SEARCH · PubMed Health

Results for “Multiplex PCR”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources

PubMed2001

Gene rearrangements in radiation-induced thyroid carcinogenesis.

BACKGROUND: Radiation is an accepted risk factor for thyroid carcinogenesis in children. Recent observations in large cohorts of children and young adults who developed papillary thyroid carcinomas (PTC) related to accidental radiation exposure after the Chernobyl reactor accident revealed typical genetic aberrations shedding light on genetic determinants and mechanisms of radiation-induced carcinogenesis. PROCEDURE: A molecular genetic analysis was performed on 191 post-Chernobyl PTC by RT-PCR, multiplex PCR, DNA sequencing, and in some cases 5'RACE. Determination of point mutations was by means of PCR and either allele-specific oligonucleotide hybridization or SSCP and DNA sequencing. RESULTS: In various sporadic thyroid tumor types of adults structural genetic aberrations have been found involving mutations of RAS (codon 12, 13, 61), p53 (exons 5 to 8), Gsalpha (codon 201 and 227), and, at a low prevalence, the receptor tyrosine kinases RET or NTRK1. In contrast, in radiation-induced PTC of children RET rearrangements are by far the most prevalent genetic aberrations. In these RET rearrangements, the transmembrane and extracellular domains of RET are lost, and are replaced by parts of other genes at the 5' end. These genes always contain coiled-coil domains with dimerization potential and lead to constitutive, ligand-independent activation of the ret tyrosine kinase domain at the 3' end of the fusion product. The most frequent radiation-induced RET gene fusions involve the ELE1 (ARA70) gene, a transcription coactivator of the androgen receptor (PTC3), and H4, a gene of unknown function (PTC1). Both rearrangements originate from DNA double strand breaks with repair by intrachromosomal balanced paracentric inversion and recombination by illegitimate DNA endjoining at small stretches of homologous nucleotide sequences and direct or inverted repeats, without significant breakpoint clusters in the involved introns. In addition, five different RET-fused genes, RIalpha, GOLGA5, HTIF, RFG7 and RFG8, have been detected leading to the PTC2, 5, 6, 7 and 8 types of RET rearrangements, respectively. Each fusion leads, in principle, to the same effect: The ret tyrosine kinase is uncoupled from its stringent physiological regulation by replacement of its 5' end and is aberrantly activated by the 5' parts of fused genes in thyrocytes that do not normally express ret tyrosine kinase. Ectopic ret expression, clonal expansion and early invasion are peculiar to the affected cells. The RET-fused gene is obviously decisive for modulating tumor development: ELE1/RET rearrangements lead to most rapid tumor progression and are related to the solid variant of PTC, in contrast to H4/RET rearrangements connected with papillary or follicular variants of PTC. CONCLUSIONS: Typical genetic aberrations are produced by radioiodine uptake in the juvenile thyroid gland. They act as determinants of phenotype, biology, and clinical course of radiation-induced papillary thyroid carcinomas.

Adolescent↗

PubMed2002

Application of a DNA analysis method for the cultivar identification of grape musts and experimental and commercial wines of Vitis vinifera L. using microsatellite markers.

A DNA-based method has been applied to the identification of several musts and wines using microsatellite markers. DNA was extracted from the solid phases of sixteen monovarietal and five multivarietal musts (mixtures of two musts down to a 4:1 proportion) and they were genotyped at seven microsatellites through a multiplex PCR reaction and automated fluorescent detection. PCR multiplexing was successful in monovarietal musts, but should be used with caution with at least some markers and in multivarietal musts. The same extraction and detection methods were unsuccessfully applied to the solid and liquid phases of five monovarietal commercial wines, even after using different concentration procedures. Nucleic acids presence was then studied in a recent must, during the fermentation process, and during the subsequent steps of winemaking. Genotyping was possible in the resulting experimental wine until decanting, when the particles in suspension were removed. These results suggest that wine authentication through DNA analysis is not possible in commercial wines, in the tested conditions.

DNA, Plant↗

PubMed2006

Powerful strategy for polymerase chain reaction-based clonality assessment in T-cell malignancies Report of the BIOMED-2 Concerted Action BHM4 CT98-3936.

