Relevant bibliographies by topics / Taqman

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  4. Book chapters
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Academic literature on the topic 'Taqman'

Author: Grafiati
Published: 4 June 2021
Last updated: 21 February 2023

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Journal articles on the topic "Taqman"

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Catsburg, Arnold, Laura van Dommelen, Vitaly Smelov, Henry J. C. de Vries, Alevtina Savitcheva, Marius Domeika, Björn Herrmann, et al. "TaqMan Assay for SwedishChlamydiatrachomatisVariant." Emerging Infectious Diseases 13, no. 9 (September 2007): 1432–34. http://dx.doi.org/10.3201/eid1309.070263.

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Watson, David E., and Baohui Li. "TaqMan Applications in Genetic and Molecular Toxicology." International Journal of Toxicology 24, no. 3 (May 2005): 139–45. http://dx.doi.org/10.1080/10915810590948299.

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Quantification of nucleic acids has become a common procedure in many toxicology laboratories. Among the technologies that accomplish this is the fluorogenic 5 ′-nuclease assay, commonly known as TaqMan. Three TaqMan applications for genetic and molecular toxicology are presented in this article: quantification of gene expression, detection of genetic polymorphisms, and quantification of chromosomal DNA deletions. Of these, quantification of gene expression is the most widely used, and established TaqMan as a benchmark technology for nucleic acid quantification. Two additional applications, polymorphism detection and quantification of DNA deletions, demonstrate the flexibility and quantitative strengths that make TaqMan so powerful, including high precision, excellent sensitivity, and broad linear dynamic range. These and similar applications improve our ability to investigate genetic and molecular dimensions of toxicological phenomena, and have promoted the widespread use of TaqMan in toxicology departments in the pharmaceutical industry. In addition to presenting these applications, the authors discuss some of the challenges of integrating TaqMan and other new technologies into the drug development process.
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Tebbs, Robert S., Yan Y. Cao, Priva Balachandran, Olga Petrauskene, and Thomas Hammack. "TaqMan Salmonella enterica Detection Kit." Journal of AOAC INTERNATIONAL 92, no. 6 (November 1, 2009): 1895–901. http://dx.doi.org/10.1093/jaoac/92.6.1895.

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Abstract Peanut butter spiked with Salmonella enterica ser. Typhimurium was prepared by an independent laboratory and sent to Applied Biosystems to determine the sensitivity and specificity of the TaqMan Salmonella enterica Detection Kit for detecting Salmonella in peanut butter. The samples were spiked at three levels: five no-spike (0 CFU/25 g); 20 low-spike (0.2 CFU/25 g); and 20 high-spike (2 CFU/25 g). They were coded to create a blind set of 45 samples. The samples were processed based on an unpaired test design that included enrichment in buffered peptone water for the candidate method and lactose broth for the reference method. In the candidate method, a 1 mL aliquot of enriched sample was extracted using PrepMan Ultra Sample Preparation Reagent; the sample was amplified on the Applied Biosystems 7500 real-time PCR system, and analyzed for detection of Salmonella using RapidFinder Version 1.0 software. All samples processed by the candidate method were confirmed by culture according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual procedures. Sensitivity, specificity, and Chi-square analysis were calculated by combining candidate method results with those of the reference method that were collected by the independent laboratory. The TaqMan Salmonella enterica Detection Kit showed 40 sensitivity, 100 specificity, and a Chi-square value equal to 1.52. Chi-square analysis indicated the candidate method and the reference method were comparable. Although the candidate method sensitivity was only 40 when compared with the reference method (unpaired samples), the sensitivity was >100 when the candidate method results were compared with those of the confirmation method (same sample enrichment).
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Li, Jin, Lilin Wang, Pasi A. Jänne, and G. Mike Makrigiorgos. "Coamplification at Lower Denaturation Temperature-PCR Increases Mutation-Detection Selectivity of TaqMan-Based Real-Time PCR." Clinical Chemistry 55, no. 4 (April 1, 2009): 748–56. http://dx.doi.org/10.1373/clinchem.2008.113381.

