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PubMed2000

A novel frameshift mutation (2436insT) produces an immediate stop codon in the autosomal dominant polycystic kidney disease 2 (PKD2) gene.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is a genetically heterogeneous disorder that can be caused by mutations in at least three different genes. Several mutations have been identified in PKD1 and PKD2 genes. Most of the mutations found in PKD2 gene are predicted to cause premature termination of the protein. METHODS: We analysed an Argentinian family characterized previously as PKD2. The PKD2 gene was amplified from genomic DNA using 17 primer pairs and the products were analysed by heteroduplex analysis. PCR products that showed a variation by heteroduplex analysis were sequenced directly. The mutation was confirmed by sequencing relatives. The segregation of the mutation in this family was verified by restriction endonuclease digestion of PCR products obtained from genomic DNA of all family members. Results and conclusions. Here, we report a novel mutation present in an Argentinian family characterized as PKD2 by linkage analysis. The mutation, shared by all affected members of the family, is a thymidine insertion at position 2436 of the gene, which results in a translation frameshift and creates an immediate stop codon. This mutation is expected to lead to a truncated protein that lacks the interacting domain with the PKD1 gene product. The thymidine insertion abolished a Ddel restriction site, allowing a rapid test for detection of PKD2 carriers in the family.

Adult↗

PubMed1996

Heteroduplex generator in analysis of Rh blood group alleles.

We describe the use of heteroduplex analysis to enhance the resolution of different rhesus-derived (Rh) isotypes. Heteroduplex analysis of different domains of the Rh D and Rh CE loci can be performed to diagnose a variety of blood group incompatibilities. One application of this technique is the ability to test for fetal-maternal blood group incompatibilities during pregnancy. Several new serotype-specific sequence variations were discovered in the mapping of the Rh locus, and used in the construction of artificial heteroduplex generators (HGs). HGs facilitate the resolution of the Rh isotypes by electrophoretic methods.

Alleles↗

PubMed1992

Histocompatibility screening by molecular techniques: use of polymerase chain reaction products and heteroduplex formation.

Novel molecular approaches have recently become available allowing improved major histocompatibility complex (MHC) matching of potential allogeneic bone marrow donors and recipients. Current cellular and serological assays are hindered by aberrant cell populations and limited reagents which only detect an individuals' phenotype. Therefore, a molecular screening protocol which discriminates at the genotypic level would be advantageous. Here we describe a two-step DNA-based approach that can be applied to large-scale screening of potential donors. A primary screen, utilizing polymerase chain reaction (PCR), reduces the potential donor population, whereas a secondary or fine resolution screen uses DNA heteroduplex analysis to determine identity or non-identity at specific loci. Heteroduplex analysis generates a DNA migration pattern that is unique for alleles at a given locus, and is more sensitive than serology in discriminating among individuals. Here we demonstrate the potential feasibility of this approach by analyzing results at one MHC locus, HLA-DQ. Since this method does not rely on typing sera or viable lymphocytes, it is not subject to the variability found in the traditional methods. In contrast to traditional methods, these molecular techniques can provide the critical information needed to select a potential bone marrow donor.

Base Sequence↗

PubMed1992

[A case of prenatal diagnosis of beta-thalassemia by polymerase chain reaction].

The prenatal diagnosis of beta-thalassemia in the Udin family, where the parents were the carriers of 2 bp deletion in the codon 8 (-AA) was undertaken using PCR. Five polymorphic restriction endonuclease sites in the beta-globin gene region were tested. They are: 2 HindIII sites in the gamma G and gamma A genes, 2 HincII sites located in the pseudogene and in its 3'-flanking region, and the AvaIII site in the second exon of the beta-globin gene. The heteroduplex analysis was also performed. Two HindIII polymorphic sites were informative and the HincII site in the pseudogene and the AvaII site in the beta-globin gene were partially informative. According to the results of the RFLP analysis, the embryo was heterozygous. The similar result was obtained by heteroduplex analysis.

Base Sequence↗

PubMedDate not supplied

The spectrum of beta-thalassaemia mutations in the Lebanon.

