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PubMed2005

Mutation analysis of BRCA1 and BRCA2 genes in Iranian high risk breast cancer families.

PURPOSE: Germline mutations in either BRCA1 or BRCA2 genes are responsible for the majority of hereditary breast and ovarian cancers. At present, over thousand distinct BRCA1 and BRCA2 mutations have been identified. Specific mutations are found to be common within particular populations, resulting from genetic founder effects. To investigate the contribution of germline mutations in these two genes to inherited breast cancer in Iran, we performed BRCA1/BRCA2 mutation analyses in ten Iranian high risk breast cancer families. This is the first study analysing the complete coding sequences of both genes that concerns the Iranian population. METHODS: BRCA1/BRCA2 mutation detection included sequencing of the coding and the 3' and 5' untranslated regions. To detect large genomic rearrangements in the BRCA1 gene semi-quantitative multiplex PCR was performed. RESULTS: Two pathogenic mutations in the BRCA2 gene were detected: a novel deletion c.4415_4418delAGAA and a previously described insertion c.6033_6034insGT. In addition, one intronic variation g.5075-53C > T and a deletion/insertion g.*381_389del9ins29 in the 3' untranslated region of BRCA1 were found in two of the investigated families. Both sequence alterations were absent in an age matched Iranian control group. The BRCA2 homozygous variation p.N372H, previously associated with an increased risk for developing breast cancer, was not identified in this study. We did not detect large genomic rearrangements in BRCA1 in patients tested negatively for disease causing mutations in both genes by standard sequencing. CONCLUSIONS: At present, the BRCA2 mutations c.4415_4418delAGAA and c.6033_6034insGT have not been identified in any investigated population except the Iranian. Whether both mutations are specific for the Iranian population or a special subgroup remains to be investigated in larger studies. The absence of BRCA1 mutations in the analysed families may suggest that penetrance or prevalence of BRCA1 mutations may be lower in Iran.

Adult↗

PubMed2005

Mutational analysis of the BRAF gene in human congenital and dysplastic melanocytic naevi.

Eighteen congenital melanocytic naevi (CMN) from 17 patients and 18 dysplastic melanocytic naevi (DMN) from 18 patients were screened for mutations in the BRAF oncogene (present study) and the N-ras oncogene (in the course of two foregoing studies) by single-strand conformational polymorphism (SSCP)/sequencing analysis. BRAF mutations were demonstrated in both types of lesion. As a whole, 17 of 18 CMN (94.4%) and five of 18 DMN (27.7%) harboured either BRAF or N-ras mutations. As the BRAF oncogene is frequently found to be mutated in human cutaneous melanomas, it may constitute a risk factor for melanoma formation within CMN and DMN.

Adolescent↗

PubMed2001

Mutation analysis of codons 345 and 347 of rhodopsin gene in Indian retinitis pigmentosa patients.

More than 100 mutations have been reported till date in the rhodopsin gene in patients with retinitis pigmentosa. The present study was undertaken to detect the reported rhodopsin gene point mutations in Indian retinitis pigmentosa patients. We looked for presence or absence of codon 345 and 347 mutations in exon 5 of the gene using the technique of allele-specific polymerase chain reaction by designing primers for each mutation. We have examined 100 patients from 76 families irrespective of genetic categories. Surprisingly, in our sample the very widely reported highly frequent mutations of codon 347 (P --> S/A/R/Q/L/T) were absent while the codon 345 mutation V --> M was seen in three cases in one family (autosomal dominant form) and in one sporadic case (total two families). This is the first report on codon 345 and 347 mutation in Indian retinitis pigmentosa subjects.

Apoptosis↗

PubMed1997

Mutational analysis of MLH1 and MSH2 in 25 prospectively-acquired RER+ endometrial cancers.

