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PubMed1993

[Sensitive detection of K-ras oncogene codon 12 mutations by nested PCR using mismatched primers and selective digestion of non-mutated PCR fragments with restriction enzyme].

Sensitive detection of K-ras oncogene mutation at codon 12 using nested polymerase chain reactions (PCR) with mismatched primers combined with selective digestion of nonmutated DNA fragments after the first PCR amplification was reported by Levi S, et al. (Cancer Res 51:3497-3502, 1991). We examined the usefulness of this novel technique in cell lines carrying various K-ras codon 12 mutations and clinical samples such as colon carcinoma tissue, corresponding normal colonic mucosa and pancreatic juice obtained from the patients with pancreatic carcinoma undergoing endoscopic retrograde pancreatography (ERP). In analysis of tumor cell lines carrying mutated K-ras at codon 12, the fragment length of the amplified DNA was 135 bp after digestion using restriction enzyme BstN1, whereas those of nonmutated cell lines were 106 bp. This method was highly sensitive to detect mutant DNA diluted at a ratio of 2048 fold with normal DNA samples obtained from peripheral blood lymphocytes. In analysis of clinical samples, 4 out of 10 colorectal carcinoma tissues were positive for K-ras gene mutation at codon 12, however, no mutations were detected in corresponding normal colonic mucosa. In analysis of pancreatic juice taken from the patients with pancreatic carcinoma, 1 out of 3 samples were positive for K-ras mutation at codon 12. Thus, this novel approach was thought to be useful for detection of minimum number of cancer cells from compound samples containing larger amounts of normal cells.

Cells, Cultured↗
PubMed1993

Sporadic mutations of the p53 gene in multiple myeloma and no evidence for germline mutations in three familial multiple myeloma pedigrees.

The recent finding that eight out of 10 multiple myeloma cell lines have p53 gene mutations prompted us to examine the p53 tumour suppressor gene in 25 non-related multiple myeloma patients. None of 19 patient bone marrow samples available for Southern blot analysis showed rearrangements in the p53 gene and only one patient showed loss of the p53 locus. DNA encompassing exons 5, 7, and 8, where p53 mutations commonly cluster, was amplified by PCR. Single-strand conformation polymorphisms of the PCR-amplified exon 5 region were detected in two patients. Direct sequencing of the mutant band revealed that one patient had a C to T transition at codon 138 (Ala to Val) and one patient had a G to C transversion at codon 139 (Lys to Asn). p53 mutations in germline cells in hereditary cancer syndromes predispose the family members to the development of malignancies. We therefore searched for p53 germline mutations in exons 5, 7, and 8 in the affected individuals from three families each with two multiple myeloma patients (these patients include three individuals from the non-related group mentioned above). Using Southern blotting, polymerase chain reaction/single-strand conformation polymorphism (PCR-SSCP) analysis and direct sequencing, no germline mutations were found. These results indicate that mutations in exons 5, 7, and 8 of the p53 gene are infrequent in multiple myeloma.

Adult↗
PubMed1995

Are two mutations sufficient to cause cancer? Some generalizations of the two-mutation model of carcinogenesis of Moolgavkar, Venzon, and Knudson, and of the multistage model of Armitage and Doll.

Some generalizations of the two-mutation carcinogenesis model of Moolgavkar, Venzon, and Knudson (to allow for an arbitrary number of mutational stages) and of the multistage model of Armitage and Doll are shown to have the property that, at least in the case when the parameters of the model are eventually constant, the excess relative and absolute risks following changes in any of the parameters will eventually tend to zero. It is also shown that when the parameters governing the processes of cell division, death, or additional mutation at the penultimate stage are subject to perturbations, there are relatively large fluctuations in the hazard function for carcinogenesis for either model, which start almost as soon as the parameters are changed. For this reason it appears that without some extra stochastic "stage" appended (such as might be provided by consideration of the process of development of a malignant clone clone from a single malignant cell) the two-mutation model is not well able to describe the pattern of excess risk for solid cancers that is often seen after exposure to ionizing radiation, although leukemia may be better fitted by the two-mutation model in this respect. An examination of the results of perturbing various of the parameters for models that require three or more mutations provides indications that these models are easier to reconcile with the results from a body of epidemiological data relating to solid cancers.

Biometry↗
PubMed1996

Mitochondrial DNA mutations associated with the 11778 mutation in Leber's disease.

