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PubMed1997

Clinical utility of heteroduplex analysis of TCR gamma gene rearrangements in the diagnosis of T-cell lymphoproliferative disorders.

We conducted this study to assess the clinical utility of heteroduplex analysis of polymerase chain reaction (PCR) products for Tgamma gene rearrangements in the diagnosis of T-cell lymphoproliferative disorders (LPDs) using a single set of consensus primers. This method was used to study 103 cases using fresh or frozen tissue. These included 62 cases of T-cell LPDs, 25 cases of B-cell LPDs, 3 cases of anaplastic large cell lymphomas of undefined lineage, and 13 cases of reactive disorders. The latter group served as the negative control group. For all cases of T-cell LPDs, the results of Tbeta Southern analysis (SA) and heteroduplex PCR analysis were compared. We also studied 10 cases of postthymic T-cell lymphoma using paraffin-embedded tissue. Heteroduplex Tgamma PCR was positive in 51 (89%) of 57 cases that were rearranged by Tbeta SA. Eight of the 10 cases of T-cell lymphoma analyzed using paraffin-embedded tissue were positive. There were no false-positive results. These results demonstrate that this method is an effective screening test in the clinical laboratory. A positive result obviates the need to perform SA. Preliminary results suggest this method is useful using paraffin-embedded tissue.

Base Sequence↗

PubMed2006

Detection of genetic polymorphism among and within Echinococcus granulosus strains by heteroduplex analysis of a microsatellite from the U1 snRNA genes.

Polymerase chain reaction of a pentanucleotide microsatellite in the U1 snRNA gene complex generated a multiple band pattern due to the priming of paralogous sequences. Denaturation and slow renaturation of polymerase chain reaction products allow the formation of heteroduplex DNA that can be detected by its differential mobility in polyacrylamide gel electrophoresis. Heteroduplex analysis was used to determine if the U1 snRNA microsatellite could be a useful genetic marker in Echinococcus granulosus. A U1 snRNA microsatellite fragment from E. granulosus was isolated and characterized by Southern blot and sequencing. Four E. granulosus strains were analyzed: sheep, Tasmanian sheep, cattle, and camel strains. The former two showed polymorphism and shared three of the six patterns found for sheep strain. The cattle strain displayed two patterns, and the camel strain was monomorphic. The electrophoretic profiles were used for statistical analysis in order to determine genetic distance and the relationship among strains. Heteroduplex analysis can be helpful in genotyping E. granulosus strains and is useful in detecting polymorphism within strains.

Animals↗

PubMed1995

Identification and characterization of new BoLA-DRB3 alleles by heteroduplex analysis and direct sequencing.

A sample of 52 mixed-breed dairy cattle (Holstein Friesian and Jersey) and 51 beef cattle (Hereford) from south-east Queensland was studied. The second exon of BoLA-DRB3 was amplified by polymerase chain reaction (PCR), and polymorphisms were detected by heteroduplex analysis. A large number of different heteroduplex patterns indicated extensive sequence polymorphism. Direct sequencing of PCR products from 17 homozygotes and cloning and sequencing of PCR product from two heterozygotes resulted in the identification and characterization of four novel alleles. The previously described allele BoLA-DRB3*2A is characterized by an amino acid deletion at position 65. We have identified three animals that are homozygous for this amino acid deletion, indicating that the deletion is unlikely to result in loss of function. Two of these animals had allele BoLA-DRB3*2A, and one had a novel allele with codon 65 deleted but differing from BoLA-DRB3*2A at a number of other amino acid positions. In conclusion, heteroduplex analysis allows rapid discrimination between homozygotes and heterozygotes, and enables rapid identification of new BoLA-DRB3 alleles.

Alleles↗

PubMed2006

Improving sensitivity of electrophoretic heteroduplex analysis using nucleosides as additives: Application to the breast cancer predisposition gene BRCA2.

A new method for the detection of unknown mutations, enhanced mismatch mutation analysis (EMMA), is proposed. It is based on electrophoretic heteroduplex analysis (HDA). The resolution is considerably improved, thanks to the combination of high-resolution block-copolymer sieving matrix, and nucleosides as additives in the electrophoretic medium. The EMMA method is compared to denaturing HPLC (DHPLC) in a large-scale study of mutations in the breast cancer-associated gene BRCA2, involving 4655 DNA amplicons from 94 patients. The rate of false positives was 0.09%. The raw success rate, without optimization of the amplicons tiling, was 94%, a value much higher than that achieved earlier with HDA, and comparable with that obtained with DHPLC. An analysis of the missed mutations suggest that the success rate could be improved up to about 97%, simply by redesigning the amplicons, while retaining the speed, cost effectiveness, and simplicity of the method.