Polymerase chain reaction (PCR) assessment of clonal T-cell receptor (TCR) and immunoglobulin (Ig) gene rearrangements is an important diagnostic tool in mature T-cell neoplasms. However, lack of standardized primers and PCR protocols has hampered comparability of data in previous clonality studies. To obtain reference values for Ig/TCR rearrangement patterns, 19 European laboratories investigated 188 T-cell malignancies belonging to five World Health Organization-defined entities. The TCR/Ig spectrum of each sample was analyzed in duplicate in two different laboratories using the standardized BIOMED-2 PCR multiplex tubes accompanied by international pathology panel review. TCR clonality was detected in 99% (143/145) of all definite cases of T-cell prolymphocytic leukemia, T-cell large granular lymphocytic leukemia, peripheral T-cell lymphoma (unspecified) and angioimmunoblastic T-cell lymphoma (AILT), whereas nine of 43 anaplastic large cell lymphomas did not show clonal TCR rearrangements. Combined use of TCRB and TCRG genes revealed two or more clonal signals in 95% of all TCR clonal cases. Ig clonality was mostly restricted to AILT. Our study indicates that the BIOMED-2 multiplex PCR tubes provide a powerful strategy for clonality assessment in T-cell malignancies assisting the firm diagnosis of T-cell neoplasms. The detected TCR gene rearrangements can also be used as PCR targets for monitoring of minimal residual disease.

Gene Amplification↗

PubMed2003

Diagnosis of Helicobacter pylori infection.

Numerous studies are still published on diagnostic tests for Helicobacter pylori, essentially for noninvasive tests. The urea breath test is applied in different types of patients, and there are attempts to have quicker and simpler protocols. Stool tests using monoclonal antibodies are now evaluated while serology is still a subject of interest. The progress in PCR (multiplex PCR, real-time PCR) has also stimulated the research in this area of invasive tests, in order to get insight into virulence factors, macrolide susceptibility and to detect H. pylori in nonconventional specimens.

Helicobacter Infections↗

PubMed2004

Comparison of different melting temperature calculation methods for short DNA sequences.

MOTIVATION: The overall performance of several molecular biology techniques involving DNA/DNA hybridization depends on the accurate prediction of the experimental value of a critical parameter: the melting temperature Tm. Till date, many computer software programs based on different methods and/or parameterizations are available for the theoretical estimation of the experimental Tm value of any given short oligonucleotide sequence. However, in most cases, large and significant differences in the estimations of Tm were obtained while using different methods. Thus, it is difficult to decide which Tm value is the accurate one. In addition, it seems that most people who use these methods are unaware about the limitations, which are well described in the literature but not stated properly or restricted the inputs of most of the web servers and standalone software programs that implement them. RESULTS: A quantitative comparison on the similarities and differences among some of the published DNA/DNA Tm calculation methods is reported. The comparison was carried out for a large set of short oligonucleotide sequences ranging from 16 to 30 nt long, which span the whole range of CG-content. The results showed that significant differences were observed in all the methods, which in some cases depend on the oligonucleotide length and CG-content in a non-trivial manner. Based on these results, the regions of consensus and disagreement for the methods in the oligonucleotide feature space were reported. Owing to the lack of sufficient experimental data, a fair and complete assessment of accuracy for the different methods is not yet possible. Inspite of this limitation, a consensus Tm with minimal error probability was calculated by averaging the values obtained from two or more methods that exhibit similar behavior to each particular combination of oligonucleotide length and CG-content class. Using a total of 348 DNA sequences in the size range between 16mer and 30mer, for which the experimental Tm data are available, we demonstrated that the consensus Tm is a robust and accurate measure. It is expected that the results of this work would be constituted as a useful set of guidelines to be followed for the successful experimental implementation of various molecular biology techniques, such as quantitative PCR, multiplex PCR and the design of optimal DNA microarrays.

Algorithms↗

PubMed1995

Screening for mutations in haemophilia A patients by multiplex PCR-SSCP, Southern blotting and RNA analysis: the detection of a genetic abnormality in the factor VIII gene in 30 out of 35 patients.