We screened 110 DNA samples from carriers of beta-thalassaemia, using the ARMS-PCR technique with primers for common Mediterranean mutations. Unidentified samples were subjected to a heteroduplex analysis with Universal Heteroduplex Generators covering the beta-globin gene, followed by DNA sequencing. In total, 16 different mutations were detected, the most frequent being IVSI-110 (40%), followed by other common Mediterranean mutations (IVSI-1, IVSII-1, IVSI-6). Other mutations detected were of Lebanese, Turkish, Iranian, Kurdish, Bulgarian and Asian Indian origin. The most heterogeneous religious group seems to be the Sunni Muslims, with 13 mutations, while only 2 mutations were detected among the Christian Maronites. Results from this study are compared with those from other Mediterranean and neighbouring countries.

Community Medicine↗

PubMed2004

Clonal proliferation of T-Cell large granular lymphocytes.

BACKGROUND: T-cell large granular lymphocyte (T-LGL) leukemia is a disorder only rarely reported in children. We diagnosed a new case of a clonal T-LGL proliferation in a 6-year-old girl presenting with severe neutropenia and pure red blood cell aplasia (PRCA). PROCEDURE: Flow cytometric analysis including TCR-Vbeta repertoire analysis and molecular studies using reverse transcriptase polymerase chain reaction (RT-PCR), PCR heteroduplex analysis and GeneScan analysis were performed to investigate the clonal nature of the T-LGL. RESULTS: Flow cytometric analysis revealed a Vbeta3 clonal nature. Molecular studies identified a clonal Vbeta3-Cbeta RT-PCR product. Both PCR heteroduplex analysis and GeneScan analysis found clonal TCRB and TCRG gene rearrangements. CONCLUSIONS: An underlying T-LGL leukemia should be investigated in the diagnostic evaluation of acquired PRCA and neutropenia in young children. Both flow cytometric and molecular analyses can be used to establish the clonal nature of T-LGL.

Child↗

PubMed1998

Mutation analysis of the c-mos proto-oncogene in human ovarian teratomas.

Female transgenic mice lacking a functional c-mos proto-oncogene develop ovarian teratomas, indicating that c-mos may behave as a tumour-suppressor gene for this type of tumour. We have analysed the entire coding region of the c-MOS gene in a series of human ovarian teratomas to determine whether there are any cancer-causing alterations. DNA from twenty teratomas was analysed by single-strand conformational analysis (SSCA) and heteroduplex analysis (HA) to screen for somatic and germline mutations. In nine of these tumours the entire gene was also sequenced. A previously reported polymorphism and a single new sequence variant were identified, neither of which we would predict to be disease-causing alterations. These results suggest that mutations in the coding region of the c-MOS gene do not play a significant role in the genesis of human ovarian teratomas.

DNA Mutational Analysis↗

PubMed1997

CNS tissue Cu/Zn superoxide dismutase (SOD1) mutations in motor neurone disease (MND).

DNA extracted from CNS tissue of 79 cases of motor neurone disease (MND) was screened by single strand conformation analysis (SSCA) and heteroduplex analysis (HA) for mutations in the Cu/Zn superoxide dismutase (SOD1) gene. The aims were to determine whether somatic mutations of SOD1 may underlie some cases of MND and to characterize the genetic abnormalities by sequencing, for subsequent correlation with the molecular pathological phenotype. In 3 cases a point mutation was found in exon 4: E100G in one familial case, and I113T in two cases (one familial, one sporadic). Two cases had previously undescribed mutations in the 3' untranslated region (3'UTR) of SOD1 and one case had a single base substitution in the intronic sequence upstream from exon 2. None of these patients had a positive family history. Non-CNS tissue was available for 3 out of the 6 cases in whom changes were found. In all 3 the same changes were consistently found in both CNS and non-CNS tissue, excluding the presence of somatic mutations in SOD1. We investigated many MND blood samples and normal controls for the presence of the 3'UTR deletions. We found the 4 bp deletion in 1/90 sporadic MND patients and 1/209 non-MND controls. If the 3'UTR deletions are pathogenic, they would have to operate via a loss of the function mechanism, and further work is necessary to define their significance.

Adult↗

PubMed1981

Structure of a naturally occurring plasmid with genes for enterotoxin production and drug resistance.

