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At least 73 records · Page 4Linked to original sources
PubMed2001

Determination of RhD zygosity: comparison of a double amplification refractory mutation system approach and a multiplex real-time quantitative PCR approach.

BACKGROUND: Rh isoimmunization and hemolytic disease of the newborn still occur despite the availability of Rh immunoglobulin. For the prenatal investigation of sensitized RhD-negative pregnant women, determination of the zygosity of the RhD-positive father has important implications. The currently available molecular methods for RhD zygosity assessment, in general, are technically demanding and labor-intensive. Therefore, at present, rhesus genotype assessment is most commonly inferred from results of serological tests. The recent elucidation of the genetic structure of the prevalent RHD deletion in Caucasians, as well as the development of real-time PCR, allowed us to explore two new approaches for the molecular determination of RhD zygosity. METHODS: Two methods for RhD zygosity determination were developed. The first was based on the double Amplification Refractory Mutation System (double ARMS). The second was based on multiplex real-time quantitative PCR. For the double ARMS assay, allele-specific primers were designed to directly amplify the most prevalent RHD deletion found in RhD-negative individuals in the Caucasian population. The multiplex real-time quantitative PCR assay, on the other hand, involved coamplification and quantification of RHD-specific sequences in relation to a reference gene, albumin, in a single PCR reaction. A ratio, DeltaCt, based on the threshold cycle, was then determined and reflects the RHD gene dosage. RESULTS: The allele-specific primers of the double ARMS assay reliably amplified the RHD-deleted allele and therefore accurately distinguished homozygous from heterozygous RhD-positive samples. The results were in complete concordance with serological testing. For the multiplex real-time quantitative PCR assay, the DeltaCt values clearly segregated into two distinct populations according to the RHD gene dosage, with mean values of 1.70 (SD, 0.17) and 2.62 (SD, 0.29) for the homozygous and heterozygous samples, respectively (P: <0.001, t-test). The results were in complete concordance with the results of serological testing as well as with the double ARMS assay. CONCLUSION: Double ARMS and real-time quantitative PCR are alternative robust assays for the determination of RhD zygosity.

Albumins↗
PubMed2002

Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification.

Real-time quantitative PCR assays were developed for the absolute quantification of different groups of bacteria in pure cultures and in environmental samples. 16S rRNA genes were used as markers for eubacteria, and genes for extracellular peptidases were used as markers for potentially proteolytic bacteria. For the designed 16S rDNA TaqMan assay, specificity of the designed primer-probe combination for eubacteria, a high amplification efficiency over a wide range of starting copy numbers and a high reproducibility is demonstrated. Cell concentrations of Bacillus cereus, B. subtilis and Pseudomonas fluorescens in liquid culture were monitored by TaqMan-PCR using the 16S rDNA target sequence of Escherichia coli as external standard for quantification. Results agree with plate counts and microscopic counts of DAPI stained cells. The significance of 16S rRNA operon multiplicity to the quantification of bacteria is discussed.Furthermore, three sets of primer pair together with probe previously designed for targeting different classes of bacterial extracellular peptidases were tested for their suitability for TaqMan-PCR based quantification of proteolytic bacteria. Since high degeneracy of the probes did not allow accurate quantification, SybrGreen was used instead of molecular probes to visualize and quantify PCR products during PCR. The correlation between fluorescence and starting copy number was of the same high quality as for the 16S rDNA TaqMan assay for all the three peptidase gene classes. The detected amount of genes for neutral metallopeptidase of B. cereus, for subtilisin of B. subtilis and for alkaline metallopeptidase of P. fluorescens corresponded exactly to the numbers of bacteria investigated by the 16S rDNA targeting assay. The developed assays were applied for the quantification of bacteria in soil samples.

Bacillus cereus↗
PubMed2006

Whole blood real-time quantitative PCR for cytomegalovirus infection follow-up in transplant recipients.