The molecular characterization of mutations in haemophilia A patients in this study was carried out by PCR-SSCP, Southern blotting, and reverse transcribed-PCR. A multiplex PCR in which four to eight exons were co-amplified was developed to reduce the time needed for screening the coding region of the factor VIII gene. PCR-SSCP was used to screen for small molecular defects, and reverse transcriptase PCR combined with Southern blotting was used to screen DNA for the inversions that occur frequently in intron 22 of the factor VIII gene. A group of 35 haemophilia A patients was analysed by these methods and 31 mutations were detected. In one patient two mutations were identified. The cases of mild and moderate haemophilia A showed changes in single nucleotides which predicted amino acid changes. The patients affected by severe haemophilia A showed two types of mutations. First, deletions or insertions that result in a frameshift in the coding DNA sequence were observed. Second, inversions were found which result in a disruption of the gene. With the screening strategies used we succeeded in elucidating an abnormality in the factor VIII gene in 30/35 haemophilia A patients.

Base Sequence↗

PubMedDate not supplied

Screening 25 dystrophin gene exons for deletions in Arab children with Duchenne muscular dystrophy.

Forty-two Arab children with Duchenne muscular dystrophy (DMD) were studied for intragenic deletions in 25 exons of the dystrophin gene using three different multiplex PCR sets each amplifying a total of 9, 9 and 6 different exons, respectively. Exon 22 was amplified individually. Deletions were found in 78, 76 and 12% of DMD patients with each of the three sets, respectively. With all the three sets, the detection rate increased to 86% (36 of 42 patients). Fifty percent of the deleted exons were located in the distal hot spot, 8% in the proximal hot spot while 42% were scattered over both. This study, the first in an Arab population and only the second to use three PCR multiplex sets, documents one of the highest deletion detection rates in DMD.

Arabs↗

PubMedDate not supplied

[Use of polymerase chain reaction for pediatric diagnosis].

Basic principles of main molecular biology techniques: polymerase chain reaction (PCR) and its variants; asymmetric PCR, ARMS, nested PCR, multiplex PCR and competitive PCR are discussed. Nucleic acids techniques are making increasing progress in molecular diagnostics. Sequence analysis of amplified DNA allows better identification of the pathogen, detection of mutant genes and more accurate prognosis and therapy of certain diseases.

Child↗

PubMed2001

Preimplantation genetic diagnosis.

Preimplantation genetic diagnosis (PGD) has now been used in human fertility centers for a decade. To this end, diagnostic analysis is conducted on polar bodies or single blastomeres from biopsied embryos before the embryos are transferred, allowing the selection of normal embryos before a pregnancy has been established. Advances in technology available for PGD are described, including fluorescent in situ hybridization (FISH), interphase chromosome conversion, comparative genomic hybridization (CGH), fluorescent polymerase chain reaction (PCR), multiplex PCR, and whole genome amplification. These techniques support the diagnosis of a number of diseases at the single-cell level.

Chromosome Aberrations↗

PubMed2004

Comparative assessment of conventional PCR with multiplex real-time PCR using SYBR Green I detection for the molecular diagnosis of imported malaria.

For the diagnosis of imported malaria, optical or immunochromatographic methods are known to be less sensitive and less specific than PCR-based methods, which are conversely more complicated and time-consuming. An original strategy, based upon the sequential use of a multiplex competitive real-time PCR detecting Plasmodium falciparum or Plasmodium spp. infection, followed by, if necessary, a single real-time PCR for species identification, was therefore performed and then tested versus conventional PCR in routine conditions. Conventional PCR has been used since October 1999 in the Department of Parasitology, University Hospitals in Toulouse, as a 2nd line diagnostic method. Out of 183 patients tested, 48 were found to be harbouring a falciparum infection by conventional microscopy, 60 by conventional PCR and 60 by multiplex competitive real-time PCR. Nine further patients had a non-falciparum infection, and concordant species identifications were obtained by both conventional PCR and single real-time PCR. The major value of PCR-based methods, when compared to microscopical techniques, was to ascertain the negativity of a suspect sample. Moreover, real-time PCR allows simplification of the operating procedure, with a diagnosis being made within 2 h.

