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Identification of forty-five novel and twenty-three known NF1 mutations in Chinese patients with neurofibromatosis type 1.

Neurofibromatosis type 1 (NF1), characterized by skin neurofibromas and an excess of café-au-lait spots, is due to mutations in the neurofibromin (NF1) gene. Identifying the genetic defect in individuals with the disease represents a significant challenge because the gene is extremely large with a high incidence of sporadic mutations across the entire gene ranging from single nucleotide substitutes to large deletions. In the present study, we have used a combination of techniques (heteroduplex analysis, sequencing, loss of heterozygosity and quantification of gene dosage) to define the genetic defect in 68 individuals from a cohort of 107 NF1 Taiwanese patients of Chinese origin. Fifty-eight were initially identified using heteroduplex analytical techniques and confirmed by sequence analysis. A further five were identified by direct sequence analysis alone. The reminders were shown to carry large deletions in the NF1 gene by demonstrating loss of heterozygosity that was confirmed by gene dosage measurements using quantitative-PCR techniques. Mis-sense, non-sense, frame-shift or splice-site mutations were identified across the entire gene of which the majority (45/68) were novel in nature. The detection rate with the various analytical techniques and the types of mutation detected are consistent with published data involving both individuals and large cohort studies from other ethnic backgrounds.

Adolescent↗

Temperature-modulated high-performance liquid chromatography for detecting variation in human genome.

Recently, temperature modulated heteroduplex analysis (TMHA) based upon ion-pair reversed-phase high-performance liquid chromatography has been developed as a tool for polymorphisms and novel mutation detection in human genome. This new approach, with increased accuracy and throughput over traditional methods. This new approach is also known as denaturing high performance liquid chromatography(DHPLC). However, the terms of both TMHA and DHPLC should be considered carefully. Firstly, it is DNA molecular that is denatured in high performance liquid chromatography but not the method or the instrument. Secondly, the temperature in the liquid chromatograph is modulated according to Tm (melting temperature) of the DNA fragments. As it is known, Tm is the temperature at which a population of double-stranded nucleic acid molecules becomes half-dissociated into single strands, and under this temperature, half of the DNA molecules is still not denaturing. Thirdly, the targets for detection are both the homoduplexes and the mismatched heteroduplexes, which are double-stranded nucleic acid molecules and are annealing. The term of DHPLC may lead to confusion in annealing and denaturing. In addition, since TMHA can be carried out using gel electrophoresis and HPLC, there is a need to distinguish HPLC from gel electrophoresis. Therefore, we suggest a new term for this technology, which is TmHPLC (temperature-modulated high- performance liquid chromatography). This term not only provides a clear definition for this new method, but also includes both TMHA and HPLC. More importantly, TmHPLC implies that the temperature in HPLC is modulated according to Tm of the DNA fragments. We also review advances in detecting variation through TmHPLC. This new approach leads to significant reduction of sequencing efforts for searching novel mutations and polymorphisms, and because of its high sample throughput, to faster data generation. This implies that TmHPLC is a sensitive, accurate, and cost effective approach to screening sequence variation in human genome.

Chromatography, High Pressure Liquid↗

Molecular diagnosis of analbuminemia: a novel mutation identified in two Amerindian and two Turkish families.

BACKGROUND: Analbuminemia is a rare autosomal recessive disorder in which individuals have little or no circulating albumin, usually the most abundant plasma protein. We describe a new mutation associated with analbuminemia. METHODS: We studied four apparently unrelated patients who had congenital analbuminemia: two of Amerindian and two of Turkish origin. The 14 exons and the flanking intron sequences of the albumin gene were amplified by PCR and screened for mutations by single-strand conformational polymorphism and heteroduplex analysis. The mutated DNA fragments were sequenced directly. RESULTS: In all four cases, analbuminemia was caused by the same mutation, an AT deletion at nucleotides 2430-2431, the 91st and 92nd bases of exon 3. This novel defect, named Kayseri, produces a frameshift leading to a premature stop two codons downstream. The predicted translation product would consist of 54 amino acid residues. CONCLUSIONS: The AT deletion at nucleotides 2430-2431 is a novel mutation associated with analbuminemia.