BACKGROUND: Cytomegalovirus (CMV) remains a major opportunistic agent among transplant recipients. While detection of CMV pp65-lower matrix protein (pp65Ag) is still widely used for monitoring CMV infection, real-time PCR assays have been recently developed for routine quantitation of CMV DNA. However, correlations are lacking between results of pp65Ag and quantitative PCR assays and there is no consensus yet as to the more appropriate blood compartment (whole blood (WB), leukocytes, plasma) to be tested with PCR assays. OBJECTIVES: The aims of the study were to determine, in a population of transplant recipients: (i) the correlation between pp65Ag and CMV quantitative real-time PCR in our setting and (ii) the utility of plasma CMV DNA quantitation in comparison to WB quantitation. METHODS: In 170 blood samples (from 61 solid organ or bone marrow transplant recipients) with pp65Ag results, CMV quantitation was performed in WB and plasma using an in-house real-time quantitative PCR. RESULTS: Real-time PCR and pp65Ag results in WB were correlated: thresholds of 10 and 50(+) cells/200,000 cells were equivalent to 3.3 log(10)copies/mL (2,000 copies/mL) and 3.8 log(10)copies/mL (6,300 copies/mL), respectively. When WB viral load was >or=3.6 log(10)copies/mL, the risk to have a negative plasma CMV DNA result was <or=2.5%. CONCLUSIONS: For the routine exploration of a single compartment, whole blood would represent a suitable compromise: easy processing for a sensitive assay. The 3.6 log(10)copies/mL threshold, which could help in identifying active CMV infection, deserves further evaluation.

Adult↗
PubMed2000

A novel closed-tube quantitative--PCR method for enumerating Porphyromonas gingivitis, Prevotella intermedia and Actinobacillus actinomycetemcomitans.

Enumeration of specific periodontopathogens in subgingival plaque samples has been problematic because of either lack of sensitivity, specificity or the time taken to identify the organisms. These problems can be overcome using PCR, but quantification by this technique is more difficult. We report a simple quantitative PCR method developed for enumerating Porphyromonas gingivalis, Prevotella intermedia and Actinobacillus actinomycetemcomitans in clinical samples. The method relies upon inclusion of ethidium bromide in a closed-tube PCR reaction and measurement of resultant amplicons by quantifying the fluorescence generated when UV-light is passed through the walls of the amplification tube. Hence, both PCR and detection are performed in the same tube. The technique was compared with a quantitative competitive PCR and a commercial colorimetric quantitative PCR and proved to be at least as sensitive, specific and reliable for enumeration of the target bacteria. However, its speed and convenience make it particularly useful for large-scale analyses in both clinical laboratories and epidemiological studies.

Aggregatibacter actinomycetemcomitans↗
PubMed2006

Practical application of fluorescent quantitative PCR on Trisomy 21 in Chinese Han population.

OBJECTIVE: To apply the fluorescent quantitative PCR method on the detection of Trisomy 21 by D21S11 locus and make a foundation for rapid prenatal diagnosis of Trisomy 21. METHODS: About 409 controls (39 amniotic fluid samples and 370 peripheral blood samples) and 35 patients (4 amniotic fluid samples and 31 peripheral blood samples) with Trisomy 21 were tested using fluorescent quantitative PCR by amplification of DNA fragment on D21S11 STR locus. The results were compared with conventional cytogenetic analysis to confirm the utility of this method. And the allele frequency distributions of D21S11 STR locus were analyzed. RESULTS: The 95% reference interval of fluorescent intensity ratios of peak heights of PCR products amplified from two alleles on D21S11 locus ranged from 0.84 to 1.42 (1.13 +/- 0.29) in heterozygous controls. About 19 out of 35 patients showed a "diallelic" pattern and their height ratio of fluorescent peaks of PCR products amplified from two alleles in patients with "diallelic" patterns were all outside of the 95% reference range of controls. The PCR products of DNA from 12 patients presented the third allele. No sample with the "monoallelic" pattern was found. Four chimeras diagnosed by cytogenetic method could not be diagnosed by this method. There were 17 and 11 alleles found in controls and patients, respectively. About 343 out of 409 controls were heterozygous and the heterozygosity was 83.86%. We did not find any significant differences in the frequency distributions of alleles on D21S11 locus between controls and patients. But there were significant differences in the frequency distributions of alleles on D21S11 locus between controls and patients. But there were significant differences in the frequency distributions of alleles on D21S11 locus among different populations. CONCLUSIONS: The fluorescent quantitative polymerase chain reaction method was rapid, accurate, and only small amount of starting material was needed, it could be applied in rapid prenatal diagnosis of Trisomy 21. D21S11 was a good marker with high heterozygosity for the screening of Trisomy 21. And the frequency distributions of alleles on D21S11 locus were significantly related to ethnic background.

