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Heteroduplex Analysis (0):
Recent article
Heteroduplex Analysis
Archives of Virology (155)6 2010
Abstract
Citrus tristeza virus (CTV) isolates from the Darjeeling hills of the Northeastern Himalayan region of India were characterized by biological indexing, multiple molecular marker (MMM) analysis, heteroduplex mobility assay (HMA) and sequence analysis. Variability was studied using the CP gene and a 5...
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PMID: 20437063
PDF is available here.
PDF is available here.
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Abstract
The aim of this study was to compare sensitivity thresholds of two pre-screening methods - the heteroduplex mobility assay (HMA) and the presence of ambiguity codes in population-based sequences - applied for detection of HIV-1 superinfection. HIV-1 env C2-C4 PCR products generated from 48 serum sam...
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PMID: 20178816
PDF is available here.
PDF is available here.
Abstract
We devised a method to detect low mutation levels in brain DNA. Different proportions of a known SOD1 mutation were prepared to determine the sensitivity of DHPLC. The fraction containing the mutant signal was collected and re-amplified ('enriched') to increase sensitivity and to dideoxy sequence th...
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PMID: 20184515
PDF is available here.
PDF is available here.
Abstract
We summarized the information of 16S rRNA including its function in cells, transcription organization, the position of variable regions and conserved regions, copies numbers of 16S rRNA gene, secondary structure, some artifacts generated during PCR amplification and the solution to avoid the artifac...
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PMID: 20344934
PDF is available here.
PDF is available here.
Abstract
We present the routine diagnostic application of EMMA (Enhanced Mismatch Mutation Analysis, Fluigent), a new, fast, reliable, and cost-effective method for mutation screening. This method is based on heteroduplex analysis by capillary electrophoresis and relies on the use of innovative matrices incr...
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PMID: 20721742
PDF is available here.
PDF is available here.
Abstract
We focused mostly on the sample preparation step that is critical for the stability of generated fractions and reproducibility of a generated result. The application of universal primer for fluorescent labeling and omitting the PCR purification step also greatly reduce the cost of mutation detection...
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PMID: 20721743
PDF is available here.
PDF is available here.
Methods in Molecular Biology (554)554 2009
Abstract
We recently developed a quantitative method based on denaturing HPLC to measure DNA mutation load, using tRNA Leu(UUR) region of the mitochondrial DNA as an example. The mutation load is determined based on the quadratic function that governs DNA reannealing and the formation of heteroduplex and hom...
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PMID: 19513681
PDF is available here.
PDF is available here.
Abstract
We document the existence of two 3'-UTR polymorphic sites, the 5711+421(G or T) and the 5711+1286(C or T). Frequency of homozygous genotype 5711+421T/T_5711+1286T/T (or T/T-T/T) in the group of BRCA1/2 neg cancer patients was triple of that seen in unaffected persons and showed a significant cancer...
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PMID: 19405875
PDF is available here.
PDF is available here.
Novel dhps and pfcrt polymorphisms in Plasmodium falciparum detected by heteroduplex tracking assay.
Abstract
We use heteroduplex tracking assays (HTAs) to analyze dhps540 mutations in 96 samples from Peru and pfcrt76 mutations in 70 samples from China. All samples had been previously analyzed by standard PCR. We detected drug-resistant minority variants and two novel non-synonymous pfcrt mutations in China...
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PMID: 19407115
PDF is available here.
PDF is available here.
Malaria Journal (8)1 2009
Abstract
Thirty one clinical P. falciparum isolates (15 primary isolates and 16 recurrent isolates) from 17 Malagasy children treated with CQ for uncomplicated malaria were genotyped for the pfcrt K76T mutation. Two (11.7%) of 17 patients harboured genetically CQ-resistant P. falciparum strains after therapy...
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PMID: 19291288
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)22 2008
Abstract
We describe a method to identify and recover minor human immunodeficiency virus type 1 (HIV-1) sequence variants from a complex population. The original heteroduplex tracking assay (HTA) was modified by incorporating a biotin tag into the probe to allow for direct sequence determination of the query...
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PMID: 18948297
PDF is available here.
PDF is available here.