Albumins↗

Albumin locust valley: a new case of analbuminemia.

OBJECTIVE: To discover and document cases of the rare disease analbuminemia. DESIGN AND METHODS: Blood specimens of a subject were analyzed by routine clinical laboratory procedures, by immunochemical tests for albumin, and by electrophoresis with immunofixation using anti-human serum albumin (HSA). Single-strand conformational polymorphism (SSCP), heteroduplex analysis (HA), and DNA sequencing of the 14 exons of the HSA gene were conducted on DNA from leukocytes. RESULTS: Albumin concentration was 0.003 g/L; serum globulins and cholesterol were elevated. Immunoelectrophoresis showed no trace of albumin in any of the serum components. The coding region plus all mRNA splice sites were normal and mutation-free, and SSCP and HA showed no abnormalities. CONCLUSIONS: Data define a bona fide case of analbuminemia. We suggest that the mutation causing the analbuminemic trait in this subject might involve a remote regulatory element.

Adult↗

Studies of variability in the islet amyloid polypeptide gene in relation to Type 2 diabetes.

AIMS: To explore whether the coding region of the islet amyloid polypeptide (IAPP) gene contains genetic variants associated with Type 2 diabetes and whether a previously reported association of the promoter variant -132g-->a with Type 2 diabetes could be reproduced in Danish Caucasians. METHODS: The coding region was analyzed using single strand conformation polymorphism (SSCP) and heteroduplex analysis in 192 Type 2 diabetic patients. Restriction fragment length polymorphism (RFLP) was employed to screen for the promoter variant in 414 Type 2 diabetic patients and 182 glucose-tolerant control subjects. RESULTS: The SSCP analysis identified an IVS+75a-->g variant in two patients. The frequency of heterozygous carriers of the promoter variant in the case-control study was 4.1% (17/414) and 7.1% (13/182), respectively. Odds ratio of the prevalence of Type 2 diabetes in carriers compared with non-carriers was estimated to be 0.47 (95% confidence interval 0.19, 1.15). CONCLUSION: Neither variability in the coding region of the IAPP gene nor the -132g-->a promoter variant was associated with Type 2 diabetes among the studied Danish Caucasians.

Amyloid↗

Frequency of the codon 807 mutation in the cGMP phosphodiesterase beta-subunit gene in Irish setters and other dog breeds with hereditary retinal degeneration.

Rod-cone dysplasia 1 (rcd1) in Irish setters is caused by a nonsense mutation in the cGMP phosphodiesterase beta-subunit gene (PDE6B). We examined the frequency of the mutant allele in the Irish setter population and determined if the defect is present in dogs of other breeds which are affected with other inherited photoreceptor diseases. Between 1994 and 1997, samples were obtained from 436 clinically normal Irish setters, a red wolf, and dogs from 23 different breeds. The mutation in codon 807 of PDE6B was detected in genomic DNA by heteroduplex analysis, allele-specific PCR, or restriction enzyme digestion. Of the 436 samples from clinically normal setters, 34 contained the mutation in one of the two PDE6B alleles (carrier rate = 7.8%). In contrast, the same mutation was not found in the red wolf or dogs of other breeds affected with PRA or inherited photoreceptor diseases. The high percentage of tested carriers, however, is not representative of the number of carriers in the population since some dogs tested were closely related and did not represent a random sample of the Irish setter breed.

3',5'-Cyclic-GMP Phosphodiesterases↗

Loss of heteroplasmy in the displacement loop of brain mitochondrial DNA in astrocytic tumors.