To clarify the characteristics of possible synergestic mitochondrial DNA (mtDNA) mutations associated with Leber's hereditary optic neuropathy (LHON), we analyzed the entire nucleotide sequences of mitochondrial genome of two Japanese patients from independent pedigrees harboring the 11778 mtDNA mutation, and compared their sequences with those of 47 disease and 6 normal controls. We have detected several unique mutations in the mtDNA in addition to the 11778 mutation. Two nucleotide substitutions, an A-to-G transition at position 856 in the 12S rRNA gene and an A-to-G transition at 14692 in the T psi C loop of the tRNA(Glu) gene, occurred at highly conserved sites among various species. These mutations in combination with the 11778 mutation might synergetically contribute to the pathogenesis of LHON.

Adolescent↗
PubMed1996

Mutation spectrum in patients with Wiskott-Aldrich syndrome and X-linked thrombocytopenia: identification of twelve different mutations in the WASP gene.

Twelve different mutations in the WASP gene were found in twelve unrelated families with Wiskott-Aldrich syndrome (WAS) or X-linked thrombocytopenia (XLT). Four frameshift, one splice, one nonsense mutation, and one 18-base-pair deletion were detected in seven patients with WAS. Only missense mutations were found in five patients diagnosed as having XLT. One of the nucleotide substitutions in exon 2 (codon 86) results in an Arg to Cys replacement. Two other nucleotide substitutions in this codon, R86L and R86H, have been reported previously, both giving rise to typical WAS symptoms, indicating a mutational hot spot in this codon. The finding of mutations in the WASP gene in both WAS and XLT gives further evidence of these syndromes being allelic. The relatively small size of the WASP gene facilitates the detection of mutations and a reliable diagnosis of both carriers and affected fetuses in families with WAS or XLT.

Base Sequence↗
PubMed1996

Genetic diagnosis of dysplasminogenemia: detection of an Ala601-Thr mutation in 118 out of 125 families and identification of a new Asp676-Asn mutation.

Dysplasminogenemia (plasminogen abnormality) is frequently found in association with thrombosis. Two types of mutation, Ala601-Thr and Val355-Phe, have already been identified; the precise genetic defects of most of these patients, however, remain unknown. In this study, we examined the genetic DNAs of two unrelated cases by single-strand conformational polymorphism and nucleotide sequencing analysis. A new mutation, designated as Asp676-Asn, has been identified in these cases. This mutation leads to the loss of a negatively-charged residue and the creation of a potential carbohydrate attachment site, which may impair the enzymatic properties of plasminogen. As many as 158 individuals with dysplasminogenemia were analyzed by a combination of in vitro amplification and restriction digestion. Among 125 unrelated families, the Ala601-Thr mutation accounted for about 94% of cases. The Val355-Phe mutation was found in four unrelated families, indicating that it is a recurring mutation and is not very rare.

Adult↗
PubMed1997

The mutational spectrum in Treacher Collins syndrome reveals a predominance of mutations that create a premature-termination codon.

Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate. The TCS locus has been mapped to human chromosome 5q31.3-32 and the mutated gene identified. In the current investigation, 25 previously undescribed mutations, which are spread throughout the gene, are presented. This brings the total reported to date to 35, which represents a detection rate of 60%. Of the mutations that have been reported to date, all but one result in the introduction of a premature-termination codon into the predicted protein, treacle. Moreover, the mutations are largely family specific, although a common 5 bp deletion in exon 24 (seven different families) and a recurrent splicing mutation in intron 3 (two different families) have been identified. This mutational spectrum supports the hypothesis that TCS results from haploinsufficiency.

Chromosomes, Human, Pair 5↗
PubMed1997

Frame shift mutation, exon skipping, and a two-codon deletion caused by splice site mutations account for pyruvate kinase deficiency.

