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PubMed1998

[Quantitative PCR system].

We evaluated a real time quantitative PCR assay using dual-labeled fluorogenic probes for clinical application. Preliminary study using the house-keeping gene, beta-actin confirmed that this method was accurate and reproducible for the quantitative detection of the genes. The system also has merit with regard to the dynamic range of the starting target molecule determination. We then investigated DNA copies of cytomegalovirus (CMV) gene in vivo. The results demonstrated on association between the quantitation of CMV-DNA copies and clinical manifestation associated with CMV infection of immunodeficiency states or infantile hepatitis. It was also successful for quantitative estimation by RT-PCR. Namely, the assay made it possible to discriminate drug-sensitive leukemia cells from resistant cells based on the MDR1 gene and dCK gene. Real time quantitative PCR assay may be useful in a variety of clinical fields.

Cytomegalovirus↗
PubMed2005

Effectiveness of real-time quantitative PCR compare to repeat PCR for the diagnosis of Charcot-Marie-Tooth Type 1A and hereditary neuropathy with liability to pressure palsies.

The majority of cases of Charcot-Marie-Tooth type 1A (CMT1A) and of hereditary neuropathy with a liability to pressure palsies (HNPP) are the result of heterozygosity for the duplication or deletion of peripheral myelin protein 22 gene (PMP22) on 17p11.2. Southern blots, pulsed-field gel electrophoresis (PFGE), fluorescence in situ hybridization (FISH) and polymorphic marker analysis are currently used diagnostic methods. But they are time-consuming, labor-intensive and have some significant limitations. We describe a rapid real- time quantitative PCR method for determining gene copy number for the identification of DNA duplication or deletion occurring in CMT1A or HNPP and compare the results obtained with REP-PCR. Six patients with CMT1A and 14 patients with HNPP [confirmed by Repeat (REP)-PCR], and 16 patients with suspicious CMT1A and 13 patients with suspicious HNPP [negative REP-PCR], and 15 normal controls were studied. We performed REP-PCR, which amplified a 3.6 Kb region (including a 1.7Kb recombination hotspot), using specific CMT1A-REP and real-time quantitative PCR on the LightCycler system. Using a comparative threshold cycle (Ct) method and beta -globin as a reference gene, the gene copy number of the PMP22 gene was quantified. The PMP22 duplication ratio ranged from 1.35 to 1.74, and the PMP22 deletion ratio from 0.41 to 0.53. The PMP22 ratio in normal controls ranged from 0.81 to 1.12. All 6 patients with CMT1A and 14 patients with HNPP confirmed by REP-PCR were positive by real-time quantitative PCR. Among the 16 suspicious CMT1A and 13 suspicious HNPP with negative REP-PCR, 2 and 4 samples, respectively, were positive by real-time quantitative PCR. Real-time quantitative PCR is a more sensitive and more accurate method than REP-PCR for the detection of PMP22 duplications or deletions, and it is also faster and easier than currently available methods. Therefore, we believe that the real-time quantitative method is useful for diagnosing CMT1A and HNPP.

Charcot-Marie-Tooth Disease↗
PubMed1995

Quantitative PCR for human herpesviruses 6 and 7.

A quantitative PCR assay for the detection of human herpesvirus 6 (HHV-6) (variants A and B) and HHV-7 DNAs in clinical samples was developed. The assay uses a nonhomologous internal standard (IS) for each virus that is coamplified with the wild-type target sequence in the same vial and with the same pair of primers. This method allows for a correction of the variability of efficiency of the PCR technique. A standard curve is constructed for each experiment by coamplification of known quantities of the cloned HHV-6 or HHV-7 target templates with the respective IS. Absolute quantitation of the test samples is then achieved by determining the viral target/IS ratio of the hybridization signals of the amplification products and plotting this value against the standard curve. Using this assay, we quantitated the amount of HHV-6 or HHV-7 DNA in infected cell cultures and demonstrated an inhibitory effect of phosphonoformic acid on the replication of HHV-6 and HHV-7 in vitro. As the first clinical application of this procedure, we performed preliminary measurements of the loads of HHV-6 and HHV-7 in lymph nodes from patients with Hodgkin's disease and AIDS. Application of this quantitative PCR method should be helpful for elucidating the pathogenic roles of HHV-6 and HHV-7.

Acquired Immunodeficiency Syndrome↗
PubMed2005

[Detection of IgH rearrangements using real-time quantitative PCR and its reaction parameters].