The aim of this study was the determination of D-loop heteroplasmy in astrocytic brain tumors. DNA fragments corresponding to the hypervariable region 2 of the mitochondrial displacement loop (D-loop) from 12 astrocytic tumors and 2 corresponding brain samples were cloned into a plasmid vector. Heteroduplex analysis revealed high sequence variability in the brain samples and a subfraction of grade 2 and grade 3 tumors. Furthermore, the results were suggestive of a very low degree of heteroplasmy in all glioblastomas. This was confirmed by direct sequencing of 223 cloned DNA samples from nine individuals. Heteroplasmy was caused in most cases by a well-known length polymorphism of a homopolymeric c-tract. Heteroplasmy of the two reference brain samples was lost in the corresponding tumors. Genes Chromosomes Cancer 26:80-83, 1999.

Adult↗

Identification of novel mutations in Arabs with cystic fibrosis and their impact on the cystic fibrosis transmembrane regulator mutation detection rate in Arab populations.

UNLABELLED: The cystic fibrosis transmembrane regulator (CFTR) gene in Arab patients with cystic fibrosis (CF) (sweat chloride > 60 mmol/l) from 61 unrelated families was screened for mutations in exons 3, 4, 5, 7, 10, 11, 16 and 19 and for mutations W1282X, N1303K and 3,849 + 10kbC --> T. Eight novel mutations were identified. These are: in exon 4: a) 425del42 (an in-frame 42 bp deletion that removes 14 amino acids and causes Gln98 --> His at the point of deletion), b) 475G --> T (Glu115 --> Stop) and c) 548A --> T (His139 --> Leu); in intron 5,711 + 1G --> A (splice site mutation); in exon 10, 1548delG (deletion of a "G" nucleotide causing a frameshift mutation that alters the amino acid sequence at residue 473 and results in translation termination at residue 526); in exon 11, a) 1729T --> C (Ph533E --> Leu) and b) 1,811 + 2 (splice site mutation) and finally in exon 19,3361A --> T (Lys1177 --> Stop). All mutations were detected by heteroduplex analysis and identified by sequencing. Of more than 850 known CFTR mutations, only 9 were encountered. The comparative frequencies of the most common mutations are: 1548delG> 1123V = deltaF508 = 3,120 + 1G --> A > H139L. Screening for these five mutations identifies 60% of the CF alleles in Arab populations. The novel mutation 1548delG is the most frequent (17%) among Arabs. CONCLUSION: Novel Arab-specific mutations were identified in the CFTR gene underlying cystic fibrosis. As a result of this study, the CFTR mutation detection rate among Arabs with cystic fibrosis is now comparable to that of other populations.

Alleles↗

Tuberous sclerosis type 1: three novel mutations detected in exon 15 by a combination of HDA and TGGE.

Tuberous sclerosis (TSC) is an autosomal dominant disorder which is genetically heterogeneous with two genes, TSC1 and TSC2. TSC1 consists of 23 exons with exon 15 being the largest one comprising 559 bp. Representing 16% of the coding region exon 15 harbors 37% of the already identified point mutations in TSC1. Mutation screening of large DNA fragments as TSC1 exon 15 by SSCP has been a problem because of the low sensitivity of this method without subdivision. Therefore, we simultaneously performed heteroduplex analysis (HDA) and temperature gradient gel electrophoresis (TGGE) which are both more suitable for evaluation of fragments of this size. DNA samples of 159 patients with the clinical diagnosis of TSC were screened and a total of seven different mutations in nine unrelated cases were identified, including the three novel mutations 1754delT, 1836delT and R500Q. Comparing the two methods applied, HDA showed a higher sensitivity in detecting frameshift mutations, while TGGE seemed to be more sensitive for the detection of base exchanges. We conclude that the combination of these two methods is appropriate to reach a high degree of sensitivity for the detection of all types of small mutations in large DNA fragments.

Electrophoresis, Polyacrylamide Gel↗

Early changes in quasispecies repertoire in HIV-infected infants: correlation with disease progression.

