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At least 793 records · Page 44Linked to original sources
PubMed2003

PCR-detectable nonneoplastic Bcl-2/IgH rearrangements are common in normal subjects and cancer patients at diagnosis but rare in subjects treated with chemotherapy.

PURPOSE: To assess whether nonneoplastic Bcl-2/IgH rearrangements act as a confounding factor in the setting of minimal residual disease analysis by evaluating their incidence in a panel of lymphoma-free subjects, including cancer-free donors and chemotherapy-naive and chemotherapy-treated cancer patients. PATIENTS AND METHODS: A total of 501 nonlymphoma subjects have been assessed: 258 cancer-free patients and 243 patients with malignancies other than lymphoma, 112 of whom were chemotherapy-naive. Patients were primarily assessed by nested polymerase chain reaction (PCR), followed by real-time quantitative PCR if they scored positive. In addition, six initially PCR-positive cancer-free donors were prospectively reassessed by qualitative and quantitative PCR after 30 and 60 days. RESULTS: The overall incidence of Bcl-2/IgH positivity was 9.6%, with a median number of 11 rearrangements per 1,000,000 diploid genomes (range, 0 to 2,845 rearrangements), as assessed by real-time PCR. The incidence was similar in healthy subjects and cancer patients at diagnosis (12% and 12.5%; P = not significant). In contrast, the incidence of this translocation was only 2.3% in chemotherapy-treated patients (P <.001). In addition, three initially PCR-positive cancer-free donors showed persistence of their rearrangements when assessed after 30 and 60 days. CONCLUSION: The low incidence of nonneoplastic Bcl-2/IgH rearrangements following chemotherapy provides further evidence of the prognostic role of persistent PCR-positivity in the posttreatment molecular follow-up of follicular lymphoma patients.

Adult↗
PubMed2004

Real-time quantitative PCR-based system for determining transgene copy number in transgenic animals.

In this paper, we describe a rapid and accurate real-time quantitative PCR-based system to determine transgene copy number in transgenic animals. We used the 2(-deltadeltaCt) method to analyze different transgenic lines without the requirement of a control sample previously determined by Southern blot analysis. To determine the transgene copy number in several mouse lines carrying a goat beta-Lactoglobulin transgene, we developed a TaqMan assay in which a goat genomic DNA sample was used as a calibrator. Moreover, we used the glucagon gene as a reference control because this gene is highly conserved between species and amplifies with the same efficiency and sensitivity in goat as in mouse. With this assay, we provide an alternative simple method to determine the transgene copy number, avoiding the traditional and tedious blotting techniques. The assay's discrimination ability from our results is of at least six copies and, similar to the limitations of the blotting techniques, the accuracy of the quantification diminishes when the transgene copy number is high.

Animals↗
PubMed2004

Guideline to reference gene selection for quantitative real-time PCR.

Today, quantitative real-time PCR is the method of choice for rapid and reliable quantification of mRNA transcription. However, for an exact comparison of mRNA transcription in different samples or tissues it is crucial to choose the appropriate reference gene. Recently glyceraldehyde 3-phosphate dehydrogenase and beta-actin have been used for that purpose. However, it has been reported that these genes as well as alternatives, like rRNA genes, are unsuitable references, because their transcription is significantly regulated in various experimental settings and variable in different tissues. Therefore, quantitative real-time PCR was used to determine the mRNA transcription profiles of 13 putative reference genes, comparing their transcription in 16 different tissues and in CCRF-HSB-2 cells stimulated with 12-O-tetradecanoylphorbol-13-acetate and ionomycin. Our results show that "Classical" reference genes are indeed unsuitable, whereas the RNA polymerase II gene was the gene with the most constant expression in different tissues and following stimulation in CCRF-HSB-2 cells.

Base Sequence↗
PubMed2002

X chromosome dosage by quantitative fluorescent PCR and rapid prenatal diagnosis of sex chromosome aneuploidies.

