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Results for “Genome quantification”

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At least 73 records · Page 4Linked to original sources
PubMed1999

Transmission rates of hepatitis C virus by different batches of a contaminated anti-D immunoglobulin preparation.

BACKGROUND AND OBJECTIVES: The aim of this study was to determine the hepatitis C virus (HCV) infection rate of recipients of different batches of anti-D immunoglobulin associated with an outbreak of HCV infection which occurred in 1977 and its relationship to the polymerase chain reaction (PCR) status of the implicated batches. This study was undertaken to determine the predictive value of HCV genome detection and quantification for subsequent infection in recipients of an HCV-contaminated anti-D immunoglobulin product for intravenous use. MATERIALS AND METHODS: Sera from recipients of anti-D were tested by HCV enzyme immunoassay and if found positive were subsequently tested by recombinant immunoblot assay and HCV PCR in a national HCV anti-D screening programme set up in 1994. The HCV status of 1,342 known recipients of infectious or potentially infectious batches has been compared to the amount of HCV RNA in the anti-D batch they received so as to determine the value of PCR in the prediction of infectivity in immunoglobulin preparations. RESULTS: It has been demonstrated that HCV-infected plasma derived from batches of anti-D showing levels of viral genome in excess of 10(4) genomes per millilitre led to infection of up to 60% of recipients. In contrast, batches with undetectable levels of HCV genome very rarely transmitted infection. CONCLUSIONS: The presence of HCV RNA in intravenous immunoglobulin preparations which have not undergone a specific viral inactivation step is a predictor of HCV infection in recipients.

Disease Outbreaks↗
PubMed1992

A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates.

A method is described for the absolute quantification by polymerase chain reaction (PCR) of nucleic acids present in low abundance. The method entails the addition to the sample of competitor DNA molecules that share the same sequence as the amplified target (including primer recognition sites), except for a 20-bp insertion in the middle, which allows easy resolution by gel electrophoresis (competitive PCR). Among the advantages of competitive PCR is that any predictable or unpredictable variable that affects amplification has the same effect on both target and competitor species and that the final ratio of amplified products reflects exactly the initial rate of targets, rendering the reaction independent of the number of amplification cycles. An easy and reliable method for the construction and quantification of competitive templates obtained as recombinant PCR products was developed. The technique was used for the absolute quantification of human genomic DNA with primers from a single copy, subtelomeric region of chromosome 19.

Base Sequence↗
PubMed2005

Specific and quantitative detection of human polyomaviruses BKV, JCV, and SV40 by real time PCR.

BACKGROUND: The polyomaviruses that infect humans, BK virus (BKV), JC virus (JCV), and simian virus 40 (SV40), typically establish subclinical persistent infections. However, reactivation of these viruses in immunocompromised hosts is associated with renal nephropathy and hemorrhagic cystitis (HC) caused by BKV and with progressive multifocal leukoencephalopathy (PML) caused by JCV. Additionally, SV40 is associated with several types of human cancers including primary brain and bone cancers, mesotheliomas, and non-Hodgkin's lymphoma. Advancements in detection of these viruses may contribute to improved diagnosis and treatment of affected patients. OBJECTIVE: To develop sensitive and specific real time quantitative polymerase chain reaction (RQ-PCR) assays for the detection of T-antigen DNA sequences of the human polyomaviruses BKV, JCV, and SV40 using the ABI Prism 7000 Sequence Detection System. STUDY DESIGN: Assays for absolute quantification of the viral T-ag sequences were designed and the sensitivity and specificity were evaluated. A quantitative assay to measure the single copy human RNAse P gene was also developed and evaluated in order to normalize viral gene copy numbers to cell numbers. RESULTS: Quantification of the target genes is sensitive and specific over a 7 log dynamic range. Ten copies each of the viral and cellular genes are reproducibly and accurately detected. The sensitivity of detection of the RQ-PCR assays is increased 10- to 100-fold compared to conventional PCR and agarose gel protocols. The primers and probes used to detect the viral genes are specific for each virus and there is no cross reactivity within the dynamic range of the standard dilutions. The sensitivity of detection for these assays is not reduced in human cellular extracts; however, different DNA extraction protocols may affect quantification. CONCLUSION: These assays provide a technique for rapid and specific quantification of polyomavirus genomes per cell in human samples.