Amniotic Fluid↗
PubMed2005

[Establishment and application of fluorescent quantitative PCR method for detecting human herpes virus type 6].

OBJECTIVE: To establish fluorescent quantitative PCR method for detecting human herpes virus type 6 (HHV6). METHODS: According to the specific sequence of human herpes virus type 6 genes, the primers and the fluorescent probe (TaqMan) were designed and synthesized. The fragment generated from HHV 6 gene as template was cloned into the pMD18-T vector which was constructed from the pUC 18. And the positive recombinant plasmid was 1:10 diluted and used as standard quantitative template to make the standard curve for sample detection. RESULTS: The standard curve indicated the linear relationship between Ct (cycle threshold) and template concentration. The clinical samples from 135 cases were detected by this system, 16 cases among 135 were positive. CONCLUSION: The fluorescent quantitative PCR method for the detection of human herpes virus type 6 is simple and accurate, and this method may be helpful to clinical diagnosis.

Adolescent↗
PubMed2004

[Establishment of a real time quantitative-PCR assay for detection of TCR VgammaI-Jgamma gene rearrangement in acute lymphoblastic leukemia patients].

OBJECTIVE: To improve the techniques for minimal residual disease (MRD) detection in acute lymphoblastic leukemia (ALL). METHODS: A real time quantitative PCR method was established for quantifying the clonal TCRVgammaI-Jgamma gene rearrangement in 36 ALL patients. RESULTS: The sensitivity of the established real time quantitative PCR was at 10(-4) level. The amount of TCRVgammaI-Jgamma gene rearrangement in newly diagnosed group, complete remission (CR) group and post hematopoietic stem cell transplantation (HSCT) group was (7.38 +/- 6.65) x 10(-2), (1.02 +/- 1.08) x 10(-2) and (3.89 +/- 5.65) x 10(-3) level, respectively. and the amount in newly diagnosed group was higher than that in CR group and HSCT group (P = 0.001). The MRD level of ALL patients in CR group was higher than that in HSCT group (P = 0.022). MRD can be detected in 6 ALL patients after HSCT, 2 of them with low MRD level (< 1 x 10(-3)) survived long disease-free survival, the other 4 with high MRD level relapsed within one year. CONCLUSION: The established real time quantitative PCR assay is simple, rapid, sensitive and specific. Use of this assay to evaluate MRD in the remission ALL cases is helpful for prognosis prediction.

Adolescent↗
PubMed2002

Evaluation of antibiotic susceptibilities of three rickettsial species including Rickettsia felis by a quantitative PCR DNA assay.

Rickettsiae grow only intracellularly, and the antibiotic susceptibilities of these bacteria have been assessed by either plaque, dye uptake, or immunofluorescence assays, which are time-consuming. We used a quantitative PCR (with the LightCycler instrument) to assess the levels of inhibition of Rickettisa felis, R. conorii, and R. typhi DNA synthesis in the presence of various antibiotics. We established the kinetics of rickettsial DNA during growth and showed that R. conorii grows more quickly than R. typhi in cell culture, with maximum replication occurring after 5 and 7 days, respectively. The MICs of the antibiotics tested for R. conorii and R. typhi by the quantitative PCR assay were similar to those previously obtained by plaque and dye uptake assays. We found that R. felis is susceptible to doxycycline, rifampin, thiamphenicol, and fluoroquinolones but not to gentamicin, erythromycin, amoxicillin, or trimethoprim-sulfamethoxazole. The resistance of this new species to erythromycin is consistent with its current taxonomic position within the spotted fever group. We believe that quantitative PCR could be used in the future to simplify and shorten antibiotic susceptibility assays of other rickettsiae and other strict intracellular pathogens.

Anti-Bacterial Agents↗
PubMed1997

[A novel quantitative PCR with fluorogenic probe].