During the past few years, rapid prenatal diagnosis of chromosome aneuploidies has been successfully achieved by quantitative fluorescent PCR (QF-PCR) amplification of chromosome-specific small tandem repeats (STR). This approach has proven to be very useful in clinical settings, since it allows the detection of major numerical disorders in a few hours after sampling. For the detection of Turner's syndrome (45,X), several highly polymorphic STR on the X chromosome are needed in order to reduce the likelihood that a normal female might be homozygous for all sequences and, consequently, that the test could fail to discriminate between samples retrieved from a Turner's and a normal female fetus. Here we report a new method for rapid and accurate detection of X chromosome copy number in prenatal samples that does not depend on STR heterozygosity. The test is based on QF-PCR amplification of the X-linked HPRT together with the autosomal D21S1411 used as internal control for quantification. In the course of this study, this assay allowed the prenatal diagnosis of a rare case of a normal female homozygous for four selected highly polymorphic X chromosome STR, as well as the assessment of the normal chromosome complement of a fetus homozygous for five chromosome 21 markers.

Amniocentesis↗
PubMed2003

Optimizing stringency for expression microarrays.

While several studies have reported methods to optimize expression microarray protocols, none have dealt directly with hybridization wash stringency. We designed a series of experiments to determine the optimal stringency conditions for microarray experiments, using reproducibility and magnitudes of log2 (test/reference) ratio values as measures of quality. Low-stringency wash conditions of cell line hybridizations led to nonspecific binding, resulting in increased intensities, decreased magnitude of ratios, and poor reproducibility. Relatively high-stringency wash conditions were found to give the best reproducibility and large magnitude ratio changes, although increasing the stringency beyond this point led to lower magnitude ratios and poorer reproducibility. The expression levels of the ERBB2 oncogene in the BT474 versus MCF7 cell lines showed that high-stringency wash conditions gave the best agreement with real-time quantitative PCR, although the magnitude of the changes by microarray was smaller than for real-time quantitative PCR. Analysis of a series of cell lines washed at the optimized stringency indicated that the rank order of relative expression levels for ERBB2 microarray clones agreed well with the rank order of ERBB2 levels, as measured by quantitative PCR. These results indicate that the optimization of stringency conditions will improve microarray reproducibility and give more representative expression values.

Artifacts↗
PubMed2001

Changes in gene expression following induction of ischemic tolerance in rat brain: detection and verification.

Tolerance against ischemic insults can be elicited in the CA1 region of rat hippocampus by inducing a short ischemic period 2-3 days prior to the ischemic insult. To detect genes whose expression changes following induction of ischemic tolerance (IT), we applied a differential display technique called restriction fragment differential display-PCR (RFDD-PCR). RFDD-PCR displays the coding region of mRNA and allows detection of differentially expressed mRNA. Double-stranded cDNA generated using a T25V primer is digested by the endonuclease TaqI, and adapters are ligated onto the cDNA fragments. When amplifying the adapter-containing cDNA fragments under high-stringency conditions, reproducible PCR profiles are obtained. By comparing these profiles from naïve and ischemia-tolerant rat brains statistically, significant expression changes of 20 fragments were identified. To verify the observed changes, quantitative PCR and in situ hybridization were performed for three fragments representing proteins with quite different functions (GluR2-flop, SC1, and p68 RNA helicase). Quantitative PCR displayed the same degree of regulation as RFDD-PCR, but in situ hybridization did not display any regulation. As the applied PCR-based techniques detect only polyadenylated mRNA, whereas in situ hybridization detects both nonadenylated and adenylated mRNA, changes in the polyadenylation state of the mRNA, rather than inconsistent changes in the total amount of mRNA, probably explain this discrepancy. Thus, our results show that the expression of genes hitherto not related to IT changes with the induction of IT and that the degree of regulation displayed by RFDD-PCR can be verified by quantitative PCR.

Activated-Leukocyte Cell Adhesion Molecule↗
PubMed2006

[Correlation of hepatitis B e antigen with hepatitis B virus DNA in the serum of chronic hepatitis B patients after treatment].