Mutations in the DNA mismatch repair (MMR) genes MLH1 and MSH2 have been linked to several human cancers which display the replication error (RER) phenotype. Germline mutations in these two genes have been implicated in about 90% of families with hereditary nonpolyposis colorectal cancer (HNPCC). A significant proportion of endometrial cancers, the second most common malignancy of the HNPCC syndrome, also exhibit RER. We screened 125 primary endometrial adenocarcinomas with seven microsatellite markers and identified 25 specimens with RER (20%). We used single-strand conformation variant analysis to search for mutations in MLH1 and MSH2. Direct sequencing of variants revealed only one germline mutation in MLH1 and a single somatic mutation in MSH2. However, six previously unreported sequence polymorphisms in MLH1 were identified. Four of these polymorphisms show clear population-based differences in allele frequency. In addition, a highly informative marker for MLH1 was characterized. The low frequency of mutations in MLH1 and MSH2 in this large series of cancers suggests that other MMR genes are responsible for the RER phenotype in endometrial cancers.

Adaptor Proteins, Signal Transducing↗

PubMed2000

Mutational analysis of beta-thalassemia cases from the Aegean region of Turkey using an allele-specific oligonucleotide hybridization technique.

The aim of the present study was to evaluate the point mutations of beta-thalassemia patients from the Aegean region of Turkey by using an allele-specific oligonucleotide hybridization technique. DNA isolated from peripheral blood samples of 75 children with beta-thalassemia major or intermedia was analyzed using a Bio-Rad mD(x)(TM)-Be Tha Gene 1 kit. We determined mutations in 56 (74.6%) patients. The allelic frequency of mutations in 150 chromosomes was as follows: IVS-I-110 (G-A) 44.1%, IVS-I-1 (G-A) 28.2%, IVS-I-6 (T-C) 13.3%, IVS-II-745 (C-G) 9.3%, IVS-II-1 (G-A) 2.7%, Cd 39 (C-T) 2.4%, -87 (C-G) 0% and Cd 6 (-A) 0%. The distribution of the mutation types was consistent with the findings of other research groups.

Alleles↗

PubMed2001

Mutational analysis of the RET and GDNF gene in children with hypoganglionosis.

Germline mutations of the RET (10q11.2) have been reported in Hirschsprung's disease (HSCR) at a rate of 15-45%. Recently, the glial cell line-derived neurotrophic factor (GDNF) was identified as one of the ligands of the RET, and GDNF (5p12-p13.1) mutations were also found in association with RET mutations in HSCR patients. We analysed the DNA sequence of RET and the GDNF of patients with hypoganglionosis. We investigated the germline mutation in 5 patients histologically diagnosed with hypoganglionosis. DNAs were extracted from peripheral blood lymphocytes of these patients. The PCR primers were designed for RET tyrosine kinase domain (exon 13-17) and GDNF (exon 1-2). The DNA sequence was determined using a direct DyeDeoxy Terminator Cycle method. The analysis of RET showed silent mutation at the codon 769 (CTT-->CTG) by DNA polymorphism in all patients. No other mutation of the RET or GDNF was evident. These results suggest that the RET or GDNF may not contribute to the pathogenesis of hypoganglionosis, which is suspected to be genetically different from HSCR.

Child↗

PubMed1994

Mutation analysis of 19 North American mucopolysaccharidosis type I patients: identification of two additional frequent mutations.

Mucopolysaccharidosis type I (MPS I) is an autosomal recessive genetic disorder caused by deficiency of the lysosomal glycosidase alpha-L-iduronidase. Patients with this disorder present with varied clinical phenotypes ranging from early severe onset of disease and death in early childhood to mild manifestations compatible with adult life. An understanding of the molecular basis of iduronidase deficiency and its correlation to clinical phenotype will improve prognostic prediction at diagnosis, aid in genetic counselling of families, and provide a framework to more accurately assess experimental treatment protocols. We have used the approach of single-strand conformational polymorphism analysis and direct sequencing of the alpha-L-iduronidase gene in an attempt to define the molecular basis of iduronidase deficiency in affected individuals. An initial series of 19 patients representing 35 independently segregating mutant alleles were studied. In addition to five previously identified mutations (W402X, Q70X, E274X, H82P, and P533R) two novel mutations (A75T and 474-2a-->g) were found. These seven mutations account for 71% of the mutant alleles and 53% of the genotypes in this group of patients. Analysis of a larger independently ascertained group of 103 MPS I patients, mainly of Northern European origin, revealed that together the two novel mutations account for 7% of mutant alleles and are associated with severe clinical phenotypes. These mutations are the most frequent MPS I mutations detected so far after W402X and Q70X. With the definition of these two mutations, a clear picture of the molecular heterogeneity of MPS I is emerging.