BK Virus↗
PubMed2004

A graph-theoretic modeling on GO space for biological interpretation of gene clusters.

MOTIVATION: With the advent of DNA microarray technologies, the parallel quantification of genome-wide transcriptions has been a great opportunity to systematically understand the complicated biological phenomena. Amidst the enthusiastic investigations into the intricate gene expression data, clustering methods have been the useful tools to uncover the meaningful patterns hidden in those data. The mathematical techniques, however, entirely based on the numerical expression data, do not show biologically relevant information on the clustering results. RESULTS: We present a novel methodology for biological interpretation of gene clusters. Our graph theoretic algorithm extracts common biological attributes of the genes within a cluster or a group of interest through the modified structure of gene ontology (GO) called GO tree. After genes are annotated with GO terms, the hierarchical nature of GO terms is used to find the representative biological meanings of the gene clusters. In addition, the biological significance of gene clusters can be assessed quantitatively by defining a distance function on the GO tree. Our approach has a complementary meaning to many statistical clustering techniques; we can see clustering problems from a different viewpoint by use of biological ontology. We applied this algorithm to the well-known data set and successfully obtained the biological features of the gene clusters with the quantitative biological assessment of clustering quality through GO Biological Process.

Algorithms↗
PubMed2004

Infection and pathogenicity of the mosquito densoviruses AeDNV, HeDNV, and APeDNV in Aedes aegypti mosquitoes (Diptera: Culicidae).

These studies compared three genetically distinct mosquito densoviruses Aedes aegypti (AeDNV), Hemagogus equinus (HeDNV), and Aedes Peruvian (APeDNV) densoviruses in a laboratory investigation to begin to evaluate their potential as mosquito control agents. A real-time polymerase chain reaction (PCR) assay for quantification of viral genomes and a standardized mosquito infection protocol were developed. Mortality associated with exposure to AeDNV increased in a dose-dependent manner, with the maximum mortality of 75.1% occurring in those organisms exposed to the highest dose of virus. The majority of death occurred as larvae. Similar results were observed with AeDNV produced from ground larvae and AeDNV produced from cell culture. Exposure of mosquitoes to HeDNV and APeDNV resulted in lower mortality, with values peaking at 33.5% for HeDNV and 27.8% for APeDNV. AeDNV-exposed larvae develop at a slower rate than nonexposed and HeDNV- and APeDNV-exposed larvae. Decreased virulence does not reflect a decrease in virus replication. PCR analysis of infectivity rates and titers in adults revealed reproduction of all three viruses, with an average viral titer of approximately 10 logs/mosquito after exposure to the highest dose of each virus. Accumulation of virus in the larval-rearing water was also observed with values approaching 10-11 logs/ml for each virus. These data indicate that there are dramatic differences in the pathogenicity among mosquito densoviruses.

Aedes↗
PubMed2001

Evaluation of CMV viral load using TaqMan CMV quantitative PCR and comparison with CMV antigenemia in heart and lung transplant recipients.

BACKGROUND: Quantitative assessment of cytomegalovirus (CMV) infection using the antigenemia test has been used to monitor CMV infection in heart and lung transplant patients enabling a preemptive treatment strategy. However, the method is labour intensive, samples have to be processed within a few hours and requires skilled interpretation. A comparative prospective evaluation of a real-time TaqMan CMV quantitative PCR (QPCR) with the CMV antigenemia was undertaken. METHODS: A real-time quantitative TaqMan CMV PCR from EDTA bloods was developed. In this study 25 heart transplant and single-lung transplant patients were monitored posttransplantation by antigenemia and TaqMan CMV QPCR. CMV DNA extracted from EDTA blood was amplified by TaqMan QPCR using primers and probe designed from the CMV glycoprotein B (gB) gene. Quantification of the genome copies is extrapolated from a standard curve generated from amplification of quantified standards. RESULTS: Antigenaemia levels and TaqMan CMV QPCR genome copies showed a linear correlation between the two assays (R=0.843, P=0.001). A clinically significant threshold of 50 CMV pp65 antigen positive polymorphonuclear leucocytes (PMNLs) per 200 000 cells previously reported was used to extrapolate an equivalent value of 40 000 (log 4.6) genome copies per ml of blood for the TaqMan CMV QPCR. CONCLUSIONS: The TaqMan system enables a rapid high-throughput of samples. The TaqMan CMV QPCR can be used as an accurate and robust alternative to the antigenemia test to predict CMV disease and to monitor effectiveness of treatment.

