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Results for “mutation scanning”

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PubMed1992

A synthetic early promoter from a baculovirus: roles of the TATA box and conserved start site CAGT sequence in basal levels of transcription.

Many baculovirus early genes and insect genes transcribed by RNA polymerase II have a conserved transcription start site sequence (CAGT) located downstream of a consensus TATA box. To examine the functions and interactions of these two motifs in initiating accurately positioned basal transcription, a 43-nt synthetic promoter was synthesized from the TATA box and start site sequences of the gp64 early promoter from the Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV). The synthetic promoter initiated accurately and was also transactivated by the baculovirus transcriptional activator, IE1. To determine the roles of sequences within the 43-nt synthetic promoter, a series of linker-scanning and spacing mutations were analyzed for transcriptional activity, start site selection, and transactivation. Linker-scanning mutations were examined in vivo by transient expression and reporter gene assays. To examine transcription start site selection, promoter constructs were used for in vitro transcription in nuclear extracts from uninfected Spodoptera frugiperda (Sf9) cells. In vivo and in vitro analyses show that the TATA box, and not the start site CAGT, is the primary element controlling start site selection. Substitution of the conserved start site CAGT sequence resulted in a reduction of both reporter gene activity and in vitro transcripts, although transcripts initiated accurately. Data from linker-scanning and spacing mutations indicate that the conserved start site CAGT sequences are not required for accurate initiation but sequences at the start site play an important role in initiation efficiency.

Baculoviridae↗
PubMed2002

Elongation of hair cell stereocilia is defective in the mouse mutant whirler.

The recessive mouse mutant whirler (wi) shows no response to sound and exhibits circling and head-tossing behaviour, indicative of both auditory and vestibular dysfunction. The wi mutation maps genetically to mouse chromosome 4. We examined the organ of Corti of whirler mutants to explore the possibility that the wi mutation affects sensory hair cells. Scanning electron microscopy (SEM) reveals that the specialised microvilli (stereocilia) that are projected by the sensory hair cells and are vital for sound transduction are abnormal in wi homozygotes. Specifically, wi homozygous inner hair cell (IHC) stereocilia are approximately half the length of equivalent stereocilia in heterozygous littermates. They are arranged normally into ranks, but the gradation in height and width of stereocilia in adjacent ranks is less prominent in wi homozygotes. Analysis of IHC stereocilia during the course of their development shows that, by embryonic day 18.5, mutant stereocilia are already significantly shorter than those in controls. Mutant stereocilia elongate at a normal rate, at least until postnatal day 1, but prematurely stop elongating between postnatal days 1 and 4. Stereocilia length then decreases. At postnatal day 15, outer hair cell (OHC) stereocilia in wi homozygotes appear short and are arranged in a rounded, "U" shape rather than the normal "W" or "V" shape. Eventually, both IHCs and OHCs degenerate. We show that the whirler locus encodes a protein(s) required for the elongation and maintenance of IHC and OHC stereocilia.

Aging↗
PubMed2005

PMUT: a web-based tool for the annotation of pathological mutations on proteins.

PMUT allows the fast and accurate prediction (approximately 80% success rate in humans) of the pathological character of single point amino acidic mutations based on the use of neural networks. The program also allows the fast scanning of mutational hot spots, which are obtained by three procedures: (1) alanine scanning, (2) massive mutation and (3) genetically accessible mutations. A graphical interface for Protein Data Bank (PDB) structures, when available, and a database containing hot spot profiles for all non-redundant PDB structures are also accessible from the PMUT server.

Amino Acid Substitution↗
PubMed1993

Twenty-four novel hemophilia B mutations revealed by rapid scanning of the whole factor IX gene in a French population sample.

Full scanning of the factor IX gene by means of denaturing gradient gel electrophoresis enabled us to determine the molecular defects in 48 out of 49 hemophiliacs and to evaluate the spectrum of factor IX mutations in the French population. Our results further document the high molecular heterogeneity of the disease and the efficiency of this rapid screening method for disease-causing mutations. This direct approach, which is based on computer-aided analysis of the whole coding, promoter and exon-flanking factor IX gene sequences, proved to be helpful for carrier detection and prenatal diagnosis in most hemophilia B families, including sporadic cases. Moreover, we were able to identify 24 novel molecular defects of various natures in the factor IX gene.

Base Sequence↗
PubMed1999

Enzymatic and chemical cleavage methods.

Cleavage-based methods of mutation detection offer a simple and intuitive means to detect and in most cases locate mutations within DNA fragment sizes ranging from 500 to 1500 bases. Their main advantages as a presequencing screening technology when scanning for unknown mutations is the potential to increase throughput by multiplexing. Combined with lower reagent costs per sample, mutation scanning methods offer significant advantages over currently available sequencing techniques and are likely to be of increasing importance as genomic sequence data becomes more readily available. Although enzymatic methods offer the advantages of simpler and less hazardous protocols, at present the most robust cleavage methods are based around chemical methods.