Acrylamides↗

PubMed1978

[Genetic heteroduplex analysis of the R6K plasmid].

The results of genetic studies of R6K Tra1- and R6Kdelta[Sm1] mutants of R6K plasmid and those of heteroduplex analysis of DNAs have shown that DNA of this drug-resistant factor contains three loops flanked by the inverted repeats. The latter are designated as IR1, IR2 and IR3 and are of 50, 100 and 120 nucleotides in size respectively. IR1 is inserted into the loop flanked by IR2. Loops with these two repeats are located in major EcoR1 fragment, IR3 having been found in minor EcoRI fragment of the plasmid. The evidence obtained from the analysis of heteroduplex R6K/RSF2124 has shown that the loop with IR1 is corresponding to transposon Tn3. The extent of the deletion deltaSm1 indicates that IR2 may be a part of a transposon bearing the resistance to streptomycin. By comparing present data with those obtaine from the analysis of the RSF1040 factor of DNA replication initiation sites (Grosa et al., 1976), it has been suggested that the loop with IR3 represents a transposon with replicative functions (TnRep). The deletion of the mutant plasmid R6Kdelta[Sm1] (7.2 . 10(6) daltons in size) which affected one of the EcoRI sites not only confers the sensitivity to streptomycin but enhances also the efficiency of conjugational transfer and results in the loss of the R6K ability to bring about integrative suppression and to inhibit the fertility of the plasmids from IncP and IncN groups. The deletion mutant proved to have lost the property of incompatibility with the initial plasmid R6K and with itself.

Conjugation, Genetic↗

PubMed1977

Heteroduplex analysis of avian RNA tumor viruses.

Electron microscopic heteroduplex analysis of avian RNA tumor viruses has been undertaken by using 35S viral RNA and long, complementary DNA synthesized in vitro. In this initial study, heteroduplex molecules were formed between complementary DNA from Rous sarcoma virus [Prague B strain (Pr-B)] and RNAs from Pr-B and Rous sarcoma virus [Prague C strain (Pr-C)] and from their transformation defective (td) derivatives, td-Pr-B and td-Pr-C. In the case of heteroduplexes with the td viruses, a deletion loop was observed of the order of two kilobases in size and less than one kilobase from the 3' terminus of the RNA. This deletion probably spans part or all of the sequences of one or more genes in the nondefective sarcoma virus which are essential for cell transformation. The sizes and the positions of the deletions in the td-Pr-B and td-Pr-C viruses were slightly, but significantly, different. No nonhomology features were observed in the Pr-B-Pr-C hybrids, thus confirming the close genetic relatedness of the two viruses. All heteroduplexes contained a proportion of circular and dimer molecules. This observation is a direct demonstration that (-) strand DNA transcription begins at an internal position of the RNA genome, proceeds to the 5' end, reinitiates at the 3' end of the RNA, and copies the remainder of the viral genome. Other implications for models of RNA tumor virus replication are also developed from these data.

Avian Sarcoma Viruses↗

PubMed2005

Rapid mutation detection in complex genes by heteroduplex analysis with capillary array electrophoresis.

Mutational analysis of large multiexon genes without prevalent mutations is a laborious undertaking that requires the use of a high-throughput scanning technique. The Human Genome Project has enabled the development of powerful techniques for mutation detection in large multiexon genes. We have transferred heteroduplex analysis (HA) by conformation-sensitive gel electrophoresis of the two major breast cancer (BC) predisposing genes, BRCA1 and BRCA2, to a multicapillary DNA sequencer in order to increase the throughput of this technique. This new method that we have called heteroduplex analysis by capillary array electrophoresis (HA-CAE) is based on the use of multiplex-polymerase chain reaction (PCR), different fluorescent labels and HA in a 16-capillary DNA sequencer. To date, a total of 114 different DNA sequence variants (19 insertions/deletions and 95 single-nucleotide substitutions - SNS) of BRCA1 and BRCA2 from 431 unrelated BC families have been successfully detected by HA-CAE. In addition, we have optimized the multiplex-PCR conditions for the colorectal cancer genes MLH1 and MSH2 in order to analyze them by HA-CAE. Both genes have been amplified in 13 multiplex groups, which contain the 35 exons, and their corresponding flanking intronic sequences. MLH1 and MSH2 have been analyzed in nine hereditary nonpolyposis colorectal cancer patients, and we have found six different DNA changes: one complex deletion/insertion mutation in MLH1 exon 19 and another five SNS. Only the complex mutation and one SNS may be classified as cancer-prone mutations. Our experience has revealed that HA-CAE is a simple, fast, reproducible and sensitive method to scan the sequences of complex genes.