Antigens, Viral↗
PubMed2000

Quantitative molecular analysis of laser-microdissected paraffin-embedded human tissues.

Laser microdissection enables the contamination-free isolation of morphologically defined pure cell populations from archival formalin-fixed paraffin-embedded tissue specimens. Cells isolated by this method have been characterized by a wide variety of qualitative molecular assays, e.g. loss of heterozygosity, point mutations, clonality and lineage origin. The recently introduced real-time PCR technology renders the reliable quantification of very small amounts of nucleic acids possible. Several groups including our own showed that this technique can be successfully applied for the quantification of DNA and RNA isolated from microdissected archival tissue sections, even after immunohistochemical staining. The exact analysis of quantitative changes of nucleic acids during the course of pathological alterations has thus become possible. In many situations these quantitative changes can be expected to be more important than qualitative changes. The new technology for the quantification of structural genomic alterations and changes in the gene expression pattern in conjunction with microdissection have equipped morphologists with a powerful tool to study reactive and neoplastic changes of tissues.

Cell Separation↗
PubMed2002

Amplification and detection of transposon insertion flanking sequences using fluorescent muAFLP.

The amplification of transposon insertionflanking sequences is the basis of a variety of techniques usedfor the detection and characterization of specific transposon insertion events. We have developed a method for the efficient size determination and quantification of amplified genomic sequences thatflank Mutator (Mu) transposon insertions in maize. Using this detection method, we have been able to optimize Mu insertion site amplification and to assess amplification from increasingly complex templates representing increasing numbers of Mu-active maize plants. This detection method should be applicablefor the characterization of transposon or transgene insertion events in a wide variety of organisms.

DNA Primers↗
PubMed2003

Recommendations for microbial source tracking: lessons from a methods comparison study.

The methods comparison study described in accompanying manuscripts demonstrated the potential value of microbial source tracking (MST) techniques, but also identified a need for method refinement. This paper provides three classes of recommendations to improve MST technology: optimization, development and evaluation. Optimization recommendations focus on library-dependent methods and include improved selection of restriction enzymes or antibiotics, better definition of appropriate library size, selection of target species and choice of statistical pattern-matching algorithms. Methods development recommendations focus on identifying new genomic targets and quantification procedures for library-independent methods. Longer-term methods development recommendations include integration of microarrays and other direct pathogen detection technology with MST. Studies defining host specificity and population dynamics should aid selection of target species during methods development. Evaluation recommendations include enhancements that should be incorporated into future methods comparison studies, along with studies to assess the value of MST results for risk characterization.

Animals↗
PubMed2005

[Large-scale genotyping in research into autism spectrum disorders and attention deficit hyperactivity disorder].

INTRODUCTION AND DEVELOPMENT: Autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) are two neuropsychiatric disorders beginning in childhood that present a high degree of familial aggregation. ASD is characterised by social interaction and communication disorders, whereas patients with ADHD display persistent inattention and/or hyperactive-impulsive behaviour. With the exception of a few cases of autism in which cytogenetic anomalies or mutations have been reported in specific genes, the aetiology of these diseases remains unknown. This is a group of multifactorial diseases with several genes having a lesser effect and there is also an environmental component. Genetic linkage studies have pointed to about 20 chromosomal regions that could well contain genes that grant susceptibility to autism, to ADHD or to both disorders. The challenge to researchers lies in the clinical characterisation, recruitment of patients with ASD and ADHD, gene dosage quantification studies, comparative genomic methylation and hybridisation in order to identify chromosomal rearrangements in patients with autism and severe mental retardation. CONCLUSIONS: Genotyping large SNP-type collections that are potentially functional in genes that are candidates for these disorders, based on pharmacological, biochemical and neuropathological data together with that coming from animal models and linkage studies in a wide collection of samples from patients and controls, will enable us to identify the genetic components of these pathologies and to define their biological foundations.