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Abstract Background: DNA genotyping with mutation-specific TaqMan® probes (Applied Biosystems) is broadly used in detection of single-nucleotide polymorphisms but is less so for somatic mutations because of its limited selectivity for low-level mutations. We recently described coamplification at lower denaturation temperature-PCR (COLD-PCR), a method that amplifies minority alleles selectively from mixtures of wild-type and mutation-containing sequences during the PCR. We demonstrate that combining COLD-PCR with TaqMan technology provides TaqMan genotyping with the selectivity needed to detect low-level somatic mutations. Methods: Minor-groove binder-based or common TaqMan probes were designed to contain a nucleotide that matches the desired mutation approximately in the middle of the probe. The critical denaturation temperature (Tc) of each amplicon was then experimentally determined. COLD-PCR/TaqMan genotyping was performed in 2 steps: denaturation at the Tc, followed by annealing and extension at a single temperature (fast COLD-PCR). The threshold cycle was used to identify mutations on the basis of serial dilutions of mutant DNA into wild-type DNA and to identify TP53 (tumor protein p53) and EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] mutations in tumors. Results: COLD-PCR/TaqMan genotyping identified G>A mutations within TP53 exon 8 (codon 273 mutation hot spot) and C>T mutations within the EGFR gene (drug-resistance mutation T790M) with a selectivity improvement of 15- to 30-fold over regular PCR/TaqMan genotyping. A second round of COLD-PCR/TaqMan genotyping improved the selectivity by another 15- to 30-fold and enabled detection of 1 mutant in 2000 wild-type alleles. Use of COLD-PCR/TaqMan genotyping allowed quantitative identification of low-level TP53 and T790 mutations in colon tumor samples and in non-small-cell lung cancer cell lines treated with kinase inhibitors. Conclusions: The major improvement in selectivity provided by COLD-PCR enables the popular TaqMan genotyping method to become a powerful tool for detecting low-level mutations in clinical samples.
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Pusterla, Nicola, Jon B. Huder, Christian M. Leutenegger, Ueli Braun, John E. Madigan, and Hans Lutz. "Quantitative Real-Time PCR for Detection of Members of the Ehrlichia phagocytophila Genogroup in Host Animals and Ixodes ricinus Ticks." Journal of Clinical Microbiology 37, no. 5 (1999): 1329–31. http://dx.doi.org/10.1128/jcm.37.5.1329-1331.1999.

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A TaqMan PCR was established for identification and quantitation of members of the Ehrlichia phagocytophila group in experimentally infected cows and in Ixodes ricinus ticks. The TaqMan PCR identified a 106-bp section of the 16S rRNA gene by use of a specific fluorogenic probe and two primers. This technique was specific for members of the E. phagocytophila group, which include E. phagocytophila, Ehrlichia equi, and the agent of human granulocytic ehrlichiosis. The TaqMan system identified 10 copies of a cloned section of the 16S rRNA gene ofE. phagocytophila. The sensitivity and specificity of the TaqMan PCR were similar to those of conventional nested PCR. The numbers of ehrlichiae in leukocytes of the two cows experimentally infected with E. phagocytophila were measured daily by TaqMan PCR and had a course similar to that of the percentages of infected leukocytes determined daily by light microscopy. The prevalence of infected free-living ticks, which were collected from areas where bovine ehrlichiosis is endemic and from regions with sporadic occurrences of granulocytic ehrlichiosis in dogs and horses, was identical as determined by nested PCR and TaqMan PCR.
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El-Sayed, Ahmed K. A., Mohamed I. Abou-Dobara, Camelia A. Abdel-Malak, and Amira A. E. El-Badaly. "Taqman hydrolysis probe application for Escherichia coli, Salmonella enterica, and Vibrio cholerae detection in surface and drinking water." Journal of Water, Sanitation and Hygiene for Development 9, no. 3 (April 8, 2019): 492–99. http://dx.doi.org/10.2166/washdev.2019.137.