To investigate the optimal reaction conditions of clonal rearrangements of immunoglobulin heavy chain (IgH) gene using polymerase chain reaction (PCR) with consensus primers and the feasibility of detecting this gene using SYBR green I real-time quantitative PCR with consensus primers, the systemic experiments were performed, which included annealing temperature, concentration of primer, the amount of Taq enzyme, concentration of dNTP and Mg(2+), number of PCR cycles. Detection of this gene on SYBR green I real-time quantitative PCR with consensus primers was carried out under the optimal reaction parameters obtained from previous study, and the sensitivity of IgH rearrangements gene was examined by using SYBR green I real-time quantitative PCR. The results indicated that the optimal annealing temperature was 60 degrees C, the optimal concentration of primers was 0.8 micromol/L, the satisfactory Taq enzyme amount was 0.5 U, the optimal concentration of dNTP was 100 micromol/L, the optimal concentration of Mg(2+) was 3.0 mmol/L, the suitable number of cycle was 40 cycles. Amplification of IgH rearrangement gene and detection of desired gene fluorescence signal on SYBR green I real-time PCR were performed. The sensitivity of IgH gene using this quantitative PCR was 10(4)/ml. It is concluded that the optimal reaction parameters for amplification of clonal IgH rearrangements gene by using PCR technique was determined, and stable and specific amplification of desired gene with consensus primers was performed. Basically, IgH rearrangement gene was successfully detected by SYBR green I real-time PCR.

Benzothiazoles↗
PubMed2006

[Real-time quantitative PCR for evaluating murine thymic function].

OBJECTIVE: To establish a real-time quantitative PCR method for detecting the levels of the signal joint T cell receptor excision circles (sjTRECs) in murine thymocytes and spleen lymphocytes for determining the amount of naive T cells and evaluating the thymic function. METHODS: The genomic DNA was extracted from murine thymocytes and splenocytes for PCR amplification of the target fragments. After purification of the PCR product, the recombination-activating gene 2 (RAG(2)) fragment was cloned into pGEMT-Easy vector to construct the standard plasmid. After PCR optimization, the standard curve was obtained and the samples (thymocytes and splenocytes of BALB/c and C(57)BL/6 mice) were detected for sjTRECs by real-time quantitative PCR. RESULTS: The standard plasmid was correctly constructed, and the standard curve with high reliability was obtained. No statistical difference was observed in sjTREC contents in the T lymphocytes between the two mouse strains. CONCLUSIONS: Real-time quantitative PCR for sjTREC analysis is established successfully, which offers an important means for thymic function analysis and a reliable model establishment for study the thymus.

Animals↗
PubMed2000

How quantitative is quantitative PCR with respect to cell counts?

Quantitative diagnostic PCR systems based upon rDNA targeted primer and probe combinations were developed for the detection of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas alcaligenes, enterococci, Staphylococcus aureus, and Staphylococcus epidermidis. Primers and probes were designed in silico using the ARB software package (TU Munich) in combination with Primer Design software of PE Applied Biosystems. Purified genomic DNA or bacterial cells of target and reference organisms were used for the evaluation of the PCR assays applying the TaqMan technique on an ABI PRISM TM 7700 Sequence Detection System (PE Applied Biosystems). Sensitive, reliable and reproducible quantification of target rDNA could be achieved applying primer-probe combinations that mediate in vitro amplification of DNA fragments smaller than 100 base pairs. Large amounts of non target DNA (1 mg per sample) remarkably affected the quantification potential of the approach resulting in an underestimation of the amounts of target DNA. One of the principal goals was to use quantitative PCR to study the correlation of gene and cell numbers depending on the growth behavior of target organisms and to explore the potential to estimate cell numbers from target DNA quantification. A clear correlation of rDNA quantification and bacterial growth was observed, however, cell numbers cannot directly be estimated from quantitative PCR data, given that the cellular genome content varies with the growth phase of the organisms. In the case of Escherichia coli the cell numbers which could be assigned to a certain number of rDNA targets varied reasonably depending upon the growth phase of batch cultures.

Bacteria↗
PubMed1997

Myosin heavy chain mRNA transform to faster isoforms in immobilized skeletal muscle: a quantitative PCR study.