Adult↗

PubMed2001

Heteroduplex analysis of T-cell receptor gamma gene rearrangement as an adjuvant diagnostic tool in skin biopsies for erythroderma.

BACKGROUND: Erythroderma, defined as red skin covering most of the body surface often accompanied or followed by exfoliation, is the clinical manifestation of at least six different underlying etiologies with allergic or irritant contact dermatitis, atopic/asteotic dermatitis, pityriasis rubra pilaris (PRP), psoriasis, and seborrheic dermatitis accounting for the majority of cases. Approximately 10% of cases are due to adverse drug reactions with roughly another 10% due to cutaneous T-cell lymphoma (CTCL), predominantly mycosis fungoides, or leukemia. It is clear from multiple studies that the clinical diagnosis of the underlying entity is often difficult, as these diseases can present in a very similar fashion. A skin biopsy is usually employed in this setting as a diagnostic tool. However, the histopathologic diagnosis of the underlying cause is complicated by the subtlety of the distinguishing histologic features. In this situation, an ancillary technique demonstrating the presence of a monoclonal T-cell proliferation could help to rule in or out CTCL in cases that clinically and histopathologically do not allow a definitive diagnosis. METHODS: We retrospectively studied 25 biopsies from sixteen patients who presented to the Stanford Dermatology Clinic with erythroderma. We examined the specimens morphologically and analyzed the gamma chain of the T-cell receptor (TCR- gamma) by polymerase chain reaction (PCR) followed by heteroduplex analysis for clonality. We then correlated the results of our PCR and heteroduplex analyses with the patients' clinical outcomes. RESULTS: Four biopsies, from three patients, contained clonal TCR-gamma rearrangements; the four biopsies, all of which were equivocal histologically, correlated to diagnoses of mycosis fungoides (MF) or Sézary syndrome (SS). Twenty-one biopsies contained polyclonal T-cell populations. Eighteen of these biopsies represent patients with inflammatory dermatoses. Three of these biopsies, all of which were taken from a single patient, correlate to a diagnosis of MF. CONCLUSION: TCR-gamma PCR heteroduplex analysis seems to represent an important adjuvant diagnostic tool that, used in conjunction with histopathology and clinical history, could help to clarify the underlying etiology of erythroderma.

Aged↗

PubMed2000

Identification of the sibling species of the Anopheles maculipennis complex by heteroduplex analysis.

The group of anopheline mosquitoes referred to as 'Anopheles maculipennis complex' includes the most important malaria vectors of the Palearctic Western region. The species belonging to this complex, however, are difficult or impossible to distinguish by morphological characters. To differentiate sibling palearctic species belonging to this complex, interspecific differences in the ITS2 sequences were used to set up a rapid and sensitive diagnostic tool based on heteroduplex analysis. The relative heteroduplex mobility allowed the following seven species to be readily distinguished: An. atroparvus, An. labranchiae, An. maculipennis s.s. , An. martinius, An melanoon, An. messeae and An. sacharovi.

Animals↗

PubMed1997

Use of heteroduplex analysis to classify legionellae on the basis of 5S rRNA gene sequences.

Seventeen different species of Legionella, 12 serogroups of Legionella pneumophila, and 2 Legionella-like amoebal pathogens (LLAP1 and Sarcobium lyticum) were examined by heteroduplex analysis of PCR products of the 5S rRNA gene. Eight different banding patterns were identified, indicating that heteroduplex analysis of this gene can be used to classify these bacteria according to base substitutions between species. This classification may have future applications in clinical and epidemiological studies.

Bacterial Typing Techniques↗

PubMed1994

Heteroduplex analysis of T-cell receptor gamma gene rearrangements for diagnosis and monitoring of cutaneous T-cell lymphomas.