Attention Deficit Disorder with Hyperactivity↗
PubMed1996

Rational use of diagnostic tools in hepatitis C.

Six years after the introduction of serological tests for the detection of antibodies to HCV these diagnostic procedures have been improved significantly. The ELISA's of the third generation contain 4-5 fragments of structural and nonstructural proteins which have increased the sensitivity and specificity for antibody detection. Several confirmatory assays have been established to detect non-specific reactions. Viremia in acute and chronic HCV infection can be detected by RT-PCR. However, studies on the quality of PCR results with serum panels in a large number of diagnostic labs indicate the urgent need to standardize the RT-PCR techniques. Quantification of viral genomes during acute and chronic HCV infection seem to be of major importance to predict the response rat to IFN. Quantitative RT-PCR techniques using internal standards and the branched DNA technology have been established. Techniques for genotyping HCV isolates have been introduced which also seemed to be important for prediction of IFN response. Recently serotyping of HCV isolates has been evaluated and seems to correlate well with genotyping by RT-PCI and specific probes. The detection of quasispecies in the 5'NCR may, in the future, be an additional prospective test for the prognosis of IFN treatment.

Enzyme-Linked Immunosorbent Assay↗
PubMed1997

Quantitative polymerase chain reaction for human herpesvirus diagnosis and measurement of Epstein-Barr virus burden in posttransplant lymphoproliferative disorder.

Human herpesviruses can cause acute diseases such as chicken pox or mononucleosis, but also may reactivate during immunosuppression and result in severe or life-threatening illnesses such as shingles or lymphoproliferative disorders. We report the development and validation of a quantitative PCR method to measure viral burden for all eight human herpesviruses (HSV1, HSV2, VZV, EBV, CMV, HHV6, HHV7, and KSHV) in patients' samples. The method uses an internal standard that is coamplified with the viral target, allowing quantification of viral genomes in absolute terms (e.g., viral targets/mL of blood) and ruling out false-negative results. We demonstrate that transplant patients with lymphoproliferative disorder carry an EBV viral burden 3 logs higher than nontransplant patients. EBV titers in transplant patients without a lymphoproliferative disorder are between these values. This quantitative PCR method may aid in differentiating clinically significant vs latent viral burden in immunosuppressed patients.

Herpesviridae Infections↗
PubMed2004

Direct quantification of Campylobacter jejuni and Campylobacter lanienae in feces of cattle by real-time quantitative PCR.

Campylobacter species are fastidious to culture, and the ability to directly quantify biomass in microbiologically complex substrates using real-time quantitative (RTQ) PCR may enhance our understanding of their biology and facilitate the development of efficacious mitigation strategies. This study reports the use of nested RTQ-PCR to directly quantify Campylobacter jejuni and Campylobacter lanienae in cattle feces. For C. jejuni, the single-copy mapA gene was selected. For C. lanienae, the three-copy 16S rRNA gene was targeted. RTQ-PCR primers were tested alone or they were nested with species-specific primers, and amplification products were detected using the intercalating dye SYBR Green. Nesting did not increase the specificity or sensitivity of C. jejuni quantification, and the limit of quantification was 19 to 25 genome copies ( approximately 3 x 10(3) CFU/g of feces). In contrast, nested RTQ-PCR was necessary to confer specificity on C. lanienae by targeting the 16S rRNA gene. The limit of quantification was 1.8 genome copies ( approximately 250 CFU/g of feces), and there was no discernible difference between the two C. lanienae secondary primer sets evaluated. Detection and quantification of C. jejuni in naturally infested cattle feces by RTQ-PCR were comparable to the results of culture-based methods. In contrast, culturing did not detect C. lanienae in 6 of 10 fecal samples positive for the bacterium and substantially underestimated cell densities relative to nested RTQ-PCR. The results of this study illustrate that RTQ-PCR can be used to directly quantify campylobacters, including very fastidious species, in a microbiologically and chemically complex substrate. Furthermore, targeting of a multicopy universal gene provided highly sensitive quantification of C. lanienae, but nested RTQ-PCR was necessary to confer specificity. This method will facilitate subsequent studies to elucidate the impact of this group of bacteria within the gastrointestinal tracts of livestock and studies of the factors that influence colonization success and shedding.