A quantitative polymerase chain reaction (PCR) method was used to measure the quantities of type I, IIa, IIx, and IIb myosin heavy chain (MHC) mRNA in total RNA preparations of the soleus, gastrocnemius, and plantaris muscles of normal and hindlimb-immobilized rats. Type IIx and even type IIb MHC mRNA were demonstrated at extremely low levels in normal soleus, 2.1 +/- 0.4 x 10(5) and 5.0 +/- 0.2 x 10(5) molecules of mRNA per microgram total RNA, respectively. Immobilization for 1 wk significantly altered the gene expression of MHC isoforms. In soleus, both type IIx and IIb MHC genes became significantly upregulated, 24-fold (P < 0.005) and 2.6-fold (P < 0.05), respectively. In gastrocnemius, the level of type IIa MHC mRNA decreased by 51% (P < 0.01) and the level of type IIx MHC mRNA increased by 140% (P < 0.05). In plantaris, the level of type IIa MHC mRNA decreased by 58% (P < 0.005). In conclusion, immobilization changed the MHC mRNA profile in three different types of skeletal muscle toward faster isoforms. The quantitative results permit reliable evaluation of changes in mRNA levels.

Animals↗
PubMed1998

Quantitative detection of t(14;18)-positive cells by real-time quantitative PCR using fluorogenic probes.

To detect t(14;18)-positive cells present in human lymphoma tissue, bone marrow aspirates and peripheral blood mononuclear cells (PBMNC), we have established an automated, real-time quantitative PCR using double-labeled fluorogenic probes. In relation to t(14;18)-positive genomic DNA or a cloned t(14;18)-DNA fragment, highly reproducible results can be obtained with initial copy numbers between 10 to 10(5). The detection of single copies has been verified by the stochastic multiple-tube approach. PBMNC cells obtained during clinical follow-up of patients with follicular lymphoma were analyzed by the one-step, real-time quantitative PCR and a two-step, semi-nested PCR combined with a limiting dilution assay. The quantitative results obtained by both assays correlate very well. Real-time quantitative PCR has several advantages: (i) it involves less critical pipetting steps, (ii) is less time-consuming and (iii) UTP, in combination with uracil-N-glycosylase, can be used to control carryover contamination. The higher specificity is due to optimized primer annealing conditions and MgCl2 concentration and the use of AmpliTaq Gold. The sensitivity is at least as high as by the two-step PCR. Real-time quantitative PCR will be very helpful in large epidemiological studies and in research for molecular staging and the detection of minimal residual tumor cells, including the analysis of blood stem-cell preparations to be used for transplantation after myelo-ablative therapy.

Cloning, Molecular↗
PubMed2003

Gene-specific monitoring of T7-based RNA amplification by real-time quantitative PCR.

T7-based RNA amplification is applied when there is insufficient RNA. The overall extent of amplification can be measured spectrophotometrically (i.e., quantifying RNA yields), but this measurement does not provide information about the RNA amplification of individual genes. Here we describe a method applying real-time quantitative PCR, which enables the monitoring of RNA amplification of individual genes. The amount of RNA before and after T7-based RNA amplification was determined by real-time quantitative PCR for three housekeeping genes: beta-2-microglobulin, porphobilinogen deaminase, and serine dehydratase, which are, respectively, a high, intermediate/low, and low copy transcript. Real-time quantitative PCR appeared to be suitable to determine the extent of RNA amplification, as was reflected by the low intra- and inter-run coefficients of variation of cycle threshold of 1.1%-2.1%. The application of real-time quantitative PCR showed that T7-based RNA amplification is reproducible but might introduce a sequence-specific bias. Real-time quantitative PCR is a novel approach to monitor RNA amplification and is particularly suited to study RNA amplification of individual genes.

Bacteriophage T7↗
PubMed1992

Accumulation of deletions in human mitochondrial DNA during normal aging: analysis by quantitative PCR.

We have developed a quantitative PCR technique to measure the amount of a specific mitochondrial DNA deletion (delta mtDNA), the so-called 'common deletion', in human tissues. Using this method, we estimate that there is a 10,000-fold increase in this delta mtDNA species in muscle during the course of the normal human lifespan. The maximum amount of common deletion observed in aged muscle was approx. 0.1%. Tissues that turn-over slowly, such as skeletal muscle and heart, contained more delta mtDNA than more rapidly dividing tissues, such as liver, in agreement with studies performed by others.