The evolution of HIV-1 quasispecies in patients during the first year of life was investigated in 10 vertically infected infants, using heteroduplex analysis of the V3-V5 region of env. Four subjects, who showed little viral evolution during the period of the study, had rapid progression of disease and early loss of CD4(+) cells. The remaining six subjects, who were slow progressors, evolved new viral variants within 6 months, and in one case by 1 month of age. Of the four patients who were PCR positive at birth, one was infected with multiple HIV-1 variants. These results show that in HIV-infected children, multiple variants may initiate infection and early quasispecies diversification is associated with a favorable clinical outcome.

Disease Progression↗

T cell activation by coxsackievirus B4 antigens in type 1 diabetes mellitus: evidence for selective TCR Vbeta usage without superantigenic activity.

Numerous clinical and epidemiological studies link enteroviruses such as the Coxsackie virus group with the autoimmune disease type 1 diabetes mellitus (DM). In addition, there are reports that patients with type 1 DM are characterized by skewing of TCR Vbeta chain selection among peripheral blood and intraislet T lymphocytes. To examine these issues, we analyzed TCR Vbeta chain-specific up-regulation of the early T cell activation marker, CD69, on CD4 T cells after incubation with Coxsackievirus B4 (CVB4) Ags. CD4 T cells bearing the Vbeta chains 2, 7, and 8 were the most frequently activated by CVB4. Up-regulation of CD69 by different TCR families was significantly more frequent in new onset type 1 DM patients (p = 0.04), 100% of whom (n = 8) showed activation of CD4 T cells bearing Vbeta8, compared with 50% of control subjects (n = 8; p = 0.04). T cell proliferation after incubation with CVB4 Ags required live, nonfixed APCs, suggesting that the selective expansion of CD4 T cells with particular Vbeta chains resulted from conventional antigen processing and presentation rather than superantigen activity. Heteroduplex analysis of TCR Vbeta chain usage after CVB4 stimulation indicated a relatively polyclonal, rather than oligo- or monoclonal response to viral Ags. These results provide evidence that new-onset patients with type 1 DM and healthy controls are primed against CVB4, and that CD4 T cell responses to the virus have a selective TCR Vbeta chain usage which is driven by viral Ags rather than a superantigen.

Adult↗

Spectrum of low density lipoprotein receptor mutations in Czech hypercholesterolemic patients.

The aim of our study was to define mutations causing familial hypercholesterolemia (FH) phenotype in Czech hypercholesterolemic individuals. A combination of heteroduplex analysis, SSCP, DGGE, DNA sequencing and PCR/restriction analysis was used for this purpose. Molecular searching in the promoter region and coding sequence of the low density lipoprotein receptor (LDLR) gene in 130 patients from 68 unrelated families resulted in the identification of 37 sequence variations. Thirty of them are most likely disease causing mutations. Nineteen mutations were novel (two nonsense, five missense, six nucleotide(s) insertions and six nucleotide(s) deletions). Their pathological effect can be predicted on the basis of their position with respect to previously reported mutations with an estimated reduction of the receptor activity and/or premature termination of translation. These results expand our knowledge of mutations responsible for FH. Seven nucleotide variations were characterized as silent polymorphisms.

Adult↗

Description of two new cathepsin C gene mutations in patients with Papillon-Lefèvre syndrome.