Animals↗
PubMed2000

Quantifying single gene copy number by measuring fluorescent probe lengths on combed genomic DNA.

An approach was developed for the quantification of subtle gains and losses of genomic DNA. The approach relies on a process called molecular combing. Molecular combing consists of the extension and alignment of purified molecules of genomic DNA on a glass coverslip. It has the advantage that a large number of genomes can be combed per coverslip, which allows for a statistically adequate number of measurements to be made on the combed DNA. Consequently, a high-resolution approach to mapping and quantifying genomic alterations is possible. The approach consists of applying fluorescence hybridization to the combed DNA by using probes to identify the amplified region. Measurements then are made on the linear hybridization signals to ascertain the region's exact size. The reliability of the approach first was tested for low copy number amplifications by determining the copy number of chromosome 21 in a normal and trisomy 21 cell line. It then was tested for high copy number amplifications by quantifying the copy number of an oncogene amplified in the tumor cell line GTL-16. These results demonstrate that a wide range of amplifications can be accurately and reliably quantified. The sensitivity and resolution of the approach likewise was assessed by determining the copy number of a single allele (160 kb) alteration.

Bacteriophage lambda↗
PubMed1996

Rapid retrovirus titration using competitive polymerase chain reaction.

A quantitative polymerase chain reaction (PCR) procedure has been developed for rapid retrovirus titration. This procedure, which is based on the simultaneous amplification of the sample with known amounts of a competitor DNA fragment (competitive PCR), was used for the quantification of viral RNA genomes in retrovirus-producing cell clone supernatants and of proviral DNA molecules formed at 24 h after infection of different reference cell lines. The results obtained from the analysis of several samples indicated that proviral DNA quantification is in complete agreement with the number of selectable colonies in a standard colony assay. Conversely, the number of viral RNA genomes in the producer cell clone supernatants is a poor predictor of the actual efficiency of infection. Repeated competitive PCR experiments for provirus copy number determination at different times after transduction indicated that the number of proviral DNA molecules remains stable over time, suggesting stable integration into the host genome. The developed procedure is rapid and simple, is applicable to retroviral constructs not containing a selectable gene and can be used to directly measure the efficiency of infection of any target cell type, thus overcoming the problem of the dependency of retroviral titer determination on the rate of expression of a selectable gene and on the efficiency of colony formation of a reference cell line.

3T3 Cells↗
PubMed2004

Tropheryma whipplei Infection of an acellular porcine heart valve bioprosthesis in a patient who did not have intestinal Whipple's disease.

Rare cases of culture-negative infective endocarditis are caused by Tropheryma whipplei, the uncommon bacterium of Whipple's disease. We evaluated an 80-year-old woman with valvular heart disease but without intestinal Whipple's disease. The diagnosis of aortic valve xenograft culture-negative infection with T. whipplei was established by multiple molecular assays and by electron microscopy. First, a PCR with broad-range primers identified the complete 16S ribosomal DNA of T. whipplei in bioprosthesis tissue. Novel real-time reverse transcription-PCR assays were developed to detect mRNAs encoding recently identified proteins determined from the T. whipplei genome, specifically Whipplei surface protein (TW113) and a DNA polymerase III subunit (TW727). The positive detection of mRNAs indicated the presence of metabolically active bacteria and suggested the viability of T. whipplei. The quantification of T. whipplei genome equivalents by real-time PCR indicated a high-density bacterial colonization of the valve tissue. Additionally, an ultrastructural examination revealed numerous rod-shaped bacteria consistent in size with T. whipplei in the extracellular collagen matrix of the bioprosthesis. We conclude that extracellular growth of T. whipplei can occur in the microenvironment of biological prosthetic valve tissue and that T. whipplei endocarditis can occur in the absence of intestinal Whipple's disease.