Endodeoxyribonucleases↗
PubMed2006

[Scanning the HNF4A gene mutation from Chinese pedigrees with early- and/or multiple-onset diabetes].

OBJECTIVE: To screen the mutation of hepatocyte nuclear factor 4 alpha gene (HNF4A) in Chinese pedigrees with early and/or multiplex-onset diabetes in Shanghai and nearby area. METHODS: By PCR-single strand conformation polymorphism (PCR-SSCP) and direct sequencing, the mutation screen of HNF4A gene was performed in 93 normal controls and 154 unrelated probands from early- and/or multiplex-onset diabetes. The PCR-RFLP was used to analyze the frequencies of the discovered mutations and variants. RESULTS: Two synonymous mutations (N153N, A158A) were found in two families, of which the N153N was co-segregated with early-onset diabetes. These two synonymous mutations were not detected in the 93 normal controls. Three variants, IVS1+308(A to G)(rs2071197), IVS1+357(A to T)(rs2071198), IVS1-5(C to T)(rs745975), were also identified in this study. The genotype and allele frequencies of the three variants had no difference between the probands and normal controls. CONCLUSION: HNF4A gene mutation is rare in Chinese pedigrees with early and/or multiplex-onset diabetes.

Adult↗
PubMed2006

[Molecular scanning of MODY1 gene mutations in pedigrees of early onset type 2 diabetes in Beijing].

OBJECTIVE: To explore MDOY1 gene mutations in pedigrees of early-onset familial type 2 diabetes. METHODS: We collected 100 early-onset type 2 diabetes pedigrees in Beijing, in which the probands were diagnosed with type 2 diabetes before the age of 40 years with at least one first-degree relative having such a diagnosis before the age of 45 years. PCR was employed to amplify all the exons and exon/intron splice sites of MDOY1 gene and the PCR products were sequenced to identify the DNA variants. RESULTS: Two DNA variants in the noncoding region including IVS1C +44A>T and IVS2 -5C>T were identified, and 3 mutations in the coding region we identified M49V, T130I, and S462S were found in these pedigrees. CONCLUSION: Currently no sufficient evidence has been obtained to identify the variation in or near MDOY1 genes as the major cause of early-onset type 2 diabetic in Chinese population.

Adult↗
PubMed2005

Detection by denaturing gradient gel electrophoresis of pncA mutations associated with pyrazinamide resistance in Mycobacterium tuberculosis isolates from the United States-Mexico border region.

Denaturing gradient gel electrophoresis (DGGE) was used to probe for mutations associated with pyrazinamide (PZA) resistance in the pncA gene of Mycobacterium tuberculosis. DGGE scans for mutations across large regions of DNA and rivals sequencing in its ability to detect DNA alterations. Specific mutations can often be recognized by their characteristic denaturation pattern, which serves as a molecular fingerprint. Five PCR target fragments were designed to scan for DNA alterations across 600 bp of pncA in 181 M. tuberculosis isolates from patients residing in the U.S-Mexico border states of Texas and Tamaulipas, respectively. A region of pncA was observed with a high GC content and a melting temperature approaching 90 degrees C that was initially refractory to denaturation, and a DGGE target fragment was specifically designed to detect mutations in this region. DGGE detected pncA mutations in 82 of 83 PZA-resistant isolates. By contrast, only 1 of 98 PZA-susceptible isolates harbored a detectable DNA alteration. The pncA gene was sequenced from 41 isolates, and 32 DNA alterations in 32 PZA-resistant isolates were identified, including 11 new mutations. DGGE also detected nine isolates whose susceptibility to PZA appeared to be incorrect, and DNA sequencing confirmed these apparent errors in drug susceptibility testing. These results demonstrate the power and usefulness of DGGE in detecting mutations associated with PZA resistance in M. tuberculosis.

Amidohydrolases↗
PubMed2000

Lisch corneal dystrophy is genetically distinct from Meesmann corneal dystrophy and maps to xp22.3.