BACKGROUND: Papillon-Lefèvre syndrome (PLS) is a rare autosomal disorder characterized by severe periodontitis and palmar plantar hyperkeratosis (PPK). PLS is caused by mutations in the cathepsin C (CTSC) gene. Dipeptidyl peptidase I (DPPI) encoded by the CTSC locus removes dipeptides from the amino terminus of the protein substrate and mainly plays an important role in immune and inflammatory processes. Several mutations have been reported in this gene in patients with PLS. This study reports two novel deletion mutation of the CTSC gene in two Indian families with PLS. METHODS: Peripheral blood samples were obtained for genomic DNA isolation from individuals belonging to two Indian families. Exon-specific intronic primers were used to amplify DNA from all individuals, and the PCR products were subsequently sequenced to detect the mutations. Heteroduplex analysis (HDA) was used to confirm heterozygosity and to determine the presence of mutations in control individuals. RESULTS: All patients from both families had a classic PLS phenotype, which included PPK and severe periodontitis. Sequence analysis of the CTSC gene revealed two novel deletion mutations, one (1213-1215delCAT) in exon 7 and the other (629-630delGA) in exon 4 of the CTSC gene. For both mutations, the patients were homozygous, whereas the parents were heterozygous. CONCLUSIONS: This study reports two novel deletion mutations in two Indian families with PLS. One of the mutations introduces a premature stop codon, thereby producing a truncated protein. In the other case, the mutation observed leads to the loss of a highly conserved histidine molecule that is present in the active site of the enzyme. In both cases, mutations may result in a conformation change, causing loss of the enzymatic activity.

Adenine↗

[Study on exons 3 and 4 of alpha-synuclein gene in Chinese familial Parkinson disease patients].

OBJECTIVE: To study the relationship of Chinese familial Parkinson disease with alpha-synuclein gene. METHODS: Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) and polymerase chain reaction-heteroduplex analysis(PCR-HA) were employed to detect the abnormal mobilization in the familial Parkinson disease and sporadic Parkinson disease patients, then it was verified by gene sequencing. RESULTS: No mutation was found in alpha-synuclein gene exons 3 and 4 by PCR-SSCP together with PCR-HA. An inserted c and an inserted t were found in intron 4, position 23 and position 67 respectively. CONCLUSION: (1) Exons 3 and 4 of alpha-synuclein gene are not the mutational hot spots of Chinese familial Parkinson disease. (2) Two polymorphisms were found in intron 4 of alpha-synuclein gene. They are 23 ins c and 67 ins t.

Adult↗

Spectrum of mutations in USH2A in British patients with Usher syndrome type II.

Usher syndrome (USH) is a combination of a progressive pigmentary retinopathy, indistinguishable from retinitis pigmentosa, and some degree of sensorineural hearing loss. USH can be subdivided in Usher type I (USHI), type II (USHII) and type III (USHIII), all of which are inherited as autosomal recessive traits. The three subtypes are genetically heterogeneous, with six loci so far identified for USHI, three for USHII and only one for USHIII. Mutations in a novel gene, USH2A, encoding the protein usherin, have recently been shown to be associated with USHII. The gene encodes a protein with partial sequence homology to both laminin epidermal growth factor and fibronectin motifs. We analysed 35 British and one Pakistani Usher type II families with at least one affected member, for sequence changes in the 20 translated exons of the USH2A gene, using heteroduplex analysis and sequencing. Probable disease-causing mutations in USH2A were identified in 15 of 36 (41.7%) Usher II families. The most frequently encountered mutation (11/15 families or 11/18 mutated alleles) was del2299G in exon 13, resulting in a frameshift and premature stop codon. Other mutations include insertions and point mutations, of which two are previously unreported. Five different polymorphisms were also detected. Our results indicate that mutations in this gene are responsible for disease in a large proportion of British Usher type II patients. Moreover, if screening for mutations in USH2A is considered, it is sensible to screen for the del2299G mutation first.

Chromosome Deletion↗

Different insulin-like 3 (INSL3) gene mutations not associated with human cryptorchidism.