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Abstract This study explored the applicability of using TaqMan qPCR (quantitative polymerase chain reaction) for Escherichia coli, Salmonella enterica and non-virulent Vibrio cholerae detection in surface and drinking water. One hundred and twenty water samples were collected monthly (January 2017–December 2017) from the surface water (input) and drinking water (output and distribution networks) of two drinking water treatment plants (DWTPs) in Damietta County, Egypt. The distribution of the studied bacteria based on their detection by TaqMan qPCR compared with membrane filtration (MF) technique showed that the higher positive samples were detected by TaqMan qPCR. The bacterial count was totally absent in all output samples. TaqMan qPCR assay (based on sequence detection of uidA, invA, and ompW) revealed 97.96%, 99.14%, and 98.3% specificity for E. coli, S. enterica, and non-virulent V. cholerae, respectively, compared with 100% specificity for all strains when MF cultures were applied. TaqMan qPCR exhibited 100% sensitivity for all strains, while it was 91.67%, 80%, and 50% using MF cultures for E. coli, S. enterica, and non-virulent V. cholerae, respectively. In conclusion, TaqMan qPCR sensitivity makes it a useful tool for urgent fast monitoring of water contamination, especially in network samples that contain low bacterial count.
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Lee, Meng-Rui, Kuei-Pin Chung, Hao-Chien Wang, Chih-Bin Lin, Chong-Jen Yu, Jen-Jyh Lee, and Po-Ren Hsueh. "Evaluation of the Cobas TaqMan MTB real-time PCR assay for direct detection of Mycobacterium tuberculosis in respiratory specimens." Journal of Medical Microbiology 62, no. 8 (August 1, 2013): 1160–64. http://dx.doi.org/10.1099/jmm.0.052043-0.

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The Cobas TaqMan MTB assay is a real-time PCR (qPCR) kit for rapid detection of Mycobacterium tuberculosis from clinical specimens. There are, however, limited studies validating its performance. We performed a prospective study in two hospitals in Taiwan on 586 respiratory specimens. By using culture as the reference method, the sensitivity and specificity of the Cobas TaqMan MTB assay were found to be 82.7 and 96.5 %, respectively. The sensitivity of the Cobas TaqMan MTB assay in acid-fast stain-negative respiratory specimens was only 34.9 %. Five specimens from five patients were positive for M. tuberculosis by the Cobas TaqMan MTB assay but were negative for M. tuberculosis by conventional culture methods. A diagnosis of pulmonary tuberculosis (TB) was made based on clinical and radiological findings as well as the response to anti-TB treatment in these five patients. Addition of data from these five specimens with discrepant results (PCR vs culture) from patients with symptoms clinically compatible with TB increased the sensitivity of the Cobas TaqMan MTB assay to 83.1 %. The Cobas TaqMan MTB assay is a rapid identification tool with a high degree of specificity for the direct detection of M. tuberculosis in respiratory specimens. The sensitivity for detecting acid-fast smear-negative respiratory specimens, however, is low.
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Harle, Alexandre, and Jean-Louis Merlin. "Comparison of COBAS 4800 KRAS, PCR TaqMan, and PCR high-resolution melting assays for the detection of KRAS somatic mutations in formalin-fixed paraffin-embedded colorectal tumors." Journal of Clinical Oncology 30, no. 30_suppl (October 20, 2012): 103. http://dx.doi.org/10.1200/jco.2012.30.30_suppl.103.