Three novel splice site mutations and two novel missense mutations were identified by molecular analysis of pyruvate kinase (PK) deficiency associated with hereditary nonspherocytic hemolytic anemia. A Nepalese PK variant, PK Kowloon, was found to have a homozygous transversion at the 5'-splice site of the seventh intervening sequence (IVS) of the L-type PK gene (Ivs7[+1]gt --> tt). Using a reverse transcription polymerase chain reaction (RT-PCR) assay, we showed that the R-type PK mRNA in the proband's reticulocytes included the seventh IVS between the seventh and eighth exon, introducing a stop codon 3 nucleotides downstream of the mutated site. Consequently, the translational product may lack 44% of the R-PK polypeptide. A transition at the last nucleotide of exon 9 (1269GCG --> GCA) was found in a Japanese PK variant, PK 'Kamata.' The mutation did not alter the amino acid sequence, but caused skipping of the ninth exonic sequence in the R-PK transcripts. As a result, the affected R-type PK lost 51 amino acid residues (373Met-423Ala del). A transversion at the splice acceptor site of the third IVS (Ivs 3[-2]ag --> tg) was identified in PK 'Aomori.' The mutation resulted in aberrant splicing at a cryptic splice site within exon 4, causing deletion of two codons in the aberrant R-PK transcript (95 Gly-96 Pro --> del). Both PK 'Kamata' and PK 'Aomori' had a missense mutation on the other allele, 1044AAG --> AAT (348Lys --> Asn) and 1075CGC --> TGC (359Arg --> Cys), respectively. Although both 348Lys and 359Arg were located in the sixth loop of A domain (beta/alpha)8 barrel, which has been shown to contain the substrate and cation binding sites, the degree of anemia was much more severe in PK 'Kamata' than PK 'Aomori,' possibly because the 51 amino acid deletion of PK 'Kamata' but the 2 amino-acid deletion of PK 'Aomori' may abolish PK catalytic activity.

Anemia, Hemolytic, Congenital Nonspherocytic↗
PubMed1997

Two novel glucose 6-phosphate dehydrogenase deficiency mutations and association of such mutations with F8C/G6PD haplotype in Chinese.

Glucose 6-phosphate dehydrogenase (G6PD) deficiency is a common genetic disease affecting 3% of the total Chinese population in Taiwan. To investigate the molecular basis of this deficiency, we analyzed blood samples from G6PD-deficient newborns using a nonradioactive polymerase chain reaction coupled with single-stranded conformation polymorphism (PCR-SSCP) analysis. We identified two novel G6PD mutations in Chinese. The first, G6PD Miaoli, involved a C-->G substitution at nucleotide (nt) 519, producing a Phe173 to Leu change in the protein. The second mutation (G6PD Keelung) involved a C-->T change at nt 1387, resulting in an Arg463 to Cys substitution. The F8C/G6PD (coagulation factor VIIIc) haplotype that spans the Xq28 region from the gene for coagulation factor VIIIc to the gene for G6PD was also investigated in Chinese using PCR and restriction enzyme digestion. Of the 16 possible haplotypes, only four were found, which suggests that these four polymorphic sites are in strong linkage disequilibrium. Analysis of the association of G6PD mutations with F8C/G6PD haplotype revealed that nt 517, 592, 835, and 1387 mutations are linked to haplotype VI+VII, whereas the nt 519 mutation is linked to haplotype III. The finding that some G6PD mutations are associated with a particular F8C/G6PD haplotype may be useful for future population studies.

Female↗
PubMedDate not supplied

Could the 185delAG BRCA1 mutation be an ancient Jewish mutation?

A predominant mutation within the BRCA1 predisposition gene, 185delAG, has been detected in about 1% of the Ashkenazi population, considered a high-risk group for breast and ovarian cancers. We examined 639 unrelated healthy Jews of Iraqi extraction, a presumed low-risk group, for the existence of this mutation. Three individuals were identified as 185delAG mutation carriers, and haplotype analysis of the Iraqi mutation carriers revealed that 2 of the Iraqis shared a common haplotype with 6 Ashkenazi mutation carriers, and 1 had a haplotype which differed by a single marker. This study suggests that the BRCA1 185delAG mutation also occurs in populations considered at low-risk for breast and ovarian cancers, and that it might have occurred prior to the dispersion of the Jewish people in the Diaspora, at least at the time of Christ.

Adult↗
PubMed1976

Control of mutation frequency by bacteriophage T4 DNA polymerase. II. Accuracy of nucleotide selection by the L88 mutator, CB120 antimutator, and wild type phage T4 DNA polymerases.

