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Automated Sequencing (automate + sequencing)
Selected AbstractsAge-Related Mitochondrial DNA Mutations in the Human LarynxTHE LARYNGOSCOPE, Issue 12 2000Jose M. Manaligod MD Abstract Objective To determine whether age-related mitochondrial DNA mutations occur in the human larynx. Study Design Genetic study of cadaveric larynx specimens. Methods Vocal fold mucosa, thyroarytenoid muscle, and cricoarytenoid joint tissue were harvested from 13 fresh postmortem larynges (age range, 2 d,82 y). DNA was extracted from each sample, and the polymerase chain reaction (PCR) was used to amplify a target DNA sequence resulting from the common age-associated, 4977,base-pair (bp) mitochondrial DNA deletion. PCR products were visualized by agarose gel electrophoresis. Automated sequencing determined the sequence of identified PCR products. Subjects Thirteen cadaveric larynges were obtained through the University of Kentucky Medical Center (Lexington, KY). Specimens from patients with a history of head and neck cancer, previous laryngeal trauma, or surgery were excluded. Results Strongly positive bands were identified in samples from three individuals. Weaker bands were seen in samples from four other samples. No band was noted from the two pediatric larynges. Different band patterns were seen among the three different tissue sites in the larynges with positive PCR products, but no consistent pattern was seen. Sequencing of the identified PCR products from selected samples confirmed that they were products of the age-associated, 4977-bp mitochondrial DNA deletion. Conclusions An age-associated mitochondrial DNA deletion was detected in several postmortem human larynges. Its presence seemed to increase in appearance with age. In the larynges in which the deletion occurred, there were individual regional differences in the occurrence of the deletion, but no consistent pattern was noted across all individuals who carried the deletion. [source] Microsatellite allelotyping differentiates chromophobe renal cell carcinomas from renal oncocytomas and identifies new genetic changesHISTOPATHOLOGY, Issue 6 2004A Nagy Aims:, The diagnosis of renal oncocytomas (ROs) and chromophobe renal cell carcinomas (RCCs) based on histological features is often uncertain. To assess the value of genetic analysis in their differential diagnosis we analysed 27 ROs and 21 chromophobe RCCs by microsatellite allelotyping. Methods and results:, Markers at the short and long arms of chromosomes specifically involved in the genetic changes of the four main types of renal cancers were selected. Allelic changes were identified by automated sequencing. Allelic changes at chromosome 1p occurred in 8/26 (31%) and at chromosome 14q in 4/27 (15%) ROs. Loss of heterozygosity (LOH) at chromosomes 1, 2, 6, 10, 13, 17 and 21 were seen in 90%, 90%, 96%, 86%, 85%, 90% and 72% of the chromophobe RCCs, respectively. Alterations of at least three of these chromosomal sites were detected in each chromophobe RCC. In addition, we found recurrent LOH at chromosomes 9p23 (43%), 18q22 (30%), 5q22 (28%) and 8p (28%) in chromophobe RCCs. Conclusions:, Chromophobe RCCs can be differentiated from ROs by analysing specific chromosomal regions with microsatellites. [source] Molecular Genetic Analysis of PRKAG2 in Sporadic Wolff-Parkinson-White SyndromeJOURNAL OF CARDIOVASCULAR ELECTROPHYSIOLOGY, Issue 3 2003CARL J. VAUGHAN Introduction: Mutations in the PRKAG2 gene that encodes the gamma2 regulatory subunit of AMP-activated protein kinase have been shown to cause autosomal dominant Wolff-Parkinson-White (WPW) syndrome associated with hypertrophic cardiomyopathy. Prior studies focused on familial WPW syndrome associated with other heart disease such as hypertrophic cardiomyopathy. However, such disease accounts for only a small fraction of WPW cases, and the contribution of PRKAG2 mutations to sporadic isolated WPW syndrome is unknown. Methods and Results: Subjects presented for clinical electrophysiologic evaluation of suspected WPW syndrome. WPW syndrome was diagnosed by ECG findings and/or by clinically indicated electrophysiologic study prior to enrollment. Echocardiography excluded hypertrophic cardiomyopathy. Denaturing high-performance liquid chromatography and automated sequencing were used to search for PRKAG2 mutations. Twenty-six patients without a family history of WPW syndrome were studied. No subject had cardiac hypertrophy, and only one patient had associated congenital heart disease. Accessory pathways were detected at diverse locations within the heart. Two polymorphisms in PRKAG2 were detected. [inv6+36insA] occurred in intron 6 in 4 WPW patients and [inv10+10delT] in intron 10 in 1 WPW patient. Both occurred in normal unrelated chromosomes. No PRKAG2 mutations were detected. Conclusion: This study shows that, unlike familial WPW syndrome, constitutional mutation of PRKAG2 is not commonly associated with sporadic WPW syndrome. Although polymorphisms within the PRKAG2 introns were identified, there is no evidence that these polymorphisms predispose to accessory pathway formation because their frequency is similarly high in both WPW patients and normal individuals. Further studies are warranted to identify the molecular basis of common sporadic WPW syndrome.