The possibility to detect markers of T-cell clonality at the T-cell receptor (TCR) beta and gamma loci in skin biopsy samples has proven to be helpful for the often difficult clinical and immunohistochemical diagnosis of cutaneous T-cell lymphoma (CTCL). However, particularly at the early stage of the neoplastic infiltration, an emerging clonal pattern at Southern may be obscured by the germline TCR configuration of the predominant dermal and epidermal cell component. Additionally, multiple TCR gamma rearranged bands of variable intensity are often observed, either in the presence or in the absence of a major clone. To overcome these difficulties, we have investigated the T-lymphocyte clonality in selected patients with variable signs of CTCL by means of heteroduplex analysis of the amplified TCR gamma VJ junctions, separated in nondenaturing polyacrylamide gel. This technique has several advantages over standard Southern blot because it is simple, rapid, not radioactive, and likely more sensitive than other polymerase chain reaction-based procedures. In particular, the cases with uncertain or contradictory TCR beta and gamma patterns were solved by the heteroduplex analysis, showing homoduplex or heteroduplex bands of clonal nature. The direct sequence of the VJ junctions, easily obtained from the homoduplex or heteroduplex bands, allowed us to confirm the same clonal marker in two apparently different skin lesions and in different biopsy samples obtained from the same patients, either at the same or different time points, thus emphasizing the utility of this method in monitoring CTCL clinical progression.

Adult↗

PubMed1995

Applications of heteroduplex analysis for mutation detection in disease genes.

Double-stranded heteroduplex molecules that form between a mutant and wild-type DNA strand are often distinguished from homoduplex molecules upon gel electrophoresis. This method, heteroduplex analysis (HA), can be performed rapidly without radioisotopes or specialized equipment. Modifications and enhancements of the HA method have been developed that increase the sensitivity of detection of single-base pair alterations.

Cystic Fibrosis↗

PubMed1997

Direct molecular genetic diagnosis and heterozygote identification in X-linked Emery-Dreifuss muscular dystrophy by heteroduplex analysis.

X-linked Emery-Dreifuss muscular dystrophy (EMD) is a very rare, relatively benign muscle disorder. The disease is associated with potentially lethal cardiac arrhythmias in affected males and some heterozygous females. X-linked EMD can be genetically distinguished from phenotypically similar autosomal EMD. Heterogenic mutations are identified as the cause of X-linked EMD. We introduced heteroduplex analysis to follow the segregation of heterogenic emerin gene mutations in the families of six unrelated EMD patients. Heteroduplex analysis was proved to be a simple, fast and reliable tool for direct molecular genetic diagnosis of EMD in male patients and identification of heterozygotes even in families where affected males are not available as index cases.

DNA Mutational Analysis↗

PubMed1994

Heteroduplex analysis of the dystrophin gene: application to point mutation and carrier detection.

Approximately one-third of the Duchenne muscular dystrophy patients have undefined mutations in the dystrophin gene. For carrier and prenatal studies in families without detectable mutations, the indirect restriction fragment length polymorphism linkage approach is used. Using a multiplex amplification and heteroduplex analysis of dystrophin exons, we identified nonsense mutations in two DMD patients. Although the nonsense mutations are predicted to severely truncate the dystrophin protein, both patients presented with mild clinical courses of the disease. As a result of identifying the mutation in the affected boys, direct carrier studies by heteroduplex analysis were extended to other relatives. We conclude that the technique is not only ideal for mutation detection but is also useful for diagnostic testing.

Base Sequence↗

PubMed1979

Heteroduplex analysis of the sequence relationships between the genomes of Kirsten and Harvey sarcoma viruses, their respective parental murine leukemia viruses, and the rat endogenous 30S RNA.