The accuracy of nucleotide selection by wild type, L88 mutator, and CB120 antimutator T4 DNA polymerases has been compared by measuring both stable incorporation of complementary and noncomplementary nucleotides into polymer and the DNA-dependent conversion of deoxynucleoside triphosphate to monophosphate. The increased accuracy of the CB120 antimutator enzyme is shown by a ratio of utilization of incorrect to correct nucleotides with poly(dA)-poly(dT) as template which is only 10 to 30% of that of the wild type enzyme. In contrast, the ratio of incorrect to correct nucleotide utilized by the L88 mutator enzyme with this template was higher than that of the wild type enzyme, in agreement with the report of Hershfield (Hershfield, M.S. (1973) J. Biol, Chem. 248, 1417-1423). The antimutator, mutator, and wild type enzymes each have a much higher apparent Km for the noncomplementary nucleotides than for complementary nucleotides with this template. The L88 mutator polymerase has a higher "Km" for poly(dA)-poly(dT) than the wild type enzyme in reactions with both complementary and noncomplementary nucleotides. The antimutator polymerase has an elevated "Km" for polymer only for reactions with noncomplementary nucleotides. The wild type and L88 mutator enzymes also utilized both noncomplementary nucleotides much more frequently than the CB120 antimutator enzymes with poly [d(A-T)] as the template-primer. The T4 gene 32DNA unwinding protein appears to facilitate the correct reading of this template since it decreases the ratio of incorrect nucleotides utilized by both the wild type and L88 mutator polymerases.

Coliphages↗
PubMed1998

Application of the restriction site mutation technique to N-methyl-N-nitrosourea-induced mutations in the rat.

The restriction site mutation (RSM) assay was developed in this laboratory for the detection of point mutations that occur within restriction endonuclease recognition sequences in the genomic DNA of the rat. Mutations were detected and identified in a number of tissues from N-methyl-N-nitrosourea (MNU)-treated rats. Resistant restriction enzyme products were detected in 5 of the 13 restriction endonuclease recognition sequences tested (NcoI, BslI, CfoI, DdeI, and HindIII). These mutations were detected in the p53 tumor suppressor gene and the H-ras protooncogene. No resistant RSM products were detected in any of the samples taken from untreated animals. The MNU-induced mutations were identified as G to A and A to G transitions. Our results describe the first successful application of the RSM assay in detecting induced mutations in the rat and highlight the usefulness of the RSM assay in the analysis of mutagen-induced base changes without the requirement for selection of a mutant phenotype. Given the increasing use of the rat as an animal model in genotoxicity studies, the development of such tests is essential for future genotoxicity investigations.

Animals↗
PubMed1999

Steroid 21-hydroxylase deficiency: mutational spectrum in Denmark, three novel mutations, and in vitro expression analysis.

We have investigated 68 unrelated 21-hydroxylase deficient Danish patients, representing 136 alleles, and determined the mutational spectrum of the CYP21 gene. The most frequent mutations detected were deletion of CYP21 and the splice mutation in intron 2 (I2-splice). Segregation analysis showed evidence of a de novo mutation in each of two patients. Three novel mutations were detected: G64E in exon 1, Q262X in exon 7, and A362V in exon 8. G64E and A362V were introduced in the CYP21 cDNA by in vitro site-directed mutagenesis, and the two corresponding proteins were transiently expressed in COS-7 cells. The activity of 21-hydroxylase was determined using the two hormone substrates 17-hydroxyprogesterone and progesterone. The analysis showed no enzyme activity for any of the substrates, a result that correlates well with the severity of the patients' disease.

Adrenal Hyperplasia, Congenital↗
PubMed2002

Mitochondrial DNA somatic mutations (point mutations and large deletions) and mitochondrial DNA variants in human thyroid pathology: a study with emphasis on Hürthle cell tumors.