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103 Background: Colorectal cancer (CRC) is the 2nd most common cancer with more than one million new cases diagnosed every year. From 2006 to 2008, several studies showed the importance of the KRAS oncogene in the treatment of metastatic CRC (mCRC) and response to anti-EGFR therapies like cetuximab or panitumumab. KRAS is a small G protein which can bear activating mutations in 40% cases of mCRC. Numerous methods have been described for the detection of KRAS mutations in FFPE tissues. Direct sequencing is the gold standard but the most sensitive methods are real time PCR assays based. The new COBAS4800 KRAS developed by Roche Diagnostics is a CE IVD validated assay using real time PCR and TaqMelt technology. This assay is validated for the detection of 19 KRAS somatic mutations on exon 2 (codons 12/13) and exon 3 (codon 61) in specimen containing at least 5% of mutated tumoral cells. Methods: We compared COBAS with previously validated PCR TaqMan and PCR High Resolution Melting (HRM) assays. The PCR TaqMan and HRM are a real time PCR based assays. TaqMan can detect accurately 0.5 to 1% of mutated tumoral DNA on codon 12 (G12A, G12C, G12D, G12R, G12S and G12V) and on codon 13 (G13D). HRM can detect 5 to 10% of tumoral DNA on codon 12 and 13. 80 FFPE samples of colorectal tumors resections or biopsies have been collected and processed with the 3 assays. Results have been compared using kappa statistics. Results: On 80 samples, 69 were interpretable with COBAS and TaqMan and 62 with COBAS and HRM. No statistically significant difference between COBAS and TaqMan was found (k=0.942 ; p<0.001). Only 2 discordant cases were found mainly regarding codon 61 mutations not detected with TaqMan. No statistically significant difference between COBAS and HRM was found (k=0.903 ; p<0.001). Three discordant cases were found two regarding codon 61, not detected with HRM and one G12S mutation (detected by COBAS and TaqMan). Conclusions: The 3 assays can detect accurately KRAS mutations. Less ininterpretable results were found with COBAS and TaqMan assays. A pre screening with COBAS and mutation characterization with TaqMan seem to be a good scheme for routine diagnostic of KRAS mutations.
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Vergara, Michelle J., I. P. Shamini Pushparajah, John F. Mackay, and Kerry R. Everett. "Testing new PCR primers and a TaqMan™ probe for detection of Phlyctema vagabunda syn. Neofabraea alba ." New Zealand Plant Protection 72 (July 28, 2019): 278. http://dx.doi.org/10.30843/nzpp.2019.72.309.

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Phlyctema vagabunda syn. Neofabraea alba is a fungal pathogen that causes bull’s eye rot (BER) of apples. Polymerase chain reaction (PCR) primers complementary to the inter-transcribed spacer region of ribosomal DNA (ITS) and the β-tubulin gene region, and a TaqMan™ probe assay were developed to detect this pathogen. These assays were compared in quantitative PCR (qPCR) reactions for amplification of DNA extracted from several fungal species and from apple tissue. Although the ITS and the β-tubulin primers amplified all N. alba isolates, both primers also amplified a few other fungal species. The TaqMan™ probe used with published primers for N. alba only amplified N. alba isolates. The TaqMan™ assay resulted in the lowest crossing threshold (Ct) values for DNA extracted from apple fruit, leaves, and spores collected on cellophane from eight apple orchards. The TaqMan™ results were correlated with percentage BER (%BER) in a 400-apple sample harvested from the same orchards. The TaqMan™ probe assay was the most sensitive and specific qPCR protocol tested, and Ct values showed the best correlation with %BER.
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Behrendt, Lars, Jeppe L. Nielsen, Søren J. Sørensen, Anthony W. D. Larkum, Jakob R. Winther, and Michael Kühl. "Rapid TaqMan-Based Quantification of Chlorophylld-Containing Cyanobacteria in the Genus Acaryochloris." Applied and Environmental Microbiology 80, no. 10 (March 14, 2014): 3244–49. http://dx.doi.org/10.1128/aem.00334-14.