Animals↗

PubMed2007

Development and application of a novel multiplex polymerase chain reaction for semi-quantitation of human Cytomegalovirus in clinical specimens.

Human Cytomegalovirus (HCMV) is an important cause of morbidity and occasional mortality in immunocompromised patients. The aims of the study were to develop and apply a multiplex PCR for semi-quantitation of HCMV in clinical specimens, compare its efficiency with pp65 antigenemia assay and real-time PCR. A multiplex PCR combining the primers targeting three regions of the HCMV genome, viz. the morphological transforming region II (mtr II), UL-83 and glycoprotein O (gO) genes for the detection of the genome of HCMV was standardized with HCMV AD169 strain. This was evaluated against pp65 antigenemia assay by applying it on 70 peripheral blood specimens obtained from 70 post-renal transplant recipients. The multiplex PCR and a real-time PCR were prospectively applied to 31 clinical specimens from 29 immunocompromised patients. The multiplex PCR was specific for HCMV. The level of antigenemia and the copy number of the viral DNA as estimated by real-time PCR in the samples positive for all the three targets was significantly higher than in those that were positive for only one or two of the targets. The multiplex PCR provides a simple and effective means of quantifying HCMV in clinical specimens with efficiency equivalent to the pp65 antigenemia assay and real-time PCR.

Cytomegalovirus↗

PubMed1992

Diagnosis of Duchenne and Becker muscular dystrophies by polymerase chain reaction. A multicenter study.

OBJECTIVE--To assess the efficiency, reliability, and ease of use of DNA diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) using the polymerase chain reaction (PCR). DESIGN--DNA from the patients was screened for deletion mutations using multiplex PCR, and the results were compared with those obtained by Southern blot analysis. The PCR multiplex reaction detects nine specific "hot-spot" exons in the dystrophin gene while the Southern analysis detects 66 specific dystrophin gene restriction fragments. The multiplex reaction requires 50-fold less DNA than Southern analysis and thus is considerably more sensitive. SETTING--Fourteen university-affiliated and private genetic disease diagnostic laboratories. PATIENTS--Male patients with clinical signs of DMD/BMD. Cases were selected for analysis randomly, without knowledge of whether a deletion was present within the dystrophin gene. MAIN OUTCOME MEASURES--The percentage of cases that were detectable by multiplex PCR in comparison with Southern analysis, the frequency, extent, and location of the detected deletion mutations. In some cases, duplication mutations were monitored. RESULTS--The accuracy of a single PCR multiplex amplification (nine exons) was compared with Southern analysis with 10 cDNA probes that cover the full length of the gene. The multiplex PCR analytic method detected 82% of those deletions detected by Southern analysis methods. In one of 745 analyses, the multiplex method suggested a single exon deletion, which was not confirmed by Southern analysis, representing a false-positive rate of 0.013%. CONCLUSIONS--Multiplex PCR represents a sensitive and accurate method for deletion detection of 46% of all cases of DMD/BMD. The method requires 1 day for analysis, is easy to perform, and does not use radioactive tracers. As such, multiplex PCR represents an efficient and rapid method for prenatal or postnatal diagnosis of DMD/BMD.

Blotting, Southern↗

PubMed2005

Characterisation of rotavirus strains among hospitalised and non-hospitalised children in Guinea-Bissau, 2002 A high frequency of mixed infections with serotype G8.

BACKGROUND: In a previous community-based cohort study in Guinea-Bissau from 1996 to 1998, characterisation of rotavirus strains showed a high frequency of less common genotypes such as G8 and G9 and a high proportion of mixed infections. OBJECTIVES AND STUDY DESIGN: In the present study, we examined the prevalence of rotavirus genotypes among 81 hospitalised and 23 non-hospitalised Guinean children with rotavirus associated diarrhoea during the 2002 seasonal rotavirus outbreak. G- and P-types were determined in a two-step procedure using reverse transcription followed by a standard multiplex PCR. The multiplex PCR for G-types was furthermore supplemented with a single locus PCR including the MW8 primer for the G8-genotype. RESULTS: The dual infection G2/P[4]P[6] (24%) appeared to be the most frequent cause of rotavirus infections followed by G2P[4] (19%), G2P[6] (16%) and G8P[6] (13%). Overall 38% of the infections were mixed and 18% of the samples had the genotype G8. However, by subjecting all samples and not only the strains, which according to the standard multiplex PCR procedure were non-typeable, to a single locus G8-PCR, we found that the genotype G8 appeared in 62% of the infections, either as a single G-strain or in combination with other G-types, especially G2. Including these results, more than 63% of infections emerged as mixed. Neither genotype (including the presence of G8) nor the presence of mixed infections, seem to influence the severity of the rotavirus infection. CONCLUSION: We found a high frequency of mixed infections especially due to G8-genotypes, which might have implications for development of rotavirus vaccine candidates for use in Africa. Our results do not suggest that a single genotype is associated with severity, but the present study is based on a modest number of samples and results should be interpreted with caution.