Amino Acid Sequence↗

PubMed2004

[Mutational analysis of the vhl gene in the sporadic renal cell carcinoma].

OBJECTIVES: To assess and characterize mutations in the vhl gene in tumor tissue samples from 30 patients undergoing surgery for renal cell carcinoma in our department. METHODS: Descriptive, observational and analytical study of 30 patients undergoing surgery for RCC, analyzing the vhl gene sequence in tumor tissue, and using healthy renal tissue from the same patients as controls. Tissues were processed by DNA extraction, PCR amplification of the three exons that conform the gene, and ulterior automatic sequence analysis of the amplified exons between intronic primers previously designed. The sequence is compared with the corresponding exons included in the GeneBank. Alterations were checked by backwards sequence analysis. RESULTS: 9 mutations (30%) were found in the tumoral samples analyzed. 7 of them were punctual (one of them intronic); the other two were deletions. Mutations were distributed among the three exons: 3 in exon 1, 4 in exon 2, 1 in exon 3 and 1 intronic. One of the samples showed 2 mutations. Control tissue was free of mutations. CONCLUSIONS: Sporadic RCC shows mutations in the vhl gene which mainly appear in the clear cell subtype. Such alterations result in severe disturbances in the protein, disturbing its tumor suppressing function.

Adult↗

PubMedDate not supplied

[Mutation analysis of functional role of amino acid residues in domain IV of elongation factor G].

Seven variants of elongation factor G (EF-G) from Thermus thermophilus with mutations Glu494Ile, Gly495Asp, Lys496Ile, His509Leu, Lys564Ile and Tyr568Lys located in the beta-sheet of its domain IV and mutation Gly553Asp in a loop between domain III and IV were constructed using polymerase chain reaction. Functional tests demonstrated that only mutation Lys496Ile, located in the vicinity of the loop 501-504, inhibits translocation effectiveness, in the presence of the mutated EF-G. The functional analysis of all mutations constructed up to now in domain IV reveals that only those located in loops 501-504 and 573-578 markedly decrease the translocation activity of EF-G. These loops are located at the tip of domain IV and close to the decoding center of the 30S ribosomal subunit upon EF-G interaction with the ribosome. The functional role of EF-G and its domain IV in ribosomal translocation is discussed.

Amino Acid Substitution↗

PubMed1998

Mutation analysis of the 6-pyruvoyl-tetrahydropterin synthase gene in Chinese hyperphenylalaninemia caused by tetrahydrobiopterin synthesis deficiency.