PURPOSE: There is an ongoing discussion whether Lisch corneal dystrophy (band-shaped and whorled microcystic dystrophy of the corneal epithelium) represents a disorder that is different from Meesmann corneal dystrophy. The purpose of this study was to evaluate at the molecular level if Lisch and Meesmann corneal dystrophies are genetically distinct. METHODS: We examined at the slit lamp a total of 48 members of a family with an aggregation of Lisch corneal dystrophy. Genomic DNA was extracted from leukocytes of the peripheral blood of seven affected and six unaffected members of this family. Mutational hotspots in the cornea-specific keratin genes K3 and K12 were scanned for mutations by single-strand conformation analysis. To test for linkage to the keratin K3 or K12 loci or for X-chromosomal inheritance, six (K3) and four (K12) microsatellite markers each flanking the keratin loci as well as 22 microsatellite markers covering the X-chromosome were typed. Linkage was analyzed using the MLINK and FASTMAP procedures. RESULTS: A total of 19 trait carriers were identified in six generations of the family. No hereditary transmission from father to son was observed. Linkage was excluded for the keratin K3 and K12 genes. Furthermore, single-strand conformation analysis detected no mutations in these genes. Multipoint linkage analysis revealed linkage with a maximum likelihood of the odds (LOD) score of 2.93 at Xp22.3. Linkage was excluded for Xp22.2 to Xqter. CONCLUSIONS: Lisch corneal dystrophy is genetically different from Meesmann corneal dystrophy. Evidence was found for linkage of the gene for Lisch corneal dystrophy to Xp22.3.

Adolescent↗
PubMed2000

A novel mutation detected by temporal temperature gradient gel electrophoresis led to the confirmative prenatal diagnosis of a Hispanic CF family.

Mutational analysis of 30 recurrent known mutations detects only about 58% of Hispanic cystic fibrosis (CF) chromosomes. The low mutation detection rate has greatly hindered prenatal diagnosis and carrier testing of Hispanic families who have multiple affected children with unidentified cystic fibrosis transmembrane conductance regulator (CFTR) mutations. We recently employed a temporal temperature gradient gel electrophoresis (TTGE) method to effectively scan unknown mutations in the entire CFTR gene. A novel mutation, 2105-2117 del13insAGAAA was identified in a Hispanic family heterozygous for delta F508. The discovery of the devastating mutation facilitated the prenatal diagnosis for this family who already had two severely affected children. The fetus was found to be a compound heterozygote of delta F508/2105-2117 del13insAGAAA. This case emphasizes the importance of whole gene mutational analysis in patients with a clinical diagnosis of CF, but without the identifiable DNA mutations by routine mutation analysis. Finding of CF mutations in the patient would allow proper genetic counselling and prenatal and carrier detection of at-risk family members.

Adolescent↗
PubMed2002

Genetic variants of insulin receptor substrate-1 (IRS-1) in syndromes of severe insulin resistance. Functional analysis of Ala513Pro and Gly1158Glu IRS-1.

AIMS: To define further the role of IRS-1 mutations in human syndromes of severe insulin resistance. METHODS: The IRS-1 gene was scanned for mutations in 83 unrelated affected subjects and 47 unaffected individuals using fluorescent single-strand conformation polymorphism (fSSCP) analysis. A novel heterozygous mutation, Gly1158Glu, was found in one affected subject. Four and two subjects were heterozygous for the previously reported variants Gly972Arg and Ala513Pro, respectively. The previously identified variant Gly819Arg was found in one affected and one unaffected subject. While Gly972Arg has been described to alter the signalling properties of IRS-1, no functional studies of Ala513Pro or Gly1158Glu have been reported. RESULTS: Chinese hamster ovary (CHO) cells stably over-expressing the insulin receptor were transiently transfected with vectors expressing either wild-type, Glu1158 or Pro513 IRS-1. A modest increase in insulin-stimulated tyrosine phosphorylation of Glu1158 IRS-1 was observed. However, this did not result in any significant change in the association of Grb2 or the p85 alpha subunit of PI3-kinase or of PI3-kinase activity. In parallel studies, the Pro513 IRS-1 variant was indistinguishable from wild-type IRS-1. CONCLUSIONS: While subtle effects of these variants cannot be excluded in this system, it is unlikely that these variants are responsible for the extreme insulin resistance seen in the subjects harbouring them. Although IRS proteins play a central role in insulin signalling, functionally significant mutations in the IRS-1 gene are a rare cause of human syndromes of severe insulin resistance.

Animals↗
PubMed2004

Characterization of cystathionine beta-synthase gene mutations in homocystinuric Venezuelan patients: identification of one novel mutation in exon 6.

This study describes for the first time the cystathionine beta-synthase (CBS) gene mutations in Venezuelan patients. A total of five disease-causing mutations were identified in 9 out of 10 independent chromosomes. Four of the mutations have been previously described (G85R, T191M, D234N, and D444N) and a novel mutation was found (Q243X). Two common polymorphisms (699C/T and 1080C/T) were found in the CBS gene. Mutation analysis was performed using a combined screening approach for CBS mutations: restriction analysis, single-strand conformational polymorphism (SSCP) scanning, and sequencing. All the mutations were detected in homozygous state, except for Q243X, detected in three heterozygous siblings. Each one of the patients studied presented a different mutation. All mutations and polymorphisms detected involved hypermutable CpG sites, except for the novel mutation Q243X. The most common mutations I278T and G307S were not found in any of the patients. The CBS mutations present in each country differ from each other depending on the demographic profile; therefore, specific mutations scanning must be performed in each population for diagnosis and prognosis purposes.

