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Gene Exons (gene + exon)
Selected AbstractsLack of genetic association of promoter and structural variants of mannan-binding lectin (MBL2) gene with susceptibility to generalized vitiligoBRITISH JOURNAL OF DERMATOLOGY, Issue 1 2009M. Dwivedi Summary Background, Vitiligo is a common depigmenting disorder resulting from the loss of functional melanocytes in the skin. It is hypothesized to be of autoimmune origin. Mannan-binding lectin (MBL) plays an important role in innate immunity. It helps in the clearance of apoptotic cells and in complement activation. Genetic variability due to structural and promoter polymorphisms in the MBL2 gene has been reported to be associated with increased risk for several autoimmune diseases including vitiligo. Objectives, The aim of this study was to explore whether MBL2 structural and promoter polymorphisms are associated with generalized vitiligo in Gujarat where the prevalence of vitiligo is alarmingly high. Materials and methods, We undertook a case,control study to investigate the association of MBL2 gene exon 1 polymorphisms , codon 52, codon 54 and codon 57 as well as promoter ,221 polymorphism in 92 patients with generalized vitiligo and 94 unaffected age-matched controls by polymerase chain reaction-heteroduplex analysis. Results, The genotype and allele frequencies of MBL2 structural and promoter polymorphisms did not differ significantly between the control and patient population (P -values: P < 0·019 for codon 52, P < 0·373 for codon 54, P < 0·855 for codon 57 and P < 0·889 for ,221 promoter polymorphisms) after Bonferroni's correction for multiple testing, which suggests that there is no association of MBL2 structural and promoter polymorphisms with generalized vitiligo. Conclusions, Our results suggest that the well-documented structural and promoter polymorphisms of the MBL2 gene may not be associated with generalized vitiligo in the Gujarat population. [source] Pleomorphic phenotypes of gastrointestinal stromal tumors at metastatic sites with or without imatinib treatmentCANCER SCIENCE, Issue 5 2010Kazuha Sakamoto Secondary resistance of gastrointestinal stromal tumors (GISTs) to tyrosine kinase inhibitors occurs after several years' administration. However, the mechanism of resistance has not been fully clarified. In this study, we analyzed the genotypes and the histologic and immunohistochemical phenotypes of metastatic GISTs with and without imatinib treatment, and clarified the pleomorphic nature of metastatic GISTs. We examined 31 autopsy cases in which the patients died of multiple metastases of GISTs, and two surgically resected specimens with and without imatinib treatment. A total of 152 primary and metastatic lesions in 33 cases of GISTs were examined for histologic and immunohistochemical expression of KIT and CD34. We analyzed the expression of other receptor tyrosine kinases (RTKs) in KIT-negative lesions, including human EGFR-related 2 (HER2), epidermal growth factor receptor (EGFR), hepatocyte growth factor receptor (MET), platelet-derived growth factor receptor-, (PDGFRA), and platelet-derived growth factor receptor-, (PDGFRB). Fifteen lesions in seven cases (9.9%) lacked KIT expression, and 74 (49%) in 22 cases lacked CD34 expression. Eight KIT-negative lesions in five cases expressed PDGFRB, one of which also expressed EGFR, and three lesions in one case expressed MET. Results for the other RTKs were negative. Missense point mutations at PDGFRB gene exon 12 were detected in one PDGFRB-positive case. Our results indicate that histomorphology, immunohistochemical phenotypes, and genotypes of metastatic GISTs vary among lesions, even in cases without imatinib treatment. A KIT-independent mechanism, such as activation of other RTKs, might participate in the proliferation of late-stage GISTs and might be a cause of secondary imatinib resistance. (Cancer Sci 2010; 101: 1270,1278) [source] A pharmacogenomic approach to Alzheimer's diseaseACTA NEUROLOGICA SCANDINAVICA, Issue 2000R. Cacabelos Single nucleotide polymorphisms (susceptibility genetics) and genomic point mutations (mendelian genetics) can be used in Alzheimer's disease (AD) for diagnostic, predictive and therapeutic purposes. Using a matrix genetic model, including APOE, PS1 and PS2 allelic variants, we have studied the distribution of 36 different genotypes in the AD population (N=479) and the genotype-related