OBJECTIVE: To analyze the correlation of hepatitis B virus (HBV) DNA with the serological markers of HB in the serum of chronic HB patients after treatment PCR method and to analyze the status of these markers and the multiplication of virus. METHODS: Peripheral blood samples were collected from 480 chronic HB patients, aged 15 - 50, who had been treated by anti-nucleotide drugs or traditional Chinese herbs and showed normal ALT/AST. Both COBAS AMPLICOR HBV MONIORTM kit (internal-standard PCR method) and Light Cycler real time fluorescent quantitative PCR instrument (external-quantitative standard PCR method) were used to measure the HBV DNAS level. 42 of the 312 patients with the HBV DNA level lower than the minimum test limit measured by COBAS AMPLICOR HBV MONIORTM kit and HBeAg positive (>4 S/CO) underwent microparticle enzyme immunoassay (MEIA) to test the HBsAg, anti-HBs, HBeAg, anti-HBe, and HBcIgG. RESULTS: Seven of the 42 patients with HBV DNA negative measured by COBAS AMPLICOR HBV MONIORTM kit lower then the minimum test limit were shown as HBV DNA positive by Light Cycler real time fluorescent quantitative PCR. The 42 patients were HBsAg (+), anti-HBs (-), HBeAg (+), anti-HBe (-), and anti-HBcIgG (-), with an average HBeAg level of 42.26 S/CO and a positive HBeAg rate of 13.46%. CONCLUSION: HBeAg positivity does not necessarily means an active multiplication of HBV. The changes of the serological markers of HBV may be not consistent with that of HBV DNA. It is more objective to undergo both internal-standard and external-quantitative standard methods.

Adolescent↗
PubMed2002

A novel medium throughput quantitative competitive PCR technology to simultaneously measure mRNA levels from multiple genes.

There is a great demand for technologies to simultaneously measure mRNA levels from multiple genes. Here we report a new quantitative competitive PCR technology and demonstrate simultaneous quantification of mRNA from multiple genes. First, a sequential 2-fold dilution series containing equal amounts of gene-specific standard DNAs for 10-12 genes is prepared. Second, the serially diluted standard DNAs are individually added to equal amounts of tissue-derived cDNA and amplified with gene-specific primers for 19-26 PCR cycles. Each gene/standard DNA pair is amplified individually. All amplified DNA products (n = 80) are resolved by one microplate array diagonal gel electrophoresis using 5% polyacrylamide. Changes in mRNA levels of approximately 15% can be detected by this technology. The mRNA levels from 10-12 genes were simultaneously quantified. mRNA levels were compared in RNA samples from rat liver, kidney and skeletal muscle. This quick, specific, sensitive, reproducible and yet inexpensive technique is ideal for simultaneously studying co-ordinate changes in mRNA levels from multiple genes.

Animals↗
PubMed2002

Comparison of quantitative competitive PCR with LightCycler-based PCR for measuring Epstein-Barr virus DNA load in clinical specimens.

The aim of this study was to develop a LightCycler-based real-time PCR assay for monitoring the Epstein-Barr virus (EBV) DNA load in unfractionated whole blood. This assay was compared with quantitative competitive PCR (Q-PCR) for EBV. The LightCycler-based assay was highly sensitive and reproducible when quantifying plasmid DNA in either the presence or absence of healthy donor blood DNA. Amplifying plasmid DNA in DNA backgrounds from different donors slightly increased the variation of quantification, indicating that clinical specimen DNA has an influence on quantification. In most transplant recipients, a good correlation was observed between EBV DNA load dynamics determined by LightCycler and Q-PCR in follow-up samples, although the correlation between absolute values of EBV DNA loads was weak and occasional samples were false negative in the LightCycler assay. In 253 cross-sectional blood samples from patients with Burkitt's lymphoma, infectious mononucleosis, or human immunodeficiency virus infection, a weak but significant correlation between the two methods was found (r(2) = 0.37, P < 0.001). Our results indicate that the clinical specimen DNA background may influence the absolute values of EBV DNA load in LightCycler analyses but that this effect is rare. LightCycler PCR is very well suited for monitoring of EBV DNA load dynamics, and its diagnostic value is comparable to that of Q-PCR. To avoid false negativity or underestimation of viral load, future internal calibration of the LightCycler is recommended. This would also enhance EBV load assay standardization and interinstitute comparisons.

DNA, Viral↗
PubMed2004

Detection of economically important viruses in boar semen by quantitative RealTime PCR technology.