Abstract
OPA1 mutation carriers (n = 158) were identified in 11 ADOA pedigrees. Sixty-nine mutation carriers were available for longitudinal follow-up. Using the right eye as the default, best-corrected visual acuity (BCVAR) remained unchanged (defined as visual acuity at or within one line of original measu...
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PMID: 18653586
PDF is available here.
PDF is available here.
Journal of General Virology (89)Pt 8 2008
Abstract
These results indicate that dual infection and recombination may be a significant source of new variation in SRLV and provide a useful tool for the rapid genetic subtyping of SRLV isolates, which could be relevant for the development of more accurate diagnosis of prevalent SRLV strains in different...
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PMID: 18632974
PDF is available here.
PDF is available here.
Journal of Virology (82)15 2008
Abstract
The frequency that multiple different subtypes of hepatitis C virus (HCV) simultaneously infect a given individual is controversial. To address this question, heteroduplex mobility analysis (HMA) of portions of the HCV core and envelope 1 region was optimized for sensitive and specific detection of...
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PMID: 18495766
PDF is available here.
PDF is available here.
Journal of Immunological Methods (335)1-2 2008
Abstract
We report the establishment and validation of a panel of Vbeta subfamily-specific semi-nested PCR assays, and a CDR3beta heteroduplex technique for analysing the clonal diversity of bovine alphabeta T cell responses. Development of these methods was based on available sequence data for 48 functional...
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PMID: 18436232
PDF is available here.
PDF is available here.
Abstract
There was a significant (p approximately 0.02) main effect of interleukin-10 haplotypes, with individuals having either the ATA/ACC or the ACC/ACC genotype experiencing around 20% fewer probing depths of >or= 4 mm compared to individuals with other genotypes. Age and smoking had significant (p < 0.0...
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PMID: 18447856
PDF is available here.
PDF is available here.
Clinical Biochemistry (41)9 2008
Abstract
DHPLC assay was established based on the analysis of 795 DNA samples from a group of various genotypes for the 20 mutations and 8 polymorphisms in beta-globin gene then validated on 319 tests in a blind study. The results obtained with this assay were in concordance with the results obtained by DNA...
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PMID: 18339318
PDF is available here.
PDF is available here.
Abstract
No relationship was found between transmission and overall maternal env diversity. Infants had less diverse HIV-1 populations than their mothers, and intrauterine-infected infants had fewer V1/V2 variants and were more likely to harbor a homogeneous V1/V2 population than infants infected intrapartum...
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PMID: 18427205
PDF is available here.
PDF is available here.
A heteroduplex assay for the rapid detection of dual Human Immunodeficiency Virus Type 1 infections.
Abstract
The predominance of circulating and unique recombinant forms (URFs) of Human Immunodeficiency Virus Type 1 (HIV-1) in Cameroon suggests that dual infection occurs frequently in this region. Despite the potential impact of these infections on the evolution of HIV diversity, relatively few have been d...
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PMID: 18314205
PDF is available here.
PDF is available here.
Abstract
We explore the possibilities offered by flow cytometric microbead analysis to develop high throughput methods for the detection of deletions/insertions and single-strand DNA lesions. The products of PCR reactions derived from reference and test samples are denatured and reannealed, then exposed to e...
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PMID: 18205197
PDF is available here.
PDF is available here.
Abstract
We present the clinical and ophthalmological findings, genetic analysis, and therapy of two siblings with NF1 and bilateral OPG. In genetic analysis, a heteroduplex profile was detected in exon 4b of the NF1 gene for the affected patients and mother. Sequencing of the DNA samples identified a C > T...
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PMID: 17514731
PDF is available here.
PDF is available here.
Legal Medicine (10)2 2008
Abstract
We propose a method to initially screen samples according to different populations. We found a unique deletion (26822-3) in an allele that 62.0% of East Asian individuals had in intron 33 of type I collagen alpha 2 (COL1A2), while most Europeans and Africans did not have it. By making a heteroduplex...
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PMID: 17897868
PDF is available here.
PDF is available here.
Journal of Virological Methods (148)1-2 2008
Abstract
Variant samples from the three genotypes of erythroviruses have already been detected using sequencing as methodology for analysis. This study aimed to investigate the efficacy of single-stranded conformation polymorphism (SSCP) analysis and heteroduplex mobility assay (HMA) as methodologies to dete...