Cryptorchidism is the most frequent congenital anomaly of the urogenital tract in the male, but its etiology is for the most part unknown. Evidence suggests that a possible genetic cause may be involved. Animal models support this hypothesis, and in particular INSL3 (Leydig insulin-like 3 hormone) has been proposed as putative gene for cryptorchidism, since male mice mutant for Insl3 exhibit bilateral abdominal cryptorchidism due to alteration of gubernaculum development. In this study, we analyzed whether mutations in INSL3 could be associated with human cryptorchidism. Heteroduplex analysis and sequencing of both exons of INSL3 in 65 ex-cryptorchid patients and a group of control subjects allowed us to find four nucleotide changes in the sequence of exon I. These mutations are all single base substitutions from G to A at position 27, 96, 126 and 178. Only the 178G-->A substitution changes codon 60 from alanine to threonine (A60T). All mutations were found in comparable distribution in ex-cryptorchid patients and non-cryptorchid men. Therefore, all mutations represent neutral polymorphisms not associated with phenotype. This study confirms previous observations and demonstrates a novel polymorphism in the INSL3 gene. In contrast to that described for the mutant mouse, these data indicate that mutations of INSL3 do not seem to represent a frequent cause of cryptorchidism.

Adult↗

DNA sequence heterogeneity in the three copies of the long 16S-23S rDNA spacer of Enterococcus faecalis isolates.

The possibility of intragenic heterogeneity between copies of the long intergenic (16S-23S rDNA) spacer region (LISR) was investigated by specific amplification of this region from 21 Enterococcus faecalis isolates. Three copies of the LISR (rrnA, B and C) were demonstrated by hybridization of the LISR to genomic DNA cleaved with I-Ceul and SmaI. When the LISR amplicon was digested with Tsp509I, two known nucleotide substitutions were detected, one 4 nt upstream from the 5' end of the tRNA(ala) gene (allele rrnB has the Tsp509I site and rrnA and C do not) and the other 22 nt downstream from the 3' end of the tRNA(ala) gene (rrnC has the Tsp509I site). Sequence differences at these sites were detected at the allelic level (alleles rrnA, B and C) and different combinations of these alleles were designated Tsp Types. Using densitometry to analyse bands from electrophoresis gels, the intra-isolate ratios of the separate alleles (rrnA:rrnB:rrnC) were determined in each Tsp Type: I (0:3:0), II (1:2:0), III (2:0:1), IV (3:0:0), V (2:1:0) and VI (1:1:1). Sequence variation between the three copies of the LISR was confirmed by the detection of at least five other intra-isolate nucleotide substitutions using heteroduplex analysis by conformation-sensitive gel electrophoresis (CSGE) that were not detected by Tsp509I cleavage. Perpendicular denaturing gradient gel electrophoresis was capable of resolving homoduplexes; six to seven out of a possible nine curves were obtained in some isolates. In the isolate where seven curves were obtained one or more further nucleotide substitutions, not detected by Tsp509I cleavage or CSGE, were detected. On the basis of LISR sequence heterogeneity, isolates were categorized into homogeneous (only one allele sequence present) and heterogeneous (two or three allele sequences present). The transition between homogeneous and heterogeneous LISRs may be useful in studying evolutionary mechanisms between E. faecalis isolates.

Base Sequence↗

Germ line BRCA1 and BRCA2 gene mutations in Turkish breast cancer patients.

Germ line BRCA1 and/or BRCA2 mutations were screened in 50 Turkish breast and/or ovarian cancer patients composed of hereditary, familial, early onset and male cancer groups. Genomic DNA samples were tested by heteroduplex analysis and DNA sequencing. Two truncating BRCA2 mutations, one novel (6880 insG) and one previously reported (3034 delAAAC), were found in two out of six (33%) hereditary breast and/or ovarian cancer patients. A novel truncating (1200 insA) and a missense (2080A-->G) BRCA1 mutation was found in two of 27 (7%) individuals in the early onset group. A total of four (8%) disease-causing mutations in 50 breast cancer patients were identified in BRCA1 and BRCA2 genes. In addition, five BRCA1 sequence variants have been identified in 23 patients. These results indicate that BRCA1 and BRCA2 genes are involved in some, but not all, forms of hereditary predisposition to breast cancer in the Turkish population.

Adult↗