Base Sequence↗

PubMed2006

Improved detection of episomal Banana streak viruses by multiplex immunocapture PCR.

Banana streak viruses (BSV) are currently the main viral constraint to Musa germplasm movement, genetic improvement and mass propagation. Therefore, it is necessary to develop and implement BSV detection strategies that are both reliable and sensitive, such as PCR-based techniques. Unfortunately, BSV endogenous pararetrovirus sequences (BSV EPRVs) are present in the genome of Musa balbisiana. They interfere with PCR-based detection of episomal BSV in infected banana and plantain, such as immunocapture PCR. Therefore, a multiplex, immunocapture PCR (M-IC-PCR) was developed for the detection of BSV. Musa sequence tagged microsatellite site (STMS) primers were selected and used in combination with BSV species-specific primers in order to monitor possible contamination by Musa genomic DNA, using multiplex PCR. Furthermore, immunocapture conditions were optimized in order to prevent Musa DNA from interfering with episomal BSV DNA during the PCR step. This improved detection method successfully allowed the accurate, specific and sensitive detection of episomal DNA only from distinct BSV species. Its implementation should benefit PCR-based detection of viruses for which homologous sequences are present in the genome of their hosts, including transgenic plants expressing viral sequences.

Badnavirus↗

PubMed2002

Multiplex polymerase chain reaction: a practical approach.

Considerable time and effort can be saved by simultaneously amplifying multiple sequences in a single reaction, a process referred to as multiplex polymerase chain reaction (PCR). Multiplex PCR requires that primers lead to amplification of unique regions of DNA, both in individual pairs and in combinations of many primers, under a single set of reaction conditions. In addition, methods must be available for the analysis of each individual amplification product from the mixture of all the products. Multiplex PCR is becoming a rapid and convenient screening assay in both the clinical and the research laboratory. The development of an efficient multiplex PCR usually requires strategic planning and multiple attempts to optimize reaction conditions. For a successful multiplex PCR assay, the relative concentration of the primers, concentration of the PCR buffer, balance between the magnesium chloride and deoxynucleotide concentrations, cycling temperatures, and amount of template DNA and Taq DNA polymerase are important. An optimal combination of annealing temperature and buffer concentration is essential in multiplex PCR to obtain highly specific amplification products. Magnesium chloride concentration needs only to be proportional to the amount of dNTP, while adjusting primer concentration for each target sequence is also essential. The list of various factors that can influence the reaction is by no means complete. Optimization of the parameters discussed in the present review should provide a practical approach toward resolving the common problems encountered in multiplex PCR (such as spurious amplification products, uneven or no amplification of some target sequences, and difficulties in reproducing some results). Thorough evaluation and validation of new multiplex PCR procedures is essential. The sensitivity and specificity must be thoroughly evaluated using standardized purified nucleic acids. Where available, full use should be made of external and internal quality controls, which must be rigorously applied. As the number of microbial agents detectable by PCR increases, it will become highly desirable for practical purposes to achieve simultaneous detection of multiple agents that cause similar or identical clinical syndromes and/or share similar epidemiological features.

Humans↗

PubMed2004

Multiplex nested PCR for Brazilian Alphavirus diagnosis.