Hyperphenylalaninemia (HPA) may be caused by deficiency of phenylalanine hydroxylase or tetrahydrobiopterin (BH4), the essential cofactor for the aromatic amino acid hydroxylases. 6-Pyruvoyl-tetrahydropterin synthase (PTPS) deficiency is a major cause of BH4 deficient HPA. In this study, seven single base mutations at nucleotides 73 (C>G), 155 (A>G), 166 (G>A), 209 (T>A), 259 (C>T), 286 (G>A), and 317 (C>T) on PTPS cDNA were detected in Chinese PTPS-deficient HPA by polymerase chain reaction and solid phase DNA sequencing. These nucleotide alterations result in R25G, N52S, V56M, V70D, P87S, D96N, and T106M amino acid substitutions, respectively. The R25G, V56M, V70D, and T106M were novel mutations found in PTPS gene. By analysis of 38 PTPS mutant alleles from 19 unrelated Chinese PTPS-deficient HPA families, the allele frequency of these mutations in Chinese PTPS-deficient HPA were determined to be approximately 5.3% (R25G), 34.2% (N52S), 7.9% (V56M), 2.6% (V70D), 36.8% (P87S), 7.9% (D96N), and 2.6% (T106M), respectively. Two common mutations, N52S and P87S, were found to account for 71% of the Chinese PTPS mutant alleles. The N52S mutation accounts for 48% of the southern Chinese PTPS mutation, but only one (9%) of the northern Chinese PTPS mutant allele was found to be N52S, which suggested that the N52S mutation might be southern Chinese. Clinically, the V56M mutation was found to associate with the mild form of PTPS deficiency. However, the R25G, N52S, P87S, and D96N were found mainly in the patients with severe clinical symptom. Using polymerase chain reaction-based mutation analysis, a fetus at risk of PTPS deficiency was diagnosed prenatally to be a carrier of N52S mutation.

Alcohol Oxidoreductases↗

PubMed2001

Mutational analysis of immunoglobulin germline derived Vlambda4B light chains in rheumatoid arthritis.

OBJECTIVE: We investigated the somatic mutational pattern of a specific Vlambda light chain variable region (V) gene in rheumatoid arthritis (RA) patients. The Vlambda4B light chain was chosen because of its location on the lambda locus and because of its previously observed use in IgM rheumatoid factors. METHODS: We sequenced 13 different mRNA transcripts of Vlambda4B from the synovium of three different RA patients. These were compared to 31 identifiable Vlambda4B sequences from GenBank, which were obtained from the PBL of patients without RA. RESULTS: A subset of Vlambda4B had a high rate of mutation, especially in the framework regions within the RA synovium. Furthermore, a set of codons within the first complementary determining region of Vlambda4B displayed frequent replacement mutations but did not possess any silent mutations. CONCLUSION: The hypermutation of RA synovial-derived Vlambda4B sequences, especially in the framework areas, may contribute to or may be the result of altered mutational mechanisms and/or prolonged B cell life.

Aged↗

PubMed2014

Single cell mutational analysis of PIK3CA in circulating tumor cells and metastases in breast cancer reveals heterogeneity, discordance, and mutation persistence in cultured disseminated tumor cells from bone marrow.

BACKGROUND: Therapeutic decisions in cancer are generally guided by molecular biomarkers or, for some newer therapeutics, primary tumor genotype. However, because biomarkers or genotypes may change as new metastases emerge, circulating tumor cells (CTCs) from blood are being investigated for a role in guiding real-time drug selection during disease progression, expecting that CTCs will comprehensively represent the full spectrum of genomic changes in metastases. However, information is limited regarding mutational heterogeneity among CTCs and metastases in breast cancer as discerned by single cell analysis. The presence of disseminated tumor cells (DTCs) in bone marrow also carry prognostic significance in breast cancer, but with variability between CTC and DTC detection. Here we analyze a series of single tumor cells, CTCs, and DTCs for PIK3CA mutations and report CTC and corresponding metastatic genotypes. METHODS: We used the MagSweeper, an immunomagnetic separation device, to capture live single tumor cells from breast cancer patients' primary and metastatic tissues, blood, and bone marrow. Single cells were screened for mutations in exons 9 and 20 of the PIK3CA gene. Captured DTCs grown in cell culture were also sequenced for PIK3CA mutations. RESULTS: Among 242 individual tumor cells isolated from 17 patients and tested for mutations, 48 mutated tumor cells were identified in three patients. Single cell analyses revealed mutational heterogeneity among CTCs and tumor cells in tissues. In a patient followed serially, there was mutational discordance between CTCs, DTCs, and metastases, and among CTCs isolated at different time points. DTCs from this patient propagated in vitro contained a PIK3CA mutation, which was maintained despite morphological changes during 21 days of cell culture. CONCLUSIONS: Single cell analysis of CTCs can demonstrate genotypic heterogeneity, changes over time, and discordance from DTCs and distant metastases. We present a cautionary case showing that CTCs from any single blood draw do not always reflect metastatic genotype, and that CTC and DTC analyses may provide independent clinical information. Isolated DTCs remain viable and can be propagated in culture while maintaining their original mutational status, potentially serving as a future resource for investigating new drug therapies.