Aging↗
PubMed1997

Engraftment of normal stem cells in W/Wv mice assessed by a novel quantitative PCR analysis.

We describe a quantitative PCR based on the unique Nsi 1 restriction site generated by the Wv mutation (C to T substitution at position 2007 of c-kit) to quantify the percentage of engraftment of wild-type stem cells in W/Wv mice. Primers flanking this mutation specifically amplify c-kit sequences from either genomic DNA or cDNA. After Nsi 1 digestion, wild-type products were identified by electrophoresis as a single 104bp (genomic DNA) or 118bp (cDNA) band whereas W/Wv products migrated as two bands: the 104-118bp band (corresponding to the W allele) and the 85bp band (corresponding to the Wv allele). The relationship between the ratio/Wv/total c-kit product versus the ratio W/Wv cells/total cells obtained in PCR amplification of artificial cell mixtures was expressed by a statistically significant linear regression. This indicated that the Wv/total c-kit ratio depends mainly upon the ratio between the two cell types in the preparation to be analysed. Therefore it is possible to determine the percentage of donor cells in tissues of W/Wv transplanted with normal stem cells by comparing the amplification ratio obtained with DNA extracted from the tissues with the ratio obtained in standard calibration curves. As applications of the technique, we determined the percentage of donor-derived cells in mononuclear blood fractions, in preparations of splenic B, T and myelomonocytic cells and in GM colonies cultured from the marrow of W/Wv mice transplanted with wild-type stem cells.

Animals↗
PubMed2004

Simple method of zygosity identification in transgenic mice by real-time quantitative PCR.

To determine zygosity in transgenic (Tg) mice, a new technology, real-time quantitative PCR, has recently been introduced in transgenic research to overcome several drawbacks (time-consuming, specialized techniques and/or ambiguity in the results) of previously established methods, for example, Southern blot hybridization, dot blot hybridization, fluorescence in situ hybridization (FISH), etc. However, the previous real-time quantitative PCR method still possesses several drawbacks, for example, it needs two sets of primers/probes and the complicated setting up of appropriate conditions, both of which are expensive and remain time-consuming. We therefore developed an improved real-time quantitative PCR system for determination of zygosity, which is easy, rapid and less expensive, because the technique needs only two experimental processes: estimation of DNA concentration and CYBR Green PCR. We found that homozygous, hemizygous and non-Tg animals could easily be distinguished among F1 littermates in crosses of hemizygous EGFP- and DsRed2-Tg mice. Our improved method will be applicable to any Tg mouse strains, when a primer set is matched to the corresponding transgene.

Animals↗
PubMed2006

Real-time quantitative PCR of Staphylococcus aureus and application in restaurant meals.

Staphylococcus aureus is considered the second most common pathogen to cause outbreaks of food poisoning, exceeded only by Campylobacter. Consumption of foods containing this microorganism is often identified as the cause of illness. In this study, a rapid, reliable, and sensitive real-time quantitative PCR was developed and compared with conventional culture methods. Real-time quantitative PCR was carried out by purifying DNA extracts of S. aureus with a Staphylococcus sample preparation kit and quantifying it in the LightCycler system with hybridization probes. The assay was linear from a range of 10 to 10(6) S. aureus cells (r2 > 0.997). The PCR reaction presented an efficiency of >85%. Accuracy of the PCR-based assay, expressed as percent bias, was around 13%, and the precision, expressed as a percentage of the coefficient of variation, was 7 to 10%. Intraday and interday variability were studied at 10(2) CFU/g and was 12 and 14%, respectively. The proposed method was applied to the analysis of 77 samples of restaurant meals in Valencia (Spain). In 11.6% of samples S. aureus was detected by real-time quantitative PCR, as well as by the conventional microbiological method. An excellent correspondence between real-time quantitative PCR and microbiological numbers (CFU/g) was observed with deviations of < 28%.

Colony Count, Microbial↗
PubMed2006

[Exon rearrangement analysis of parkin gene in patients with isolated early-onset parkinsonism using semi-quantitative PCR].