A physical map of the 117-kilobase conjugative plasmid pCG86 was constructed using electron microscope heteroduplex analysis. This plasmid carries the genes elt, for heat-labile enterotoxin, and estA, for heat-stable enterotoxin, as well as the genes for resistance to tetracycline, streptomycin, sulfonamides, and mercury. These genes were mapped using deletions and Tn5 insertions as physical markers. Analysis of a heteroduplex between pCG86 and a previously described enterotoxin plasmid (EntP307) showed a 48-kilobase region of complete homology which included the genes elt and estA. An 8.8-kilobase BamHI fragment of EntP307 carrying elt, cloned by others, was also shown to be completely homologous with pCG86. The position of elt on the fragment was verified, and it was shown to carry estA as well. A 44-kilobase region of pCG86 showed partial homology with the region of EntP307 previously shown to contain conjugal transfer genes. The gene for tetracycline resistance is carried on a stem-loop structure with the dimensions of Tn10, and the genes for the other drug resistance markers are carried on a 14.6-kilobase segment that forms an insertion loop in heteroduplexes with EntP307. These studies suggest that pCG86 arose either by recombination between an enterotoxin plasmid of incompatibility group FI, like EntP307, and a multiple resistance factor of incompatibility group FII, or by transposition into EntP307 of two transposons.

Cloning, Molecular↗

PubMed2004

Screening of the myelin protein zero gene in patients with Charcot-Marie-Tooth disease.

The myelin protein zero gene (MPZ) coding for the most abundant protein of the peripheral myelin was shown to be mutated in Charcot-Marie-Tooth type 1B disease (CMT1B). Later on MPZ mutations have been shown in axonal type of CMT (CMT2). Recently three novel MPZ gene mutations were reported in congenital hypomyelinating neuropathy (CHN). In contrast to the previously reported studies, focused on CMT1B disease, we aimed to analyze the coding and promoter sequences of the MPZ gene in a group of patients with three CMT phenotypes i.e.: CMT1, CMT2 and CHN. Over 500 PCR products were screened by single strand conformation polymorphism analysis (SSCP) and heteroduplex analysis (HA). In one CMT2 family we founded the E56K mutation in the MPZ gene and in one CHN patient the T124K substitution was detected. In agreement with previously reported studies we conclude that MPZ gene screening should be performed for wide phenotype spectrum of CMT.

Amino Acid Substitution↗

PubMed2006

Characterization of T-cell population in children with prolonged fetal exposure to dexamethasone for anti-Ro/SS-A antibodies associated congenital heart block.

The objectives of the study were to characterize the production, function and survival of T lymphocytes of children with prolonged fetal exposure to dexamethasone for anti-Ro/SS-A antibodies associated congenital complete heart block. The analysis of thymic function, studied by measuring the level of T-cell receptor excision circles, was performed by real time PCR, the composition of T-cell subpopulation was evaluated by flow cytometry and the T-cell diversity was assayed by heteroduplex analysis. T-cell competence was gauged at two functional levels by determining the proliferation and the number of T-cell divisions and by measuring gamma-interferon production after mitogenic stimulation. We observed that the thymic output, distribution of T-cell subsets, thymidine incorporation, number of T-cell divisions, and y-interferon production were comparable to those of age-matched control. On the contrary, heteroduplex analysis demonstrated the presence of both polyclonal and oligoclonal peripheral T-cell repertoires. In conclusion, the analysis of the T-cell compartment in children with prolonged intrauterine exposure to high dose dexamethasone did not disclose any relevant abnormality, except a restriction of T-cell receptor diversity in some patients.

Antibodies, Antinuclear↗

PubMed2000

A proposal for the integration of immunohistochemical staining and DNA-based techniques for the determination of TP53 mutations in human carcinomas.