In an attempt to progress in the understanding of the relationship of mitochondrial DNA (mtDNA) alterations and thyroid tumorigenesis, we studied the mtDNA in 79 benign and malignant tumors (43 Hürthle and 36 non-Hürthle cell neoplasms) and respective normal parenchyma. The mtDNA common deletion (CD) was evaluated by semiquantitative polymerase chain reaction. Somatic point mutations and sequence variants of mtDNA were searched for in 66 tumors (59 patients) and adjacent parenchyma by direct sequencing of 70% of the mitochondrial genome (including all of the 13 OXPHOS system genes). We detected 57 somatic mutations, mostly transitions, in 34 tumors and 253 sequence variants in 59 patients. Follicular and papillary carcinomas carried a significantly higher prevalence of non-silent point mutations of complex I genes than adenomas. We also detected a significantly higher prevalence of complex I and complex IV sequence variants in the normal parenchyma adjacent to the malignant tumors. Every Hürthle cell tumor displayed a relatively high percentage (up to 16%) of mtDNA CD independently of the lesion's histotype. The percentage of deleted mtDNA molecules was significantly higher in tumors with D-loop mutations than in mtDNA stable tumors. Sequence variants of the ATPase 6 gene, one of the complex V genes thought to play a role in mtDNA maintenance and integrity in yeast, were significantly more prevalent in patients with Hürthle cell tumors than in patients with non-Hürthle cell neoplasms. We conclude that mtDNA variants and mtDNA somatic mutations of complex I and complex IV genes seem to be involved in thyroid tumorigenesis. Germline polymorphisms of the ATPase 6 gene are associated with the occurrence of mtDNA CD, the hallmark of Hürthle cell tumors.

Adenoma, Oxyphilic↗
PubMed2004

Detection of point mutation and insertion mutations in DNA using a quartz crystal microbalance and MutS, a mismatch binding protein.

MutS protein is a mismatch binding protein that recognizes mispaired and unpaired base(s) in DNA. In this study, we incorporate the MutS protein-based mutation recognition into quartz crystal microbalance (QCM) measurements for DNA single-base substitution mutation and 1-4 base(s) insertion (or deletion) mutation detection. The method involves the immobilization of single-stranded probe DNA on a QCM surface, the hybridization of target DNA to form homoduplex or heteroduplex DNA, and finally the application of MutS protein for the mutation recognition. By measuring the MutS binding signal, DNA containing a T:G mismatch or unpaired base(s) is(are) discriminated against perfectly matched DNA at target concentrations ranging from 1nM to 5 microM. Furthermore, the QCM damping behavior upon MutS-DNA complex formation is studied using a Network Analyzer. The measured motional resistance changes per coupled MutS unit mass (deltaR/deltaf) are found to be indicative of the viscoelastic or structural properties of the bound protein, corresponding to different binding mechanisms. In addition, the deltaR/deltaf values vary remarkably when the MutS protein binds at different distances away from the QCM surface. Thus, these values can be used as a "fingerprint" for MutS mismatch recognition and also used to quantitatively locate the mutation site.

Adenosine Triphosphatases↗
PubMed2000

Mutation detection in 65 families with a possible diagnosis of ornithine carbamoyltransferase deficiency including 14 novel mutations.

The high new mutation rate and the wide spectrum of mutations found in patients with ornithine carbamoyltransferase (OCT) deficiency means that direct mutation analysis is essential for providing accurate carrier detection and prenatal diagnosis in affected families. We present our strategy for mutation detection in the OCT gene and summarize the results from 31 families with a confirmed diagnosis and 34 families with a suspected diagnosis of OCT deficiency, and describe 14 previously unreported mutations.

Alternative Splicing↗
PubMed2002

Mutation analysis of thyroid peroxidase gene in Chinese patients with total iodide organification defect: identification of five novel mutations.

Total iodide organification defect (TIOD), where the iodide in the thyroid gland cannot be oxidized and/or bound to the protein, is caused by a defect in the thyroid peroxidase (TPO) gene. Single strand conformation polymorphism analysis was used to screen for mutations in the TPO gene from five unrelated TIOD patients in Taiwan, and five novel mutations were detected. Three of these were frameshift mutations: a single T insertion between nucleotide position 2268 and 2269 (c.2268-2269 insT) in exon 13 and two single C deletions at nucleotide positions 843 (c.843 delC) and 2413 (c.2413 delC) in exon 8 and 14 respectively. The other two were single nucleotide substitutions (c.G1477>A and c.G2386>T) located in exons 9 and 13 respectively. While the former would result in amino acid substitution (Gly493Ser) in the highly conserved region of the TPO polypeptide, the latter would result in either amino acid substitution (Asp796Tyr) or alternative splicing. Of those identified TPO mutations, c.2268-2269 insT was most prevalent and was detected as heterozygous in all but one TIOD patients. All five TIOD patients investigated in this study were compound heterozygous. The method presented in this study could be used for carrier assessment and mutation analysis of newly identified TIOD patients.

Amino Acid Sequence↗