The polymerase chain reaction(PCR) is a powerful tool to amplify small amounts of DNA or RNA for various molecular analysis. However, in these analyses, PCR only provides qualitative results. The availability of quantitative PCR provides valuable additional information in various applications. It is difficult to establish absolute quantitation, because PCR amplification is a complicated reaction process of exponential growth. To trace the amplification process, the initial amount of template and the efficiency of amplification in each cycle, has to be determined. Conventional methods have not achieved absolute quantitative analysis. The ABI PRISM 7700 Sequence Detection System has solved these problems with real-time monitoring of the PCR process. The real-time detection system provides essential information to quantify the initial target copy number, because it can draw an amplification curve. Using the 5' nuclease assay, a specific fluorescent signal is generated and measured at every cycle during a run. This system can perform a variety of applications including, quantitation, allele discrimination, PCR optimization and viral screening. Using the ABI PRISM 7700 Sequence Detection System, the rice genome has been quantitatively analyzed. To monitor maturation of the chloroplast genome from proplastid during germ development, 5' nuclease assay set up for Cab and rbcL genes which are located in the nuclear genome and chloroplast genome, respectively. Cab was used as an internal standard for normalization of cell numbers. The maturation process of chloroplast was estimated using the ratio of gene dosage, [rbcL]/[Cab]. After development of cotyledon, a significant increase in copy numbers of the chloroplast was observed. These results indicate that a light-induced chloroplast maturation process is coupled with an increase in chloroplast genome copy numbers.

Chloroplasts↗
PubMed2005

Real-time, fluorescence-based quantitative PCR: a snapshot of current procedures and preferences.

Real-time fluorescence-based quantitative PCR has become established as the benchmark technology for the quantification of nucleic acids, offering an immense choice of protocols, chemistries and instruments. However, whilst there are comparatively few technical problems associated with DNA-targeted quantitative PCR, this is not the case for real-time reverse transcription PCR assays, and there is considerable uncertainty regarding biological or clinical relevance of many real-time reverse transcription PCR results. A survey of working practices of nearly 100 delegates carried out prior to the Third qPCR Symposium held in London, UK, April 25-26, 2005, reveals some of the reasons underlying the variability of reported real-time reverse transcription PCR results. Specifically, the survey reveals extensive interlaboratory variation in assay design, validation and analysis that, together with other dubious practices, are the likely cause for the publication of variable results. These results emphasize the urgent need for the establishment of best practice guidelines for this technology, particularly in the context of its mounting adaptation as a high-throughput clinical diagnostic assay.

DNA Primers↗
PubMed2005

Validation of a cotton-specific gene, Sad1, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic cottons.

Genetically modified (GM) cotton lines have been approved for commercialization and widely cultivated in many countries, especially in China. As a step towards the development of reliable qualitative and quantitative PCR methods for detecting GM cottons, we report here the validation of the cotton (Gossypium hirsutum) endogenous reference control gene, Sad1, using conventional and real-time (RT)-PCR methods. Both methods were tested on 15 different G. hirsutum cultivars, and identical amplicons were obtained with all of them. No amplicons were observed when DNA samples from three species of genus Gossypium, Arabidopsis thaliana, maize, and soybean and others were used as amplified templates, demonstrating that these two systems are specific for the identification and quantification of G. hirsutum. The results of Southern blot analysis also showed that the Sad1 gene was two copies in these 15 different G. hirsutum cultivars. Furthermore, one multiplex RT-quantitative PCR employing this gene as an endogenous reference gene was designed to quantify the Cry1A(c) gene modified from Bacillus thuringiensis (Bt) in the insect-resistant cottons, such as Mon531 and GK19. The quantification detection limit of the Cry1A(c) and Sad1 genes was as low as 10 pg of genomic DNA. These results indicate that the Sad1 gene can be used as an endogenous reference gene for both qualitative and quantitative PCR detection of GM cottons.

DNA, Plant↗
PubMed2006

[Real-time fluorescence quantitative PCR in detecting ribosome protein S13 (RPS13) gene expression in NK/T cell lymphoma].