cognitive response to a multifactorial therapy in AD patients with mild-to-moderate dementia. The 10 most frequent AD genotypes are the following: 1) E33P112P2+ (17.75%), 2) E33P112P2, (15.55%), 3) E33P111P2+ (10.85%), 4) E34P112P2+ (9.60%), 5) E34P112P2, (7.56%), 6) E33P111P2, (7.10%), 7) E34P111P2+ (4.80%), 8) E33P122P2+ (4.38%), 9) E34P111P2, (4.18%), and 10) E34P122P2+ (3.55%). APOE-4/4-related genotypes represent less than 3% in the following order: E44P112P2+> E44P111P2+=E44P111P2,>E44P112P2+>E44P122P2+= E44P122P2,. Multifactorial therapy with CDP-choline (1000 mg/day)+piracetam (2400 mg/day)+anapsos (360 mg/day) did improve mental performance during the first 6,15 months in a genotype-specific fashion. The best responders in the APOE series were patients with APOE-3/4 genotype (r=+0.013), while the worst responders were APOE-4/4 patients (r=,0.93). PS1-related genotypes responded in a similar manner; and patients with a defective PS2 gene exon 5 (PS2+) always showed a poorer therapeutic response than PS2, patients. All these data suggest that the therapeutic outcome in AD exhibits a genotype-specific pattern, and that a pharmacogenomic approach to AD might be a valuable strategy for drug development and monitoring. [source] Molecular identification and localization of cellular titin, a novel titin isoform in the fibroblast stress fiberCYTOSKELETON, Issue 6 2007Peter J. Cavnar Abstract We previously discovered a large titin-like protein,c-titin,in chicken epithelial brush border and human blood platelet extracts that binds ,-actinin and organizes arrays of myosin II bipolar filaments in vitro. RT-PCR analysis of total RNA from human megakaryoblastic (CHRF-288-11) and mouse fibroblast (3T3) nonmuscle cells reveal sequences identical to known titin gene exon sequences that encode parts of the Z-line, I-band, PEVK domain, A-band, and M-line regions of striated muscle titins. In the nonmuscle cells, these sequences are differentially spliced in patterns not reported for any striated muscle titin isoform. Rabbit polyclonal antibodies raised against expressed protein fragments encoded by the Z-repeat and kinase domain regions react with the c-titin band in Western blot analysis of platelet extracts and immunoprecipitate c-titin in whole platelet extracts. Immunofluorescent localization demonstrates that the majority of the c-titin colocalizes with ,-actinin and actin in 3T3 and Indian Muntjac deer skin fibroblast stress fibers. Our results suggest that differential expression of titin gene exons in nonmuscle cells yields multiple novel isoforms of the protein c-titin that are associated with the actin stress fiber structures. Cell Motil. Cytoskeleton 2007. © 2007 Wiley-Liss, Inc. [source] An optimized microchip electrophoresis system for mutation detection by tandem SSCP and heteroduplex analysis for p53,gene exons,5,9ELECTROPHORESIS, Issue 19 2006Christa N. Hestekin Abstract With the complete sequencing of the human genome, there is a growing need for rapid, highly sensitive genetic mutation detection methods suitable for clinical implementation. DNA-based diagnostics such as single-strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are commonly used in research laboratories to screen for mutations, but the slab gel electrophoresis (SGE) format is ill-suited for routine clinical use. The translation of these assays from SGE to microfluidic chips offers significant speed, cost, and sensitivity advantages; however, numerous parameters must be optimized to provide highly sensitive mutation detection. Here we present a methodical study of system parameters including polymer matrix, wall coating, analysis temperature, and electric field strengths on the effectiveness of mutation detection by tandem SSCP/HA for DNA samples from exons,5,9 of the p53 gene. The effects of polymer matrix concentration and average molar mass were studied for linear polyacrylamide (LPA) solutions. We determined that a matrix of 8%,w/v 600,kDa LPA provides the most reliable SSCP/HA mutation detection on chips. The inclusion of a small amount of the dynamic wall-coating polymer poly- N -hydroxyethylacrylamide in the matrix substantially improves the resolution of SSCP conformers and extends the coating lifetime. We investigated electrophoresis temperatures between 17 and 35°C and found that the lowest temperature accessible on our chip electrophoresis system gives the best condition for high sensitivity of the tandem