OBJECTIVE: To investigate the value of fluorescence semi-quantitative PCR in analysis of the exon rearrangement of parkin gene in Chinese patients with isolated early-onset parkinsonism (EOP). METHODS: fluorescence semi-quantitative PCR was used to analyze the exon rearrangements of parkin gene in 61 isolated patients with EOP. RESULTS: Exon deletions in parkin gene were found in 4 of the 61 isolated patients with EOP. One of them failed to show the PCR product of exon 4 and had homozygous deletions of exon 4. The normalized ratios (NRs) of exon 2, exon 3, and exon 4 of the other 3 patients were 0.47, 0.52, and 0.49 respectively, showing that they had heterozygous deletions of exon 2, 3, and 4 respectively. No exon multiplication was found in this study. CONCLUSION: Exon rearrangement of parkin gene exists in Chinese patients with isolated EOP.

Adolescent↗
PubMed2004

Evaluation of semi-quantitative PCR and IgG & IgM ELISA in diagnosis of toxoplasmosis in females with miscarriage.

One hundred female (age 20-42 yrs) patients were classified into group I: 40 patients presented with abortion in the first trimester; group II: 33 patients with abortion in the second trimester and group III: 27 patients with intrauterine fetal death (IUFD). The positive percentages of semi-quantitative PCR and both IgG & IgM ELISA were 38% and 35% respectively. Ten (26.3%) cases out of 38 were positive for toxoplasmosis by both PCR and ELISA-IgG, while 5 (13.2%) cases out of 38 were positive by both PCR and ELISA-IgM, whereas 16 (42.1%) cases out of 38 PCR positive cases were positive by both ELISA IgG & IgM. Sensitivity and specificity of both ELISA IgG and IgM were 81.57% & 93.54% respectively. False negative by ELISA were found in 7 cases out of 38 positive toxoplasmosis cases detected by semi-quantitative PCR. Three cases out of the 7 cases with false negative by ELISA were detected with a trophozoite copy load of 10(1) trophozoite /mL in the blood sample by semi-quantitative PCR. So, the semi-quantitative PCR detected low levels of parasite DNA recommending its usefulness especially in the early stages of the disease when low amount of antibodies can't be detected by serological method or even by the conventional PCR.

Abortion, Spontaneous↗
PubMed1998

Developments in quantitative PCR.

In recent years the growing interest in quantitative applications of the polymerase chain reaction (PCR) has favoured the development of a large number of assay procedures suitable for this purpose. In this paper we review some basic principles of quantitative PCR and in particular the role of reference materials and calibrators and the different strategies adopted for nucleic acid quantification. We focus on two methodological approaches for quantitative PCR in this review: competitive PCR and real-time quantitative PCR based on the use of fluorogenic probes. The first is one of the most common methods of quantitative PCR and we discuss the structure of the competitors and the various assay procedures. The second section is dedicated to a recent promising technology for quantitative PCR in which the use of fluorogenic probes and dedicated instrumentation allows the development of homogeneous methods. Assay performance of these methods in terms of practicability and reliability indicates that these kinds of technologies will have a widespread use in the clinical laboratory in the near future.

Animals↗
PubMedDate not supplied

One step screening of retroviral producer clones by real time quantitative PCR.

BACKGROUND: Recombinant retroviruses are obtained from either stably or transiently transfected retrovirus producer cells. In the case of stably producing lines, a large number of clones must be screened in order to select the one with the highest titre. The multi-step selection of high titre producing clones is time consuming and expensive. METHODS: We have taken advantage of retroviral endogenous reverse transcription to develop a quantitative PCR assay on crude supernatant from producing clones. We used Taqman PCR technology, which, by using fluorescence measurement at each cycle of amplification, allows PCR product quantification. Fluorescence results from specific degradation of a probe oligonucleotide by the Taq polymerase 3'-5' exonuclease activity. Primers and probe sequences were chosen to anneal to the viral strong stop species, which is the first DNA molecule synthesised during reverse transcription. The protocol consists of a single real time PCR, using as template filtered viral supernatant without any other pre-treatment. RESULTS: We show that the primers and probe described allow quantitation of serially diluted plasmid to as few as 15 plasmid molecules. We then test 200 GFP-expressing retroviral-producing clones either by FACS analysis of infected cells or by using the quantitative PCR. We confirm that the Taqman protocol allows the detection of virus in supernatant and selection of high titre clones. Furthermore, we can determine infectious titre by quantitative PCR on genomic DNA from infected cells, using an additional set of primers and probe to albumin to normalise for the genomic copy number. CONCLUSION: We demonstrate that real time quantitative PCR can be used as a powerful and reliable single step, high throughput screen for high titre retroviral producer clones.

Animals↗
PubMed2001

Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data.

Algorithms↗