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PMID: 18054089
PDF is available here.
PDF is available here.
Journal of Virological Methods (148)1-2 2008
Abstract
Automated, high-throughput detection methods for single-nucleotide polymorphisms have been applied to the routine genotyping of genetic polymorphisms influencing drug metabolism. Melting curve analysis with LCGreen was introduced recently as one such technique which can be performed rapidly and easi...
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PMID: 18201770
PDF is available here.
PDF is available here.
Clinical Biochemistry (41)3 2008
Abstract
The high-resolution melting curve analysis successfully genotyped the c.1138G>A mutation in exon 8 of the FGFR3 gene in all 40 patients with achondroplasia without the need of further assays. The technique had a sensitivity and specificity of 100%. CONCLUSION: High-resolution melting analysis is a s...
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PMID: 18199430
PDF is available here.
PDF is available here.
New Phytologist (180)3 2008
Abstract
* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping...
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PMID: 18684160
PDF is available here.
PDF is available here.
Abstract
Genomic variations in HIV-1 represent a major problem in understanding disease progression, studying drug resistance and developing effective vaccines. Heteroduplex Mobility Assay (HMA) was used for analyzing HIV-1 subtypes resulting from genetic similarity or divergence of C2 -V3 -V5 region of enve...
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PMID: 18723957
PDF is available here.
PDF is available here.
BMC Biotechnology (8)1 2008
Abstract
We used two highly-specific mutation screening methods, mismatch-specific endonuclease and denaturing high-performance liquid chromatography, to identify mutations in the HBB gene. The sensitivity and specificity of these two methods were compared. We successfully distinguished mutations in the HBB...
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PMID: 18694524
PDF is available here.
PDF is available here.
Abstract
We report missense mutations in COL1A1 of several OI patients. Two novel mutations were found in the D1 period. One caused a substitution of glycine 200 by valine at the N-terminus of D1 in OI type I/IV, lowering collagen stability by 50% at 34 degrees C. The other one was a substitution of valine 3...
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PMID: 18670065
PDF is available here.
PDF is available here.
Abstract
These results suggest that the HDA is a simple yet powerful and inexpensive tool for the detection of both intersubtype and intrasubtype dual infections, and that the HDA harbors significant potential for reliable, high-throughput screening for dual infection. As these infections and the recombinant...
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PMID: 18275354
PDF is available here.
PDF is available here.
Abstract
Real-time polymerase chain reaction (PCR) has become a standard tool in both quantitative gene expression and genetic variation analysis. Data collection is performed throughout the PCR process, thus combining amplification and detection into a single step. This can be achieved by combining a variet...
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PMID: 18695963
PDF is available here.
PDF is available here.
Chinese Medical Journal (120)24 2007
Abstract
The genetic diversity within HVR1 was consistently higher than that in the E1 and E2 regions outside HVR1 in individuals with persistent viremia, but did not change markedly over time in those with clearance of viremia. For individuals with persistent viremia, the rate of nonsynonymous substitutions...
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PMID: 18167197
PDF is available here.
PDF is available here.
Electrophoresis (28)23 2007
Abstract
We searched for mutations in a cohort of 38 patients and investigated the relationship between mutation type and allele-specific transcription from the wild-type versus mutant alleles. Quantification of relative mRNA transcript numbers was done by Pyrosequencing, a novel real-time sequencing method...
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PMID: 18041031
PDF is available here.
PDF is available here.
Abstract
Analysis of 400 samples sent in duplicate revealed one error that was associated with reporting rather than the methodology. Of 5327 samples received, 1122 were for family testing, 2470 for diagnostic testing and in 1735 cases no reason was given. Overall, homozygosity for C282Y was found in 14% of...
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PMID: 17079357
PDF is available here.
PDF is available here.
Abstract
Premature ovarian failure (POF) occurs in 1% of the general population and affects approximately 10% of non-ovulating women, resulting in infertility and sex steroid deficiency. The forkhead domain transcription factor (FOXL2) gene is one of the candidate genes associated with POF. This case-control...
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PMID: 18028747
PDF is available here.
PDF is available here.