The sequence relations between Kirsten murine sarcoma virus (Ki-SV), Harvey murine sarcoma virus (Ha-SV), and a rat endogenous 30S RNA were studied by electron microscope heteroduplex analysis. The sequence relationships between the sarcoma viruses and their respective parental murine leukemia viruses (Kirsten and Moloney murine leukemia viruses), as well as between the two murine leukemia viruses, were also studied. The only observed nonhomology feature of the Kirsten murine leukemia virus/Moloney murine leukemia virus heteroduplexes was a substitution loop with two arms of equal length extending from 1.80 +/- 0.18 kilobases (kb) to 2.65 +/- 0.27 kb from the 3' end of the RNA. It is believed that this feature lies in the env gene region of the viral genomes. The Ha-SV and Moloney murine leukemia virus genomes (respective lengths, 6.0 and 9.0 kb) were homologous in a 1.0 +/- 0.05-kb region at the 3' end and possibly over a 200-nucleotide region at the 5' ends; otherwise, they were nonhomologous. Ha-SV and Ki-SV (length, 7.5 kb) were homologous in the first 4.36 +/- 0.37-kb region from the 3' end and in a 0.70 +/- 0.15-kb region at the 5' end. In between, there was a nonhomology region, possibly containing a short (0.23-kb) region of partial or total homology. The heteroduplex analysis between rat endogenous 30S RNA and Ki-SV shows that there are mixed regions of sequence homology and nonhomology at both the 5' and 3' ends. However, there is a large (4-kb) region of homology between Ki-SV and the rat 30S RNA in the center of the genomes, with only a small nonhomology hairpin feature. These studies help to define the regions of homology between the Ha-SV and Ki-SV genomes with each other and with the rat endogenous 30S RNA. These regions may be related to the sarcoma genicity of the viruses. In particular, the 0.7-kb region of homology of Ha-SV with Ki-SV at the 5' ends may be related to the formation of a 21,000-dalton phosphoprotein in cells transformed by either virus.

Animals↗

PubMed2003

Evaluation of multiplex capillary heteroduplex analysis: a rapid and sensitive mutation screening technique.

Bardet-Biedl syndrome (BBS) is a heterogeneous disease; to date seven loci have been mapped and five identified (BBS1, BBS2, BBS4, BBS6, and BBS7). Inheritance in some families is complex with multiallelic participation making linkage analysis difficult. Previous mutation screens have been carried out by direct sequencing but with an increasing number of patients to be screened for five relatively large genes, a more rapid and cost-effective mutation assay for BBS was required. We have adapted the technique of heteroduplex analysis for use on the MegaBACE 1000, a capillary-based DNA fragment analyser, to improve the resolution and sensitivity of the system. Twelve known alterations (insertions, deletions, missenses, and SNPs) in BBS1, BBS2, BBS4, and BBS6 were used to test the sensitivity of the assay and subsequently used to screen new patients for mutations. We achieved a 100% detection rate while dramatically increasing the sample throughput by virtue of multiplexing up to six PCR products in each capillary. In addition, four novel variants were identified: two in BBS2 [c.522T>A (p.D174E) and c.805-20A>G] and two in BBS4 [c.332+27_28insA and c.1414A>G (p.M472V)]. Compared with sequencing and alternative screening methods, multiplex capillary heteroduplex analysis (MCHA) is extremely cost effective. Hum Mutat 22:151-157, 2003.

Bardet-Biedl Syndrome↗

PubMed1999

Use of a DNA toolbox for the characterization of mutation scanning methods. I: construction of the toolbox and evaluation of heteroduplex analysis.

A systematic characterization of the effects of important physical parameters on the sensitivity and specificity of methods in searching for unknown base changes (mutations or single nucleotide polymorphisms) over a relatively long DNA segment has not been previously reported. To this end, we have constructed a set of molecules of varying G+C content (40, 50, and 60% GC) having all possible base changes at a particular location - the "DNA toolbox". Exhaustive confirmatory sequencing demonstrated that there were no other base changes in any of the clones. Using this set of clones as polymerase chain reaction (PCR) templates, amplicons of various lengths with the same base mutated to all other bases were generated. The behavior of these constructs in manual and automated heteroduplex analysis was analyzed as a function of the size and overall base content of the fragment, the nature and location of the base change. Our results show that in heteroduplex analysis, the nature of the mismatched base pair is the overriding determinant for the ability to detect the mutation, regardless of fragment length, GC content, or the location of the mutation.

DNA, Viral↗

PubMed1979

Heteroduplex analysis of the RNA of clone 3 Moloney murine sarcoma virus.

Heteroduplex analysis of the RNA isolated from purified virions of clone 3 Moloney murine sarcoma virus (M-MSV) hybridized to cDNA's from Moloney murine leukemia virus (M-MLV) and clone 124 M-MSV shows that the main physical component of clone 3 RNA is missing all or most of the 1.5-kilobase (kb) clone 124 M-MSV specific sequence denoted beta s (S. Hu et al. Cell 10:469--477, 1977). This sequence is either deleted in clone 3 RNA or substituted by a very short (0.3-kilobase) sequence. In other respects, clone 3 and clone 124 RNAs show the same heteroduplex structure relative to M-MLV. Since beta s is believed to contain the src gene(s) of clone 124 RNA, this result leaves as an unresolved question the nature of the src gene(s) of the clone 3 M-MSV RNA complex.

Base Sequence↗