The objective of this study was to develop quantitative real-time polymerase chain reaction (ReTi-PCR) tests for the detection of five economically important viruses in swine semen namely, pseudorabies virus (PRV), classical swine fever virus (CSFV), foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), and porcine reproductive and respiratory syndrome virus (PRRSV). Each ReTi-PCR test was validated for specificity, analytical sensitivity (detection limits), and experimental infection studies were performed to compare the conventional virus isolation methods with the newly developed ReTi-PCR tests. All five developed ReTi-PCR tests are very rapid compared to virus isolation, highly specific, and even more sensitive (lower detection limits) than conventional virus isolation methods for the detection of mentioned viruses in semen. In semen of experimentally infected boars, viruses were detected much earlier after infection and more frequently by ReTi-PCR tests than by virus isolations. The high throughput of these rapid ReTi-PCR tests makes it possible to screen large number of semen samples for the presence of viruses prior to insemination. This is a substantial advantage, in particular for boar semen the quality of which deteriorates quickly after storage. In general, the newly developed ReTi-PCR tests are valuable tools for the early, reliable and rapid detection of five economically important viruses, namely PRV, CSFV, FMDV, SVDV, and PRRSV in boar semen. These ReTi-PCR tests will improve the control of viral diseases transmitted via semen.

Animals↗
PubMed2005

Quantitative PCR-enhanced immunoassay for measurement of enteroviral immunoglobulin M antibody and diagnosis of aseptic meningitis.

A PCR-enhanced immunoassay (PIA) to detect enterovirus (EV) immunoglobulin M (IgM) for diagnosis of recent EV infection was recently developed. This test was compared with another EV IgM capture technique, the solid-phase reverse immunosorbent test (SPRIST). Fourteen of 43 serum samples from aseptic meningitis patients were positive by PIA, whereas 10 were positive by SPRIST. One of 39 control serum samples was weakly positive by PIA. A single-serum-dilution real-time PCR-based PIA for EV IgM (quantitative PIA [QPIA]) was also developed and evaluated against PIA, SPRIST, an EV IgM radioimmunoassay (RIA), and clinical data. A mixture of 12 EVs was used as the antigen. Results from investigating four groups of serum samples were as follows. (i) The nine PIA-positive serum samples in group 1 were all positive by QPIA. (ii) Group 2 consisted of 59 serum samples from aseptic meningitis patients. Nineteen of 30 serum samples (63%) taken at hospital admission were positive by QPIA. Of these, 17 were positive in EV PCR. (iii) None of the 30 control serum samples in group 3 were positive by QPIA. (iv) For the 24 serum samples in group 4, of which 11 were positive and 13 were negative by RIA, the QPIA results were completely concordant. The sensitivity and specificity of QPIA for diagnosis of EV infection were 70 and 80%, respectively. QPIA provides a rational strategy for the detection of EV IgM, allows the use of viral antigens with minimal purification, and needs no virus-specific reagents apart from those in the PCR. QPIA is a generally applicable method for the detection of viral IgM in IgM capture assays.

Antibodies, Viral↗
PubMed1998

[Utility of quantitation of human cytomegalovirus(HCMV) DNA in plasma and cerebrospinal fluid by quantitative competitive PCR in AIDS patients].

Persons with advanced HIV infection may have active HCMV infection for months before clinically recognized HCMV disease. The qualitative detection of HCMV-DNA in plasma by PCR is more useful than either urine or blood culture in identifying over time those persons with advanced HIV disease who will develop HCMV disease. Quantitation of HCMV DNA in plasma has identified an association between levels of HCMV DNA in plasma and risk for development of HCMV disease. Thus, quantitative competitive PCR has potential as a marker for the identification of persons who are at highest risk of developing HCMV disease and in helping to guide decisions regarding prophylaxis for HCMV disease. AIDS patients with HCMV-related central nervous system(CNS) disease have high quantities of HCMV DNA in their cerebrospinal fluid(CSF), and quantities of HCMV DNA in CSF are higher in persons with HCMV-related polyradiculopathy than encephalitis. Additionally, quantitation of HCMV DNA can be a useful marker for monitoring the antiviral efficacy of therapies of HCMV-related CNS disease.

AIDS-Related Opportunistic Infections↗
PubMed2003

Oligodendrocyte dysfunction in schizophrenia and bipolar disorder.