Cystathionine beta-Synthase↗
PubMed2003

In-depth mutation and SNP discovery using DHPLC gene scanning.

Denaturing high-performance liquid chromatography (DHPLC) is a new technology used in the discovery of genetic variations (mutations), such as single-base substitutions (or single nucleotide polymorphisms) and small deletions or insertions. These genetic variations can be routinely detected by DHPLC gene scanning at the germ-line and somatic levels. Epigenetic alterations, such as changes in DNA methylation status at defined loci, can also be assessed using DHPLC-based methodologies. The biological impact of these genetic variations depends on the location and identity of the DNA sequence alteration. The discovery of functionally relevant genetic variations can be exploited throughout the drug discovery and development processes. Examples of the application of DHPLC for sequence variant detection will be presented and discussed, with emphasis on target validation by candidate gene scanning and mutation detection in disease pathway genes, as well as the discovery of therapeutically significant mutations associated with drug metabolism and resistance.

Animals↗
PubMed2005

Alteration of p73 in acute myelogenous leukemia.

The frequency of p73 mutation is low in hematologic malignancies as well as solid tumors. In the present study, we scanned for mutations in the exons 4, 5, 6, and 7 of p73, as well as methylation of the CpG island in the untranslated region of exon 1, in 100 de novo AML patients. Four patients showed mutation in exon 5 and one in exon 6, and none of the patients showed mutation in exons 4 and 7. None of the patients showed p73 gene methylation. The expression level of p73 mRNA was also examined in 40 AML samples using reverse transcriptase-polymerase chain reaction. Only six AML patients showed p73 mRNA expression, as analyzed by RT-PCR analysis. However, p73 over-expression in 30% of patients was demonstrated by immunocytochemistry and Western blot analysis. Further, mutation of p73 has been correlated with p73 mRNA and p73 protein status. The results show the presence of over-expressed p73 mRNA and protein in the samples with mutated p73 gene. Thus, it is presumed that mutation of p73 might lead to production of defective p73 protein and p73 mRNA, and this might have a role in the process of leukemogenesis of AML. This report is the first demonstrating the presence of mutations in p73 gene in acute myelogenous leukemia.

Adult↗
PubMed2002

Molecular heterogeneity of glucose-6-phosphate dehydrogenase deficiency in Malays in Malaysia.

Multiplex polymerase chain reaction (PCR) using multiple tandem forward primers and a common reverse primer (MPTP) was recently established as a comprehensive screening method for mutations in X-linked recessive diseases. In the work reported here, MPTP was used to scan for mutations of the glucose-6-phosphate dehydrogenase (G6PD) gene. Mutations in exons 3,4,5,6,7,9, 11, and 12 of the G6PD gene were screened by MPTP in 93 unrelated Malaysian patients with G6PD deficiency. Of the 93 patients, 80 (86%) had identified mutations. Although all of these were missense mutations, identified nucleotide changes were heterogeneous, with 9 mutations involving various parts of the exons. These 9 mutations were G-to-A nucleotide changes at nucleotide 871 of the G6PD gene (G871A), corresponding to G6PD Viangchan, G6PD Mediterranean (C563T), G6PD Vanua Lava (T383C), G6PD Coimbra (C592T), G6PD Kaiping (G1388A), G6PD Orissa (C131G), G6PD Mahidol (G487A), G6PD Canton (G1376T), and G6PD Chatham (G1003A). Our results document heterogeneous mutations of the G6PD gene in the Malaysian population.

DNA Mutational Analysis↗
PubMed1999

DGGE screening of PKD1 gene reveals novel mutations in a large cohort of 146 unrelated patients.

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most commonly inherited renal diseases. ADPKD is a genetically heterogeneous disorder involving at least three different genes. PKD1, the major locus mapped to chromosome 16p13.3 accounts for approximately 85% of ADPKD cases. The search for mutations is a very important step in understanding the molecular mechanisms underlying ADPKD. Despite intense screening by many groups, only a small number of mutations have been described so far. We undertook the first study using denaturing gradient gel electrophoresis (DGGE) to scan for mutations in the non-duplicated region of the PKD1 gene in a large cohort of 146 French unrelated ADPKD patients. We successfully identified novel mutations: 3 are frameshift mutations, 2 nonsense mutations, 2 missense mutations, 1 is an insertion in the frame of 9 nucleotides, 3 intronic variations and several polymorphisms. One of these mutations is the fourth de novo mutation described in this gene. We also describe a family with possible clinical anticipation. DGGE is an effective method for detecting nucleotide changes in the PKD1 gene.

Adult↗