Abstract
This study contributes to enlarging the adenomatous polyposis coli gene mutations spectrum and to defining new biomarkers for the early diagnosis of Turkish patients with familial adenomatous polyposis....
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PMID: 17882487
PDF is available here.
PDF is available here.
Abstract
Two distinct patterns of blood/CSF viral population dynamics can be observed in SIV-infected macaques, and the patterns may be associated with different neurological disease outcomes....
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PMID: 17763329
PDF is available here.
PDF is available here.
Abstract
Human immunodeficiency virus type 1 (HIV-1) can be acquired through oropharyngeal tissues in breastfeeding infants. Efforts to better understand the determinants of breast milk transmission are hampered by the lack of a relevant oral human mucosa model and well-defined breast milk-derived viruses. T...
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PMID: 17919104
PDF is available here.
PDF is available here.
Abstract
Histological progression of hepatitis C is tightly associated with homogenization of HCV quasispecies, perhaps reflecting immune failure and/or selective outgrowth of aggressive viral variants....
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PMID: 17570111
PDF is available here.
PDF is available here.
Abstract
Median age of patients was 26 years (1-79 range), 68.7% (279/406) females, 69.9% (269/385) sexual exposure, 14.3% parenteral risk, 15.8% vertical cases. Overall 69.9% (284/406) of HIV-1 subtypes were concordant B(env)/B(gag), 1.7% F(env)/F(gag) and 1% C(env)/C(gag). Discordant HIV-1 isolates were 14...
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PMID: 17537671
PDF is available here.
PDF is available here.
Clinical Chemistry (53)7 2007
Abstract
High-resolution melting analysis is a highly accurate heteroduplex scanning technique. With many exons, however, use of single-sample instruments may lead to clerical errors, and routine use of difference analysis is recommended. Common variants can be identified by their melting curve profiles and...
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PMID: 17525106
PDF is available here.
PDF is available here.
Clinical Chemistry (53)6 2007
Abstract
Clinical Chemistry (53)6 2007
Abstract
We observed a quadratic relationship between the heteroduplex peak areas and mutant loads, consistent with the kinetics of heteroduplex formation reported by others. This was modeled mathematically and used to quantify mtDNA mutation load. The method was able to detect a mutation present in a concen...
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PMID: 17446331
PDF is available here.
PDF is available here.
Abstract
We have developed a multiple site-specific heteroduplex tracking assay (MSS-HTA) that can detect pfcrt 76T mutant parasites consisting of as little as 1% of the parasite population. In clinical samples, no pfcrt 76T was detected in 87 pregnant Malawian women by standard PCR. However, 22 (25%) contai...
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PMID: 17553226
PDF is available here.
PDF is available here.
Abstract
We systematically searched for HIV-1 co-infections by means of a heteroduplex mobility assay in 660 HIV-1 seroconverters from the two ANRS SEROCO and PRIMO cohorts. Our results strongly suggest that HIV-1 co-infection remains a rare phenomenon in HIV-1 seroconverters infected in France between 1986...
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PMID: 17457105
PDF is available here.
PDF is available here.
Journal of Virology (81)10 2007
Abstract
We describe the first documented case of coinfection and viral recombination in two naturally infected goats. DNA fragments encompassing a variable region of the envelope glycoprotein were obtained from these two animals by end-limiting dilution PCR of peripheral blood mononuclear cells or infected...
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PMID: 17344293
PDF is available here.
PDF is available here.
Journal of Virology (81)10 2007
Abstract
We characterized human immunodeficiency virus type 1 env V4/V5 genetic populations in multiple blood plasma samples collected over an average of 7 months from 24 chronically infected human subjects. We observed complex and dynamic V4/V5 genetic populations in most subjects. Comparisons of V4/V5 and...
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PMID: 17329337
PDF is available here.
PDF is available here.
Abstract
We conducted a retrospective study of pregnant women over the time period 1989-2000. From a total of 300 women sampled, we defined subtypes by heteroduplex mobility assay for 230 subjects and by partial sequencing and phylogenetic analyses of the env gene for 216 subjects. Subtypes A and D were most...
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PMID: 17531003
PDF is available here.
PDF is available here.