Bone Marrow↗

PubMed2002

Prenatal diagnosis of a lethal form of Netherton syndrome by SPINK5 mutation analysis.

Netherton syndrome (NS) is a severe autosomal recessive ichthyosis with no specific treatment or prenatal diagnosis available at present. The recent identification of SPINK5, which encodes a serine protease inhibitor, as the defective gene enables DNA based prenatal diagnosis to be carried out. Here we report the first direct molecular prenatal diagnosis of a lethal form due to a recurrent SPINK5 mutation in three consanguineous Turkish families. XmnI restriction enzyme digestion and DNA sequencing demonstrated that each deceased affected child was homozygous for mutation 153delT inherited from each parent. Analysis of fetal DNA from amniotic fluid cells in Family 1 and from a chorionic villus sampling in Family 3 showed that the fetus was heterozygous for 153delT in both cases. The pregnancies were carried to term and the newborns were unaffected. In Family 2, fetal DNA analysis from chorionic villus biopsy showed in a first pregnancy that the fetus was homozygous for 153delT. The pregnancy was terminated at 13 weeks and DNA analysis of fetal keratinocytes confirmed the prenatal prediction. In a second pregnancy in Family 2, fetal DNA analysis showed heterozygosity for 153delT, and the pregnancy was continued. Direct SPINK5 mutation analysis in families at risk for NS represents the first early, rapid and reliable method for prenatal diagnosis of this life threatening form of ichthyosis.

Amniocentesis↗

PubMed2007

Distal RTA with nerve deafness: clinical spectrum and mutational analysis in five children.

Distal renal tubular acidosis (RTA) with nerve deafness is caused by mutations in the ATP6V1B1 gene causing defective function of the H+ -ATPase proton pump. We report five acidotic children (four males) from four unrelated families: blood pH 7.21-7.33, serum bicarbonate 10.8-14.7 mEq/l, minimum urinary pH 6.5-7.1 and fractional excretion of bicarbonate in the presence of normal bicarbonatemia 1.1-5.7%. Growth retardation and nephrocalcinosis, but not hypercalciuria, were common presenting manifestations. Hearing was normally preserved in one of the patients whose sister was severely deaf. One child was homozygous for a known mutation in exon 1: C>T (R31X). Three children were homozygous for a splicing mutation, intron 6 + 1G>A. The other patient was a compound heterozygote, having this mutation and a previously unreported mutation in exon 10: G>A (E330K). Our report shows that hearing loss is not always present in the syndrome of distal renal tubular acidosis with nerve deafness and the absence of hypercalciuria at diagnosis and describes a new mutation responsible for the disease in the ATP6V1B1 gene.

Acidosis, Renal Tubular↗

PubMed2000

Germ-line mutation analysis in patients with von Hippel-Lindau disease in Japan: an extended study of 77 families.