A reverse-transcriptase PCR (RT-PCR) and a multiplex nested PCR were developed for the rapid detection and identification of 14 Brazilian alphaviruses. Using Alphavirus genus-specific primers in a RT-PCR, we obtained amplified products of 434 bp. Species-specific primers were selected and simultaneously tested in a multiplex nested PCR. The nested PCR increased the test sensitivity 1000-fold and was capable of identifying Brazilian Alphavirus showing the expected bands with diagnostic sizes for Venezuelan (400 bp), Eastern (124 bp), and Western (208 bp) equine encephalitis, Aura (86 bp), and Mayaro (270 bp) viruses. This strategy for diagnosis is fast, sensitive, specific and it can be used as a reliable alternative for routine Brazilian Alphavirus diagnosis.

Alphavirus Infections↗

PubMed2004

Presence of insertion sequences (IS elements) in group B streptococci of bovine origin.

BACKGROUND & OBJECTIVES: Streptococcus agalactiae (group B streptococci, GBS) is one of the leading causative agents of human and animal infections. Recently it was demonstrated that integration of different IS elements could inactivate some of the GBS virulence properties. The presence of IS elements in human isolates has been studied while the bovine isolates were not investigated till now. The objective of the study was to perform IS analysis of a large number of bovine GBS and to use the IS elements for classification and molecular epidemiology of GBS strains. METHODS: A total of 101 GBS isolates obtained from the dairy cows were tested. These were analyzed by PCR and multiplex PCR. Southern hybridization was accomplished with the Enzo(TM) DNA Labeling and Detection Kit. The computer techniques were used for selection of the specific primers and for analysis of the sizes of PCR products. RESULTS: GBS isolates collected at three different dairy farms were studied for the presence of IS elements. Multiplex PCR was used for the fast screening. It was found that IS861 presented in 29 GBS isolates (28.7%), IS1548 in 9 (8.9%), ISSa4 in 48 (47.5%) and IS1381 in 26 isolates (25.7%). A total of 28 bovine GBS isolates (27.7%) did not possess any of the IS elements, 36 (35.6%) possessed, 35 (34.7%) possessed two and 2 (1.9%) possessed three different IS elements. The GBS with four different IS elements were not found. Taken together, 10 different variants of GBS strains were discovered. Two out of 10 variants being specific for 51 isolates (50.5%) were predominant in bovine GBS. The results of the study demonstrated that the presence of IS elements significantly varied in bovine GBS. INTERPRETATION & CONCLUSION: The present data demonstrated that variants of IS elements present in GBS genome could be used as effective criteria for molecular epidemiology. In future this approach could probably be used as an additional tool for the epidemiological control and prevention of other bacterial infections.

Animals↗

PubMed1998

Androgen responsiveness of stromal cells of the human prostate: regulation of cell proliferation and keratinocyte growth factor by androgen.

PURPOSE: Growth and development of the prostate are androgen dependent and mainly influenced by stromal-epithelial interaction. It is believed that indirect androgenic activation of paracrine factors like keratinocyte growth factor (KGF) in the prostatic stroma influences the growth of epithelial cells. In this study we investigated the role androgen plays in stromal cell growth and stimulation of KGF in the human prostate. MATERIALS AND METHODS: Stromal cells were derived from explant primary culture of human normal or benign prostatic tissue. The effect of different dihydrotestosterone (DHT) concentrations on cell proliferation was measured using 3[H]thymidine incorporation assay. The effect of DHT on levels of KGF protein was determined by Western blotting. The effect of DHT on levels of KGF gene expression was measured by various cycles of polymerase-chain-reaction (PCR) and multiplex PCR. RESULTS: Characterization of stromal cells showed epithelial cells less than 9.5% in all passages. DHT stimulated human prostate stromal cells in a dose dependent fashion over a concentration range of 0.001-10 nM. Immunocytochemical evaluation of KGF after DHT exposure showed a higher staining intensity. Relative quantitation of Western blotting showed a 1.93-fold increase in KGF protein in the androgen treated stromal cells. At 1 nM DHT conventional and multiplex PCR revealed a significant stimulation of the KGF mRNA expression. CONCLUSIONS: These data show for the first time that androgen stimulates cell proliferation as well as KGF protein and gene expression in human prostate stromal cells. This supports the hypothesis that androgen-induced stromal-derived KGF stimulates prostate epithelial cell growth.

Aged↗