(J Cardiovasc Electrophysiol, Vol. 14, pp. 263-268, March 2003) [source] Mutations in the von Hippel-Lindau (VHL) gene refine differential diagnostic criteria in renal cell carcinomaJOURNAL OF SURGICAL ONCOLOGY, Issue 1 2002Nandita Barnabas PhD Abstract Background and Objectives Renal cell carcinomas (RCC) with abundant granular cytoplasm include oncocytomas, eosinophillic variants of chromophobe RCC, papillary RCC, collecting duct carcinoma, and some conventional (clear cell) RCC. Tumors with predominantly clear cell cytoplasm include typical chromophobe RCC and conventional (clear cell) RCC. The objective of this study was to determine if mutations in the VHL gene can serve as auxiliary diagnostic criteria in refining histology based subtyping of renal epithelial neoplasia. Methods The study cohort of 67 cases included 24 conventional RCC, 14 chromophobe RCC, 14 papillary RCC, and 15 oncocytomas. Single strand conformational polymorphism (SSCP) was used as a screening procedure for mutations followed by automated sequencing to identify mutations. Results Thirteen of the 14 mutations identified were novel, seven of which were in the coding region. In chromophobe RCC, mutations clustered in the 5,UTR/promoter region and have not been previously reported. Exon 3 appeared to favor conventional (clear cell) RCC and correlated with a more aggressive phenotype. Mutations were absent in the papillary and oncocytoma RCC subtypes. Conclusions Exon 3 mutations permitted a morphological distinction between conventional (clear cell) RCC and chromophobe RCC with clear cells. Mutations in the VHL gene refine histologic diagnostic criteria in RCC serving as adjuncts to the present morphology based diagnosis of RCC. J. Surg. Oncol. 2002;80:52,60. © 2002 Wiley-Liss, Inc. [source] The rothein peptides from the skin secretion of Roth's tree frog Litoria rothii.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 18 2005Sequence determination using positive, negative ion electrospray mass spectrometry The secretion from the dorsal glands of the frog Litoria rothii contains a series of new peptides including rothein 1 (SVSNIPESIGF-OH, a neuropeptide which contracts smooth muscle), a number of inactive rothein 2 and 3 peptides (e.g. rothein 2.1, AGGLDDLLEPVLNSADNLVHGL-OH), and a new proline rich peptide, named rothein 4.1 (AEILFGDVRPPWMPPPIFPEMP-OH), which shows neither antimicrobial nor neuronal nitric oxide synthase (nNOS) activity. Two known neuropeptides of the caerulein family [e.g. caerulein, pEQDY(SO3)TGWMDF-NH2] together with a series of known caerin 1 antibiotic and nNOS-inhibiting peptides (e.g. caerin 1.1, GLLSVLGSVAKHVLPHVVPVIAEHL-NH2) were also identified. Positive ion electrospray mass spectrometry (ES-MS) was used as the primary method to investigate the sequences of the new peptides. Negative ion ES-MS was used to fill in any gaps in the positive ion data and, finally, Edman automated sequencing was used to differentiate between Leu and Ile and to confirm the sequences determined by mass spectrometry. Copyright © 2005 John Wiley & Sons, Ltd. [source] New Mutations of EXT1 and EXT2 Genes in German Patients with Multiple OsteochondromasANNALS OF HUMAN GENETICS, Issue 3 2009Wolfram Heinritz Summary Mutations in either the EXT1 or EXT2 genes lead to Multiple Osteochondromas (MO), an autosomal dominantly inherited disorder. This is a report on clinical findings and results of molecular analyses of both genes in 23 German patients affected by MO. Mutation screening was performed by using denaturing high performance liquid chromatography (dHPLC) and automated sequencing. In 17 of 23 patients novel pathogenic mutations have been identified; eleven in the EXT1 and six in the EXT2 gene. Five patients were carriers of recurrent mutations in the EXT2 gene (p.Asp227Asn, p.Gln172X, p.Gln258X) and one patient had no detectable mutation. To demonstrate their pathogenic effect on transcription, two complex mutations in EXT1 and EXT2 and three splice site mutations were characterized by mRNA investigations. The results obtained provide evidence for different aberrant splice effects , usage of new cryptic splice sites and exon skipping. Our study extends the mutational spectrum and understanding of pathogenic effects of mutations in EXT1 and EXT2. [source] 2461: Increasing complexity of ocular genetic diseases : the case of BEST diseaseACTA OPHTHALMOLOGICA, Issue 2010M ABITBOL Purpose Monogenic diseases until recently appeared simple from a molecular genetics point of view but correlations between genotypes and phenotypes still remain difficult to establish in many diseases and for many genes. For autosomal dominant diseases such as Best Vitelliform Macular Dystrophy, supposed to be a juvenile disease, it appears that mutations of BEST1 gene can cause multiple phenotypes including early onset and late onset phenotypes as well as unexpected phenotypes such as RP. We report several novel mutations and their associated phenotypes and describe phenotypes linked to previously reoported mutations for which the phenotype had not been describe at all previously. The role of SOX9, MITF and OTX2 in the incomplete penetrance and the variable expressivity of BVMDs is duscussed as well the potential roles of SNPs occuring in coding exons Methods We used genomic PCR with appropriate primers flanking all the exons of the BEST1 gene in order to amplify them. This Genomic PCR was followed by automated sequencing and careful analysis of the sequences obtained. Results We report the case of an unusual family where the Mother II2 of the proband III1, his maternal aunt II3, his brother III3 and his first cousin IIIIV, the son of his maternal aunt, carry a missense mutatation causing apparently only electrophysiological abnormalities. The Father II1 of the proband III1 turned out to carry a stop codon instead of the fifth normal BEST1 codon. The father did not display any electrophysiological nor any clinical abnormality and has a perfect monocular and binocular vision. In contrast the proband III1 carries both mutations with a severe phenotype. Conclusion This report exemplifies the necessity to study all family members in the case of BVMDs. [source] | ||||||||||