The p53 protein plays an important role in the control of the cell cycle and DNA repair. Mutations in the TP53 gene may be a prognostic factor for certain forms of human cancer, with specific mutation sites being associated with significantly worse prognosis, particularly for colorectal and breast cancer. Thus, standardization of accurate, rapid, and cost-effective techniques for the detection of TP53 mutations is a high priority. At present, the only widely available technology that reliably detects and defines all mutations is DNA sequencing. However, the routine sequencing of the entire TP53 gene in all breast and colorectal cancer cases in hospital laboratories is prohibitively costly, complex, and time consuming. In order for the analytical power of DNA to be accessed by the routine laboratory, initial screening using immunohistochemistry, which is widely used as a test for detection of accumulated, mutated protein, followed by heteroduplex analysis of exons 4 to 9 to detect frameshift mutations in immunohistochemistry-negative cases, is proposed. To illustrate the effectiveness of this approach, 28 cases of head and neck squamous-cell carcinomas that were known to contain TP53 mutations were retrospectively analyzed. All missense mutations stained positive on immunohistochemistry using the monoclonal antibody DO7, and all insertions and deletions, even those involving a single nucleotide, were positive using an extremely simple heteroduplex analysis. Only rare nonsense mutations were not detected by this strategy. Nevertheless, application of these results to published data suggests that the prescreening would detect 80% of mutations but would result in a 75% reduction in the sequencing load of the laboratory.

Antibodies, Monoclonal↗

PubMed2001

Oligoclonal T cell repertoire in cerebrospinal fluid of patients with inflammatory diseases of the nervous system.

OBJECTIVE: To evaluate the T cell receptor beta chain variable region (TCRBV) gene usage ex vivo in CSF cells and peripheral blood mononuclear cells (PBMCs) collected from patients with autoimmune and inflammatory diseases of the nervous system. METHODS: A novel sensitive seminestedpolymerase chain reaction coupled with heteroduplex analysis was developed. RESULTS: Under these experimental conditions, the minimal number of cells required for the analysis of the whole T cell repertoire was established at 2.5x10(4)-sufficient to evaluate most of the samples collected during diagnostic lumbar punctures. In the 21 patients examined, restrictions in TCRBV gene family usage were not seen. However, using heteroduplex analysis, oligoclonal T cell expansions were found in the CSF of 13 patients and monoclonal expansions in five patients. The T cell abnormalities found did not correlate with intrathecal IgG production or with any clinical variable considered. CONCLUSION: T cell clonal expansions, useful for further characterisation of pathogenetic T cells, can be found during the course of nervous system inflammations, but this abnormality is probably not disease specific.

Adult↗

PubMed2003

Ineffective hematopoiesis linked with a mitochondrial tRNA mutation (G3242A) in a patient with myelodysplastic syndrome.

In a patient with refractory anemia with excess blasts (RAEB), a somatic mutation of mitochondrial transfer RNA(Leu(UUR)) was detected in bone marrow cells. Heteroduplex analysis indicated that 40% to 50% of mitochondrial DNA (mtDNA) molecules in the bone marrow (BM) carried the novel G3242A mutation. The proportion of mutant mtDNA was higher in CD34(+) cells than in the unfractionated sample. Surprisingly, the mutation was not detectable by heteroduplex analysis in the peripheral blood (PB). However, PB CD34(+) cells selected by immunomagnetic beads harbored the mutation with a proportion of approximately 50%. In hematopoietic colony assays, CD34(+) cells from BM and PB yielded only colonies with wild-type mtDNA. These results indicate that the mtDNA mutation in CD34(+) cells was associated with a maturation defect. Mitochondrial tRNA mutations impair mitochondrial protein synthesis, thereby causing dysfunction of the mitochondrial respiratory chain. We propose that this effect contributed to ineffective hematopoiesis in our patient.

Aged↗

PubMed1999

[Cloning the representative strains of China HIV-1 subtypes B, C and E for heteroduplex mobility analysis (HMA)].

OBJECTIVE: To clone the HIV-1 env gene and establish the HMA reagents suitable for use with the Chinese HIV strains. METHODS: Using Nest-PCR technique, we amplified env gene from representative strains which contain the most proximate consensus of China HIV-1 subtypes B, C and E. The genes were then cloned into pGEM-Teasy vector for HMA subtyping. RESULT: The env gene of representative strains of China HIV-1 subtypes B, C and E were amplified and cloned into plasmids. The plasmids were used in HMA and compared with those standard env gene of other countries. The heteroduplex bands obtained with ours env genes were more proximate to homoduplex bands. The homogeneity of the corresponding China HIV-1 subtypes with standard TH14(B), IND868(C), MA959 (C) and TH22(E) are 90.2%(B), 88.3%(C), 83.7(C)% and 92.3%(E) respectively. CONCLUSION: The HMA reagents we established in this study have higher sensitivity in HMA analysis for China HIV-1 strains when compared with the international HMA reagents. The HMA reagents also provide new reference reagents for UNAIDS HIV isolation network.