BACKGROUND: Results of array studies have suggested abnormalities in expression of lipid and myelin-related genes in schizophrenia. Here, we investigated oligodendrocyte-specific and myelination-associated gene expression in schizophrenia and bipolar affective disorder. METHODS: We used samples from the Stanley brain collection, consisting of 15 schizophrenia, 15 bipolar affective disorder, and 15 control brains. Indexing-based differential display PCR was done to screen for differences in gene expression in schizophrenia patients versus controls. Results were cross-validated with quantitative PCR, which was also used to investigate expression profiles of 16 other oligodendrocyte and myelin genes in schizophrenia and bipolar disorder. These genes were further investigated with an ongoing microarray analysis. FINDINGS: Results of differential display and quantitative PCR analysis showed a reduction of key oligodendrocyte-related and myelin-related genes in schizophrenia and bipolar patients; expression changes for both disorders showed a high degree of overlap. Microarray results of the same genes investigated by quantitative PCR correlated well overall. INTERPRETATION: Schizophrenia and bipolar brains showed downregulation of key oligodendrocyte and myelination genes, including transcription factors that regulate these genes, compared with control brains. These results lend support to and extend observations from other microarray investigations. Our study also showed similar expression changes to the schizophrenia group in bipolar brains, which thus lends support to the notion that the disorders share common causative and pathophysiological pathways.

Bipolar Disorder↗
PubMed2002

LPS-induced cytokine production in the monocytic cell line THP-1 determined by multiple quantitative competitive PCR (QC-PCR).

BACKGROUND: Quantifying cytokines on the protein level can be problematic because of low concentrations or degradation during sample handling. Aiming towards finding a simple method by which to quantify cytokines on the mRNA level, we combined existing and established molecular biology techniques. Based on the principle of quantitative competitive RT-PCR with a DNA-competitor, IL-1beta, IL-6, IL-12alpha and the housekeeping enzyme GAPDH are measured at levels down to 200 copies of mRNA. METHODS: As a source of mRNA, the total RNA from 4 samples of 5 x 10(6) THP-1 cells stimulated with LPS (1 microg/ml for 24 h) was isolated. For competitors, we constructed sequences similar to the target sequences, but with deletion or insertion of 10-15% of the target length. For validating this method, we performed first strand synthesis on different days using different amounts of RNA (1-4 microg) isolated from the same pool of cells. Quantitative competitive PCR was accomplished using different amounts of cDNA (0.125-4 microL). Using IL-1beta as an example, the assay was validated for a dynamic range of 5-300 x 10(3) copies. RESULTS: A linear correlation was found between output and amount of RNA for cDNA synthesis, signifying that the final result of the analysis was linearly related to the amount of RNA or cDNA when operating within the range 1-4 microg (RNA isolation). CONCLUSION: The quantitative, competitive RT-PCR produces highly reproducible results within a 60-fold dynamic range.

Cell Line↗
PubMed2005

Application of real-time PCR for quantitative detection of Clostridium botulinum type A toxin gene in food.

The TaqMan real-time PCR method for the quantitative detection of C. botulinum type A was developed based on sequence-specific hybridization probes. The validity of this assay was verified by using 10 genera of 20 strains, including reference strains of C. botulinum types A, B, C, D, E and F. The detection limit of this assay was evaluated on C. botulinum type A, using a 10-fold dilution series of DNA and spores . The DNA and spores were detected up to level of 0.1 ng/ml and 10(2)spores/ml, respectively. Spore spiked food sample preparation prior to the real-time PCR was performed by two methods, heat treatment and GuSCN. The detection limits after heat treatment showed 10(2) spores/ml for spiked sausage slurry, and 10(3) spores/ml for spiked canned corn slurry, while detection limits after GuSCN precipitation showed 10(2) spores/ml in both sausage and canned corn. Therefore the real-time PCR assay after GuSCN precipitation is useful for the quantification of C. botulinum type A because it showed identical CT values in both pure spore solutions and food slurries. We suggest that quantitative analysis of C. botulinum type A by TaqMan real-time PCR can be a rapid and accurate assessment method for botulinal risk in food samples.

Botulinum Toxins, Type A↗
PubMed2006

Development of an improved method of detection of infectious parvovirus B19.