OBJECTIVE: To quantitatively detect the expression level of ribosome protein S13 (RPS13) in NK/T cell lymphoma. METHODS: The total RNA isolated from the parafin-embedded tissue of NK/T cell lymphoma was reversely transcribed into cDNA. The real-time fluorescence quantitative PCR technology method was used to analyze the expression level of RPS13 gene. RESULTS: The real-time fluorescence quantitative PCR technology was successfully performed to precisely detect the mRNA level. The expression level of RPS13 gene in tumor tissue of 20 cases of NK/T cell lymphoma was dramatically lower than that in normal peripheral blood lymphocyte of healthy controls. CONCLUSION: The RPS13 gene has lower expression level in tumor tissue cells of NK/T cell lymphoma than in normal lymphocyte, indicating that it plays an role in the development of the NK/T cell lymphoma.

Humans↗
PubMed1995

Gene amplification for c-erbB-2, c-myc, epidermal growth factor receptor, int-2, and N-myc measured by quantitative PCR with a multiple competitor template.

We recently proposed a quantitative PCR procedure for the absolute measurement of c-erbB-2 oncogene amplification, based on the simultaneous polymerase chain reaction (PCR) amplification of the target gene and of a competitor DNA molecule acting as internal standard. To increase the number of assayable oncogenes and the accuracy of the quantitative comparison of gene amplification degree within the same tumor, we have now constructed a single synthetic competitor for int-2, c-myc, N-myc epidermal growth factor receptor, and c-erbB-2 genes, and for the reference gene beta-globin. This competitor was constructed by a two-step recombinant PCR procedure and inserted as a 297-bp sequence in a plasmid. The order of primer insertion was designed to obtain competitors of comparable sizes to those of the respective genomic targets, but still easily recognizable from the latter ones by gel electrophoresis. The clone competitor was tested to evaluate the linearity range for each assay. The present application of quantitative PCR based on a multiple competitor represents the first approach for the achievement of a single reagent for the evaluation of a panel of genes potentially amplified in human tumors.

Base Sequence↗
PubMed1993

Regulation of human renin secretion and renin transcription by quantitative PCR in cultured chorionic cells: synergistic effect of cyclic AMP and protein kinase C.

A quantitative PCR was developed to measure human renin mRNA in chorionic cells under various stimuli. An internal standard consisting of a mutated renin mRNA with an insertion of 60 bp was designed to quantify the reaction. Quantitative PCR is a suitable tool for studying human renin gene transcription from a low number of cells. Forskolin alone had no effect on either renin mRNA levels or renin production whereas 10(-7)M PMA stimulated renin mRNA levels and renin production 5- and 2.6-fold, respectively, after 24 hours incubation. PMA and forskolin acted synergistically to increase both renin mRNA levels and renin production in a dose-dependent manner.

Base Sequence↗
PubMed2005

Comparison of quantitative PCR and antigenemia in cytomegalovirus infection in renal transplant recipients.

UNLABELLED: Cytomegalovirus infection is a common complication of renal transplantation. Antigen pp65 levels serve as indicators of viral load, although the technique is difficult to perform and interpret. We sought to determine whether quantitative PCR had a higher sensitivity and predictive value in CMV infection. METHODS: The study included 100 renal transplant recipients who were screened for IgM and IgG at the time of admission. On days 7, 15, 30, 45, 60, 75, 90, 120, 180, and 360, antigenemia tests were performed on blood (pp65) and urine, and a quantitative PCR on blood. Among 59 patients recruited between November 2003 and August 2004 the mean age was 54.5 +/- 12.9 years. Two patients did not reach 90 days follow-up (3%); four patients have not surpassed 90 days (7%); 22, 120 days (37%); and 31, 180 days (53%). Ninety-three percent of patients showed anti-IgG CMV-positive titers with all being IgM CMV-negative at baseline. The patients at risk for infection were given valgancyclovir as prophylaxis throughout the study. RESULTS: At 474 visits, 8 samples (2.4%) were positive with urine; 5 (1.4%) with pp65, and 15 (4.7%) with PCR. Among the 15 positive samples, two (>100,000 and 3250 copies) revealed agreement of positive IgM and shellvial test on urine; two (15,100 and 5670 copies), antigen pp65 1+; one (17,400 copies) with pp65 2+ and shellvial urine; two (99,400 and 28,300 copies) with pp65 1+ and shellvial urine; and eight remaining determinations, 749, 2250, 686, 928, 2250, 26600, 777, and 2790 copies. The rest of the tests were negative. CONCLUSION: The preliminary results of this study demonstrated that quantitative PCR was a useful rapid tool for diagnosing and monitoring CMV infections.