Abstract
OPA1 mutations were identified in 11/17 (65%) of the ADOA pedigrees in this study. The penetrance in our cohort was lower than originally described (82.5% vs 98%) but higher than some recent studies since the availability of genotyping. It is anticipated that this figure would be even lower as more...
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PMID: 17306754
PDF is available here.
PDF is available here.
Haematologica (92)4 2007
Abstract
Two versions of conformation sensitive gel electrophoresis, fluorescent (F-CSGE) and manual (M-CSGE) techniques, were compared for mutation analysis of the von Willebrand factor gene. 56 PCRs were used to amplify all 52 exons of the gene in seven type 1 von Willebrand disease cases, plus a healthy c...
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PMID: 17488667
PDF is available here.
PDF is available here.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics (24)2 2007
Abstract
Two mutations were found from 500 samples: 966G > A mutation in exon 9 and C > A mutation in 67th site of intron 7, both with no amino acid change. The mutation rate was 4/1000. No mutation was found as missed in using PCR-RF-SSCP combined with heteroduplex. CONCLUSION: PCR-RF-SSCP combined with het...
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PMID: 17407078
PDF is available here.
PDF is available here.
Abstract
We rely more on TCRG clonal markers to quantitate the minimal residual disease in T-ALL.
Copyright (c) 2006 Wiley-Liss, Inc....
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PMID: 17133429
PDF is available here.
PDF is available here.
Abstract
We developed a quick genetic approach to screen variants of the intimin gene (eae) by using a heteroduplex mobility assay (HMA) that targets the 5' conserved region of eae. The eae variants were categorized into 4 major HMA types and 10 minor subtypes.
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PMID: 17229860
PDF is available here.
PDF is available here.
Cancer Letters (245)1-2 2007
Abstract
We have previously reported a frameshift mutation of this gene and the down-regulation of its expression in chronic lymphocytic leukemia. In this study, we have determined the expression levels of Dok1 in Burkitt's lymphoma (BL) cell lines, lymphoblastoid cell lines from patients with X-linked lymph...
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PMID: 16338067
PDF is available here.
PDF is available here.
Folia Microbiologica (52)5 2007
Abstract
We evaluated the association of the LIF gene mutation and the levels of antiphospolipid antibodies (aPLs) in the peripheral blood of infertile women (the aPLs examination was part of our routine immunological test during the infertility check-up). Eight infertile mutation-positive women were diagnos...
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PMID: 18298054
PDF is available here.
PDF is available here.
Abstract
The most promising approach for detection of random point mutations relies upon the DNA chemical cleavage near associated mismatching base pairs. In our study, the series of heteroduplexes with all types of mismatches and extrahelical nucleotide residues surrounded by both A x T and G x C pairs were...
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PMID: 17685231
PDF is available here.
PDF is available here.
Abstract
Seventeen samples from HIV positive FSWs were genotyped by env HMA, showing the presence of 9 subtype F, 6 subtype B and 2 subtype C. Sequence analysis of the protease/RT region on 16 of these showed that 10 were BF recombinants, three were subtype B, two were subtype C, and one sample presented a d...
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PMID: 17697319
PDF is available here.
PDF is available here.
Familial Cancer (6)1 2007
Abstract
I (NF1) were referred for NF1 diagnostic testing over a 2 year period. Mutation analysis of the entire NF1 coding region and the flanking splice sites was carried out, and included the use of a combination of FISH, dHPLC and MLPA. Possible disease causing mutations were identified in 109 (64%) cases...
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PMID: 16944272
PDF is available here.
PDF is available here.
Abstract
We have already found that a single silver (I) cation specifically binds to a single C:C mismatch base pair in heteroduplex, which increases the melting temperature of heteroduplex involving a single C:C mismatch base pair by about 4 degrees C. Here, to examine the thermodynamic properties involving...
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PMID: 18029647
PDF is available here.
PDF is available here.
Abstract
We have already found that a single mercury (II) cation specifically binds to a single T:T mismatch base pair in heteroduplex, which increases the melting temperature of heteroduplex involving a single T:T mismatch base pair by about 4 degrees C. Here, to examine the thermodynamic properties involvi...
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PMID: 18029648
PDF is available here.
PDF is available here.