Actinomycetales↗
PubMed2001

Multiple groups of novel retroviral genomes in pigs and related species.

In view of the concern over potential infection hazards in the use of porcine tissues and organs for xenotransplantation to humans, we investigated the diversity of porcine endogenous retrovirus (PERV) genomes in the DNA of domestic pigs and related species. In addition to the three known envelope subgroups of infectious gamma retroviruses (PERV-A, -B, and -C), classed together here as PERV group gamma 1, four novel groups of gamma retrovirus (gamma 2 to gamma 5) and four novel groups of beta retrovirus (beta 1 to beta 4) genomes were detected in pig DNA using generic and specific PCR primers. PCR quantification indicated that the retroviral genome copy number in the Landrace x Duroc F(1) hybrid pig ranged from 2 (beta 2 and gamma 5) to approximately 50 (gamma 1). The gamma 1, gamma 2, and beta 4 genomes were transcribed into RNA in adult kidney tissue. Apart from gamma 1, the retroviral genomes are not known to be infectious, and sequencing of a small number of amplified genome fragments revealed stop codons in putative open reading frames in several cases. Analysis of DNA from wild boar and other species of Old World pigs (Suidae) and New World peccaries (Tayassuidae) showed that one retrovirus group, beta 2, was common to all species tested, while the others were present among all Old World species but absent from New World species. The PERV-C subgroup of gamma1 genomes segregated among domestic pigs and were absent from two African species (red river hog and warthog). Thus domestic swine and their phylogenetic relatives harbor multiple groups of hitherto undescribed PERV genomes.

Animals↗
PubMed2003

Frequent infection with a viral pathogen, parvovirus B19, in rheumatic diseases of childhood.

OBJECTIVE: To find further evidence of the association of parvovirus B19 infection with juvenile rheumatic diseases, and to get new insights into the immunopathogenesis of these diseases. METHODS: Paired serum and synovial fluid samples from 74 children with rheumatic disease were analyzed with respect to their content of viral DNA and antibodies directed against the B19 viral proteins VP1, VP2, and NS1. Control sera from 124 children with noninflammatory bone diseases or growth retardation were also analyzed. The sequence of the viral DNA, amplified by polymerase chain reaction (PCR), was determined. IgG-complexed virus was isolated from sera and synovial fluid by adsorption to protein A beads. The amount of free virus versus immunocomplexed virus particles was determined by quantification of the viral genomes by quantitative PCR. RESULTS: Twenty-six of the 74 patients (35%) had detectable amounts of parvovirus B19 DNA in the serum (n = 22 [30%]) and/or the synovial fluid (n = 16 [22%]), whereas only 9 of the 124 control sera (7%) were positive for the viral DNA (P < 0.0001). Forty-six patients (62%) had serum IgG against the structural proteins, indicating past infection with B19. NS1-specific antibodies were detected in sera from 29 patients (39%) and 27 controls (22%) (P < 0.001). In addition, 3 patients (4%) showed VP2-specific IgM. In 15 patients, viral DNA could be repeatedly detected in followup samples of serum and synovial fluid. Sequencing revealed low-degree nucleotide variations that are in the range of genotype 1 of parvovirus B19. Immunocomplexed virus was present in varying amounts, both in the sera and in the synovial fluid samples. CONCLUSION: Parvovirus B19 is frequently found in serum or synovial fluid of children with rheumatism. The rate of persistent B19 infection in these patients is significantly higher than in age-matched controls.

Adolescent↗