SSCP/HA method, especially for the SSCP conformers. Finally, the use of electrical fields between 350 and 450,V/cm provided rapid separations (<10,min) with well-resolved DNA peaks for both SSCP and HA. [source] CASRdb: calcium-sensing receptor locus-specific database for mutations causing familial (benign) hypocalciuric hypercalcemia, neonatal severe hyperparathyroidism, and autosomal dominant hypocalcemia,HUMAN MUTATION, Issue 2 2004Svetlana Pidasheva Abstract Familial hypocalciuric hypercalcemia (FHH) is caused by heterozygous loss-of-function mutations in the calcium-sensing receptor (CASR), in which the lifelong hypercalcemia is generally asymptomatic. Homozygous loss-of-function CASR mutations manifest as neonatal severe hyperparathyroidism (NSHPT), a rare disorder characterized by extreme hypercalcemia and the bony changes of hyperparathyroidism, which occur in infancy. Activating mutations in the CASR gene have been identified in several families with autosomal dominant hypocalcemia (ADH), autosomal dominant hypoparathyroidism, or hypocalcemic hypercalciuria. Individuals with ADH may have mild hypocalcemia and relatively few symptoms. However, in some cases seizures can occur, especially in younger patients, and these often happen during febrile episodes due to intercurrent infection. Thus far, 112 naturally-occurring mutations in the human CASR gene have been reported, of which 80 are unique and 32 are recurrent. To better understand the mutations causing defects in the CASR gene and to define specific regions relevant for ligand-receptor interaction and other receptor functions, the data on mutations were collected and the information was centralized in the CASRdb (www.casrdb.mcgill.ca), which is easily and quickly accessible by search engines for retrieval of specific information. The information can be searched by mutation, genotype,phenotype, clinical data, in vitro analyses, and authors of publications describing the mutations. CASRdb is regularly updated for new mutations and it also provides a mutation submission form to ensure up-to-date information. The home page of this database provides links to different web pages that are relevant to the CASR, as well as disease clinical pages, sequence of the CASR gene exons, and position of mutations in the CASR. The CASRdb will help researchers to better understand and analyze the mutations, and aid in structure,function analyses. Hum Mutat 24:107,111, 2004. © 2004 Wiley-Liss, Inc. [source] H intragenic polymorphisms and haplotype analysis in the ornithine transcarbamylase (OTC) gene and their relevance for tracking the inheritance of OTC deficiency,,HUMAN MUTATION, Issue 5 2002Consuelo Climent Abstract The "private" nature of most mutations causing ornithine transcarbamylase (OTC) deficiency makes mutation identification in the patients difficult. Further, the PCR-amplification technology generally used for the genetic diagnosis of the deficiency misses large deletions in carrier females. Intragenic OTC polymorphisms may allow detection of these deletions and may represent an alternative to mutation detection for prenatal diagnosis and carrier identification in families with a history of inherited OTC deficiency. A new highly informative polymorphism (allele frequencies, 0.66/0.34) in intron 3 of the OTC gene (IVS3-39_40insT) is reported here, and allelic frequencies of 16 additional intragenic OTC polymorphisms are determined in 133-35 (average per polymorphism, 72) unrelated chromosomes. In addition to the novel polymorphism, only three of the studied polymorphisms (Lys46Arg, allelic frequency 0.68/0.32; IVS3-8A>T, 0.34/0.66; Gln270Arg, 0.97/0.03) are confirmed to be informative. These provide, together with another reported polymorphism (IVS4-7A>G; reported allelic frequency 0.71/0.29; Plante and Tuchman, 1998), a set of highly valuable markers of the OTC gene. Nevertheless, the combined informativity of the studied polymorphisms is limited by their distribution in only four haplotypes with one of them predominating (65% of the sampled chromosomes). Although this haplotype composition may be restricted to the Iberian peninsula (the origin of the samples), more informative polymorphisms are required to increase the diagnostic potential and, particularly, to identify large deletions affecting OTC gene exons 5-10, where only one polymorphism of weak diagnostic value is known. © 2002 Wiley-Liss, Inc. [source] | |||||||||||||