We have previously reported on the analysis of germ-line mutations in Japanese von Hippel-Lindau disease (VHL) patients and found mutations in 26 families. We have now extended these studies to include an additional 41 VHL families. Germ-line mutation of the VHL gene was screened by DNA-SSCP, direct sequencing, and Southern blot analysis. To summarize all of the data we have studied in this and our previous report, germ-line mutations have been detected in 55 of 77 (73%) (type 1: 41/62 (66%) and type 2: 14/15 (93%)) families. We found similarities in the nature of germ-line mutations including mutational incidence, location, and DNA substitution patterns between Japanese and Western VHL. These similarities may reflect the predominance of endogenous mutational processes. We also found several interesting characteristics in Japanese VHL. Twenty of 41 (49%) intragenic mutations were unique and not reported in the Western VHL. Four mutations (Arg113Stop, Gln132Stop, Leu158Val, and Cys162Tyr) previously characterized as type 1 mutations were identified in the type 2 (with pheochromocytoma) Japanese families. Genotype-phenotype correlation study suggested non-missense mutations predicted to result in the loss of VHL function were associated with the occurrence of renal cell carcinoma, as in sporadic tumors. Our data add to the diversity of VHL germ-line mutations and provide a better understanding of VHL disease in terms of both clinical management and molecular pathogenesis.

Genotype↗

PubMed2006

Mutation analysis in Irish families with glomuvenous malformations.

BACKGROUND: Glomuvenous malformations (GVMs) are rare bluish lesions that can affect the skin and mucosal surfaces. They represent defects in vasculogenesis. Lesions can occur sporadically or in an autosomal dominant mode of inheritance. Recent studies have shown that mutations in the glomulin gene (GLMN) on chromosome 1p21-22 are responsible for familial GVMs. OBJECTIVES: To search for mutations in GLMN in Irish families with GVMs. METHODS: We identified four Irish families with GVMs and confirmed linkage to chromosome 1p21-22 in these cases. We sequenced the glomulin gene in all affected and unaffected members of the families. Results Linkage analysis showed that affected individuals from the families shared a common haplotype. Mutation analysis revealed a delAAGAA mutation in exon 3 of the glomulin gene in all four families with GVMs. CONCLUSIONS: We confirm that mutations in the glomulin gene are responsible for GVMs and suggest a founder Irish mutation in the glomulin gene in four Irish families.

Adaptor Proteins, Signal Transducing↗

PubMed1999

Mutation analysis of BRCA1 and BRCA2 in Turkish cancer families: a novel mutation BRCA2 3414del4 found in male breast cancer.

Since the identification of the BRCA1 and BRCA2 breast-ovarian cancer susceptibility genes, mutation analyses have been carried out in different populations. Here we screened 15 Turkish breast and breast-ovarian cancer families for mutations in both genes by conformation-sensitive gel electrophoresis (CSGE) and the protein truncation test (PTT), followed by DNA sequencing. Three families included a male breast cancer case, one without family history. Three germline mutations were identified, two in BRCA1 and one in BRCA2. The two BRCA1 mutations, 5382insC and 5622C-->T, were found in breast-ovarian cancer families. The BRCA2 3414delTCAG is a novel mutation detected in a site-specific breast cancer family that included 1 case of male breast cancer. These first results of Turkish families show that the frequency of germline BRCA1 or BRCA2 mutations appears to be high in families with at least 3 breast and/or ovarian cancer cases.

Age of Onset↗

PubMed2002

BRCA1 and BRCA2 mutation analysis of early-onset and familial breast cancer cases in Mexico.

The entire coding regions of BRCA1 and BRCA2 were screened for mutations by heteroduplex analysis in 51 Mexican breast cancer patients. One BRCA1 and one BRCA2 truncating mutation each was identified in the group of 32 (6%) early-onset breast cancer patients (< or =35 years). Besides these two likely deleterious mutations, eight rare variants of unknown significance, mostly in the BRCA2 gene, were detected in six of 32 (19%) early-onset breast cancer cases and in three of 17 (18%) site-specific breast cancer families, one containing a male breast cancer case. No mutations or rare sequence variants have been identified in two additional families including each an early-onset breast cancer case and an ovarian cancer patient. The two truncating mutations (BRCA1 3857delT; BRCA2 2663-2664insA) and six of the rare variants have never been reported before and may be of country-specific origin. The majority of the alterations appeared to be distinct, with only one of them being observed in more than one family.

Adult↗