Acquired Immunodeficiency Syndrome↗

PubMed2000

Identification of two LDL receptor mutations causing familial hypercholesterolemia in Indian subjects.

Familial hypercholesterolemia (FH) is a genetic disorder caused by numerous mutations in the low-density lipoprotein receptor (LDLR) gene. Mutational analyses of Indians in South Africa suggest the possibility of a high frequency of FH in India. This study aimed at identifying mutations in exons 3, 4, 9, and 14 of the LDLR gene among Indians and at eventually developing population-directed molecular-based screening assays. DNA samples from 25 hypercholesterolemic patients with clinical features of FH and 25 normal controls were analyzed for four known point mutations: W66G (exon 3), E207K (exon 4), E387K (exon 9), and P664L (exon 14), which are those most reported among Indian immigrants in South Africa. Subsequently, samples were screened for other mutations by modified heteroduplex analysis in these exons. Point mutations predicted to be common among Indians were absent in the samples analyzed. Heteroduplex analysis and sequencing revealed the presence of novel insertion mutations in two patients. Both mutations are single-nucleotide "G" insertions at position 242 in exon 3 and position 397 in exon 4. The observed mutations are predicted to cause a translational frameshift, encoding truncated LDLR proteins due to premature termination. The mutant proteins are likely to be degraded intracellularly and, therefore, are pathogenic.

Apolipoproteins B↗

PubMed2006

[Analysis of ethambutol drug-resistance gene mutation in Mycobacterium tuberculosis by specific endonuclease].

OBJECTIVE: Surveyor nuclease is a member of the family of plant endonucleases that cleave heteroduplexes DNA with high specificity at sites of base substitution mismatch and DNA distortion. Heteroduplex analysis by Surveyor nuclease is a relatively new method. The purpose of this study was to explore the application of this method in analysis of drug-resistance gene mutation in Mycobacterium tuberculosis. METHODS: Surveyor nuclease was used to analyze embB gene mutation of 60 Mycobacterium tuberculosis isolates, among which 45 were EMB-resistant and embB gene mutation was found by sequencing, and 15 EMB-susceptible isolates without embB mutation. PCR amplification was carried out first, and then hybridized with products of H37Rv to form heteroduplex, cleaved by Surveyor nuclease, and lastly the results were shown by polyacrylamide gel electrophoresis and mutation was judged according to electrophoresis profile. RESULTS: Forty-five EMB-resistant isolates were found harboring embB gene mutation, while in the 15 EMB-susceptible isolates no mutation was found. All the 45 EMB-resistant isolates were revealed to harbor embB gene hotspot codon 306 mutation, among which 33 with ATG-->GTG, 3 with ATG-->ATT, 5 with ATG-->ATA, 2 with ATG-->ATC, 2 with ATG-->CTG. These results from Surveyor nuclease method was completely parallel to those of sequencing. CONCLUSION: Heteroduplex analysis by Surveyor nuclease may become a useful method for drug-resistance gene mutation analysis for Mycobacterium tuberculosis because of its simplicity, stability, low-cost, and high sensitivity and specificity.

Antitubercular Agents↗

PubMed1981

Human DNA sequences complementary to the small nuclear RNA U2.

Clones containing sequences complementary to the small nuclear RNA U2 were isolated from a human DNA library (1). Three clones, designated U2/4, U2/6 and U2/7 were purified and characterized by restriction enzyme cleavage, hybridization and heteroduplex analysis. Hybridization showed that the three clones each contained one single region which is complementary to U2 RNA. Restriction enzyme cleavage revealed furthermore that the inserted fragments in the three recombinants are different. Heteroduplex analysis identified a 240-380 bp long duplex region in each heteroduplex which includes sequences complementary to U2 RNA. Heteroduplexes between clones U2/4 and U2/7 as well as between U2/4 and U2/6 revealed two additional approximately 200 bp long homologies. The remainder of the inserts were found to lack measurable sequence homology. Two fragments from clone U2/4 were subcloned in the pBR322 vector and the subclones were used to determine the nucleotide sequence of a region in clone U2/4 which is complementary to U2 RNA. A comparison between the established sequence and the sequence for rat U2 RNA (2) reveals several discrepancies.

Base Sequence↗