational heterogeneity at the WD locus. The test helps clinicians for therapeutic intervention in suspect WD cases by copper chelating agents prior to manifestation of overt clinical symptoms.

Adolescent↗
PubMed2002

Mutations in MYOC gene of Indian primary open angle glaucoma patients.

PURPOSE: Glaucoma is the second leading cause of blindness worldwide after cataract. Defects in the myocilin gene (MYOC) have been shown to be associated with Primary Open Angle Glaucoma (POAG), the most common form of the disease, especially in its juvenile form. Most of the reported mutations in MYOC are in POAG patients of Caucasian origin. A few studies have been reported on Asian patients (such as Chinese, Japanese, and Koreans) but none from the Indian subcontinent. The purpose of this study was to investigate the molecular basis of POAG among Indians, using MYOC as the candidate gene, and broaden our understanding on the pathogenesis caused by MYOC. METHODS: Fifty-six unrelated POAG patients, comprising 39 sporadic cases and 17 patients having familial history for POAG were enrolled in this study. The coding sequence of the gene was amplified by polymerase chain reaction (PCR) using genomic DNA from 30 POAG patients, followed by sequencing of the PCR products. Nucleotide changes were detected by identifying double peaks in the chromatogram due to heterozygosity and pairwise BLAST analysis of the sequence output data against the normal copy of the MYOC cDNA. Alteration of restriction sites due to nucleotide changes was identified. Twenty-six patients (not sequenced) and controls were screened for nucleotide changes by allele specific restriction digestion of the PCR products followed by separation of the digested DNA fragments by polyacrylamide gel electrophoresis. RESULTS: From a pool of 56 unrelated POAG patients two mutations were identified. A putative novel mutation (144 G->T; Gln48His) of a conserved amino acid was detected in the exon 1 of MYOC from three unrelated patients but none in the 51 control samples examined. The other mutation (1109 C->T; Pro370Leu), located in exon 3 and detected in a family affected with POAG, cosegregated with the disease and was not present in control samples. Two single nucleotide polymorphisms (SNPs) were identified; one in the promoter region (-83 G->A) and the other in the coding sequence (227 G->A; Arg76Lys). These two SNPs were found to be highly heterozygous both in the control (0.480) and the patient (0.477) populations, and were observed to be in linkage disequilibrium. CONCLUSIONS: The presence of a novel non-conservative change in codon 48 of MYOC in 3 POAG patients, but none in the healthy controls, suggests a causal association of the mutation with the disease, either singly or in combination with other genetic loci. The other point mutation (Pro370Leu) detected in the members of an affected POAG family represents a hotspot of mutation in the gene. Two identified SNPs (-83 G->A and 227 G->A) are not associated with the disease phenotype but could be used as highly informative markers in POAG affected families to determine any causal association of MYOC with the disease, and for identification of presymptomatic carriers in the family, where applicable. A comparison of our data with other studies revealed that these two polymorphisms are in complete linkage disequilibrium among Asians, but not among other ethnic groups studied so far.

Adolescent↗
PubMed2002

Distribution of p53 codon 72 polymorphism in Indian primary open angle glaucoma patients.

PURPOSE: Glaucoma is a complex neurodegenerative disorder of the eye. Primary Open Angle Glaucoma (POAG) is the most common type, accounting for over half of the total cases. Recently, a significant difference in the distribution of the codon 72 polymorphism of the tumor suppressor gene p53 between control subjects and POAG patients of Chinese origin (p=0.00782) was demonstrated. The proline residue at codon 72 of the p53 gene was significantly over represented in the POAG patients relative to healthy controls. The purpose of this study was to investigate whether the reported association between the p53 polymorphism and POAG is a common phenomenon irrespective of geographical location or ethnicity of the population. METHODS: Sixty seven unrelated POAG patients, ranging from 10-65 years of age (mean+/-SD of 41.16+/-18.52 years), and 112 control subjects having a similar age range of 18-63 years (mean+/-SD of 36.64+/-14.65 years) were enrolled in this study. A region of the p53 gene encompassing two polymorphic sites, a 16 bp duplication in intron 3 and a BstU I RFLP in exon 4, were amplified by polymerase chain reaction from Indian POAG patients and normal healthy controls. A single base change (G to C) in codon 72 alters the amino acid residue from arginine to proline and removes the polymorphic BstU I site mentioned above. The amplified DNA fragments were digested with the restriction enzyme and the digestion patterns of the fragments were used to identify the alleles for both the polymorphic sites. RESULTS: No significant association between p53 alleles and Indian POAG patients were observed by analyzing either codon 72 polymorphism (p=0.5627) or the intronic 16 bp duplication polymorphism (p=0.059). Haplotype analysis, reported to be a better predictor of association of the p53 gene with different types of cancer, was also performed and no association of any haplotype was detected with POAG (p=0.1831). CONCLUSIONS: Association between the p53 gene encoding for proline at codon 72 and POAG presumably exists in some ethnic populations but cannot be used as a predictor for the role of the gene as a common regulator of cell death of retinal ganglions leading to POAG.

Adolescent↗
PubMed2002

Did myocilin evolve from two different primordial proteins?

PURPOSE: Myocilin, a 57 kDa glycoprotein, has been of much interest because of its association with primary open-angle glaucoma, lack of understanding of its biological function, and sequence homology of its N- and C-termini with two distinctly different proteins, myosin and olfactomedin, respectively. In that context, the molecular evolution of myocilin was investigated. METHODS: The human myocilin protein was used as query in sequence alignment program and the similar protein sequences were searched in the protein databases for different species. The secondary structure analysis of human myocilin and the prediction of disulfide bonded cysteine residues in the protein were done using PSIPRED and CYSPRED software, respectively. Presence of putative motifs in the protein sequences was determined using the ScanProsite tool with the option of including patterns with the high probability of occurrence. The phylogenetic analyses of human, mouse, rat, and bovine myocilin were done at the DNA Data Bank of Japan (DDBJ) server. RESULTS: It was observed that while two different protein sequences from Drosophila melanogaster contained significant homology with either C-terminal or N-terminal of myocilin, a single protein from Xenopus laevis showed homology covering entire C-terminal and most of the N-terminal region of myocilin. These observations are noteworthy in the context of the previously reported homology of N-terminal domain of myocilin with a single protein (non-muscle myosin) in Dictyostelium discoideum, and C-terminal domain with a single protein (olfactomedin-like) in Caenorhabditis elegans, both representing lower organisms. Further, specific amino acids and putative functional motifs were observed to be conserved between the two sets of proteins having homology to two ends (N- and C-termini) of myocilin. At the secondary structure level, myocilin shows two distinctly different domains: (a) the N-terminal region is primarily a-helical type, and (b) the C-terminal region consists mostly of beta-sheet and turn. CONCLUSIONS: These observations led to the hypothesis that during evolution myocilin might have resulted from fusion of genes for at least two different proteins with functional implications relevant to mammals. It is noteworthy that mutations in the myocilin gene, causal to Primary Open Angle Glaucoma, have only been detected in the first exon (corresponding to myosin like region) and the last exon (corresponding to olfactomedin domain) but not the region (exon 2) between the two domains. Phylogenetic analysis of mammalian myocilin revealed that rat and mouse myocilins demonstrate a closer relationship compared to its human or bovine homologues.

Amino Acid Sequence↗