BACKGROUND: Parvovirus B19, the only known pathogenic human parvovirus is the aetiologic agent of erythema infectiosum, transient aplastic crisis, pure red cell aplasia, and hydrops fetalis. Transmission is either by respiratory secretions or, as it can be present at high titre in plasma, by blood and blood products. B19 is only cultured with difficulty in vitro, and there is no readily available assay for detecting B19 infectivity or neutralizing antibodies. OBJECTIVES: In this study, we evaluated different methods to detect viral infection for the purpose of developing automated methods for large-scale testing of viral infectivity, development of neutralizing antibody and viral inactivation assays. STUDY DESIGN: Different cell lines were evaluated for their ability to support B19 infection and assays tested for sensitivity and ease of performing. A high-throughput assay was validated by determining infectious virus in blood pools and for determining neutralizing antibody in sera. RESULTS: B19 protein production was detected by immunofluorescence (IF) staining and increased viral DNA production by dot blot hybridization and quantitative PCR. The detection of RNA transcripts by RT-PCR assay and quantitative RT-PCR (qRT-PCR) was used as an indirect marker for infection. Of the cell lines tested, the subclone UT7/Epo-S1 showed the greatest sensitivity to B19 infection, with detection of viral transcripts by qRT-PCR the preferred assay. The assays were validated by experiments to determine the infectious titre of sera from acutely infected humans, to evaluate the presence of infectious virus in human donor plasma pools and to measure neutralizing antibodies.

Antibodies, Viral↗
PubMed2004

The use of fluorescent molecular beacons in real time PCR of IgH gene rearrangements for quantitative evaluation of multiple myeloma.

UNLABELLED: BACKGROUND AND OBJECTIVES Fluorescent molecular beacons have been employed as hybridization probes in real time quantitative PCR to quantify residual disease in multiple myeloma (MM). DESIGN AND METHODS: After clinical diagnosis of MM, the CDR1, CDR2 and CDR3 regions of the IgH gene were analysed and sequenced to identify its clonal nature. Unique sequences of the clonal IgH rearrangement were used to design specific molecular beacon probes for each MM patient. A molecular beacon probe for the beta-globin gene was used as a reference control to calculate relative amounts of the clonal B-cell population. RESULTS: Optimization of probe design resulted in the use of a competitive sequence at the IgH area target between the loop and part of the stem of the molecular beacon. Cycling conditions and fluorescence temperature acquisition were optimized for a Light Cycler. To validate this method for the follow-up of treated MM patients, we investigated accuracy, as well as interassay and intrassay reproducibility. CONCLUSIONS: Our results indicated that real time PCR with specific molecular beacons provides a feasible, accurate and reproducible method for the determination of minimal residual disease in MM.

DNA Probes↗
PubMed2005

Detection of chromosome abnormalities by quantitative fluorescent PCR in ectopic pregnancies.

OBJECTIVE: To evaluate the potential value of quantitative fluorescent polymerase chain reaction (QF-PCR) in the detection of chromosome abnormalities in ectopic pregnancies. METHODS: Seventy chorionic villi samples of ectopic pregnancies were studied by QF-PCR. Primers for chromosomes 16, 21, X and Y in chorionic villi were evaluated. Fluorescence in situ hybridization (FISH) was performed when results of QF-PCR showed aneuploidy, in case of unexplicable QF-PCR peaks, and in 10 cases with normal QF-PCR results. RESULTS: QF-PCR produced a result for chromosomes X and Y in 66 cases (94%), for chromosome 16 in 62 cases (89%) and for chromosome 21 in 55 cases (79%). Overall, QF-PCR produced a result for the chromosomes tested in 54 ectopic pregnancy cases (77%). Fifty-two of these results were normal disomic (96%) and two were abnormal, one trisomy 16 (2%) and one triploidy (2%). In 16 cases (23%) no definite QF-PCR results could be obtained for all chromosomes, 11 due to amplification failure, and 5 due to unexplicable QF-PCR peaks. In 10 cases with normal QF-PCR results, disomy was confirmed by FISH. The trisomy 16 was also confirmed by FISH. Furthermore, a result was obtained with FISH in 5 of the cases without definite QF-PCR results. CONCLUSION: Although QF-PCR can establish the chromosomal status in ectopic pregnancies for chromosomes 16, 21, X and Y in the majority of cases, the technical failure rate is still considerable and does not improve results when compared to cytogenetic techniques.

Adult↗