Antigens, Viral↗
PubMed2005

Effect of tissue fixatives on telomere length determination by quantitative PCR.

Telomere length is a well established marker of cellular senescence and thus biological age. Quantitative PCR allows the determination even from very low amounts of tissue by using telomere specific and single copy gene primers. Comparing a directly processed tissue sample to a 4% formaldehyde fixed one showed a significantly reduced efficiency of PCR reactions (mainly in single copy gene experiments) in a storage time-dependent manner resulting in an artificial increase in reported relative telomere length. This effect was not seen when the tissue was stored in RNA later solution. In summary, telomere length determination from formaldehyde fixed material by quantitative PCR is not a reliable method. Unfortunately therefore, many easily accessible tissue samples from pathology laboratories are unsuitable for this technique.

Cellular Senescence↗
PubMed2005

Standardisation of data from real-time quantitative PCR methods - evaluation of outliers and comparison of calibration curves.

BACKGROUND: As real-time quantitative PCR (RT-QPCR) is increasingly being relied upon for the enforcement of legislation and regulations dependent upon the trace detection of DNA, focus has increased on the quality issues related to the technique. Recent work has focused on the identification of factors that contribute towards significant measurement uncertainty in the real-time quantitative PCR technique, through investigation of the experimental design and operating procedure. However, measurement uncertainty contributions made during the data analysis procedure have not been studied in detail. This paper presents two additional approaches for standardising data analysis through the novel application of statistical methods to RT-QPCR, in order to minimise potential uncertainty in results. RESULTS: Experimental data was generated in order to develop the two aspects of data handling and analysis that can contribute towards measurement uncertainty in results. This paper describes preliminary aspects in standardising data through the application of statistical techniques to the area of RT-QPCR. The first aspect concerns the statistical identification and subsequent handling of outlying values arising from RT-QPCR, and discusses the implementation of ISO guidelines in relation to acceptance or rejection of outlying values. The second aspect relates to the development of an objective statistical test for the comparison of calibration curves. CONCLUSION: The preliminary statistical tests for outlying values and comparisons between calibration curves can be applied using basic functions found in standard spreadsheet software. These two aspects emphasise that the comparability of results arising from RT-QPCR needs further refinement and development at the data-handling phase. The implementation of standardised approaches to data analysis should further help minimise variation due to subjective judgements. The aspects described in this paper will help contribute towards the development of a set of best practice guidelines regarding standardising handling and interpretation of data arising from RT-QPCR experiments.

Biotechnology↗
PubMedDate not supplied

Detection and quantification of the iap gene of Listeria monocytogenes and Listeria innocua by a new real-time quantitative PCR assay.

A real-time quantitative polymerase chain reaction (PCR) assay for direct detection and enumeration of Listeria monocytogenes and Listeria innocua was developed and applied to artificially contaminated milk samples. The iap gene present in both species was used as a target for amplification of a 175-bp (L. monocytogenes) and a 309-bp (L. innocua) fragment. To ensure that L. monocytogenes and L. innocua are specifically detectable, tests were carried out using 42 L. monocytogenes strains and 33 L. innocua strains belonging to different serovars. Specificity was also confirmed using 22 bacterial strains not belonging to the genus Listeria, including closely related bacteria. In addition to specificity, the reported assay is characterized by a wide dynamic range of quantification and a high sensitivity, as we could detect as few as six copies of the iap gene per PCR using purified DNA as template. When applied to direct detection and quantification of L. monocytogenes in milk, the more rapid real-time quantitative PCR assay was as sensitive as the traditional plate count method, but real-time quantitative PCR-derived iap gene copy numbers were one to two logs higher than colony-forming units obtained by the plate count method.

Animals↗