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ABSTRACTReports of the chlorophyll (Chl)d-containing cyanobacteriumAcaryochlorishave accumulated since its initial discovery in 1996. The majority of this evidence is based on amplification of the gene coding for the 16S rRNA, and due to the wide geographical distribution of these sequences, a global distribution ofAcaryochlorisspecies was suggested. Here, we present a rapid, reliable, and cost-effective TaqMan-based quantitative PCR (qPCR) assay that was developed for the specific detection ofAcaryochlorisspecies in complex environmental samples. The TaqMan probe showed detection limits of ∼10 16S rRNA gene copy numbers based on standard curves consisting of plasmid inserts. DNA from fiveAcaryochlorisstrains, i.e., MBIC11017, CCMEE5410, HICR111A, CRS, and Awaji-1, exhibited amplification efficiencies of >94% when tested in the TaqMan assay. When used on complex natural communities, the TaqMan assay detected the presence ofAcaryochlorisspecies in four out of eight samples of crustose coralline algae (CCA), collected from temperate and tropical regions. In three out of these TaqMan-positive samples, the presence of Chldwas confirmed via high-performance liquid chromatography (HPLC), and corresponding cell estimates ofAcaryochlorisspecies amounted to 7.6 × 101to 3.0 × 103per mg of CCA. These numbers indicate a substantial contribution of Chld-containing cyanobacteria to primary productivity in endolithic niches. The new TaqMan assay allows quick and easy screening of environmental samples for the presence ofAcaryochlorisspecies and is an important tool to further resolve the global distribution and significance of this unique oxyphototroph.
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Dissertations / Theses on the topic "Taqman"

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Borodina, Tatiana. "Entwicklung des Ligationsdetektionreaction (LDR)-Taqman Assay eine neue SNP-Genotypisierungsmethode /." [S.l.] : [s.n.], 2005. http://www.diss.fu-berlin.de/2005/298/index.html.

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Armbruster, Katrin. "Entwicklung einer Multiplex-TaqMan-PCR zur Diagnostik der viralen Enzephalitis." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:25-opus-49607.

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Savill, Rachel. "Validering av realtids-PCR-metod för Herpes simplex- och Varicella-zoster virus." Thesis, Hälsohögskolan, Högskolan i Jönköping, HHJ, Avd. för naturvetenskap och biomedicin, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:hj:diva-27225.

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Scheer, Carola. "Nachweis von Aspergillus-fumigatus-Infektionen aus dem Respirationstrakt mittels TaqMan-PCR." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2006. http://dx.doi.org/10.18452/15415.

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Die invasive Aspergillose (IA) wird mehr und mehr zu einem lebensbedrohlichen Problem bei immunsupprimierten Patienten. Der Hauptverursacher der IA ist der Aspergillus fumigatus. Es existieren verschiedene DNS-Extraktions-Methoden und PCR Assays, um Aspergillus fumigatus DNS in Bronchiallavagen (BAL) nachzuweisen. Häufig sind diese Methoden langwierig und verdeutlichen den Bedarf an einer klinisch relevanten Methode, mit der der Aspergillus-fumigatus-DNS Nachweis schnell und zuverlässig erbracht werden kann. Wir haben eine schnelle Methode entwickelt, mit der wir quantitative Ergebnisse innerhalb sechs Stunden erhalten können. Es wurde ein Extraktionsverfahren auf mechanischer Basis (FastPrep), in Kombination mit einer real-time-PCR, basierend auf der TaqMan- Technologie, etabliert. Dazu wurde eine Aspergillus-fumigatus-spezifischeSonde entwickelt und ein Aspergillus-fumigatus-spezifisches Primerpaar eingesetzt. Durch den Einsatz einer Standardreihe wurden die Ergebnisse quantifiziert. Es wurden hauptsächlich Bronchiallavagen sowie andere Materialien von 204 Patienten untersucht. Die Patienten wurden hinsichtlich ihres Verdachtes an einer IA erkrankt zu sein, anhand bestimmter Kriterien (EORTC) in bestimmte Gruppen eingeteilt. Die Ergebnisse wurden innerhalb der einzelnen Gruppen analysiert. Bei allen 8 Patienten mit bewiesener IA gelang der Nachweis von Aspergillus-fumigatus-DNS. In dieser Gruppe konnten quantitativ die höchsten Werte gemessen werden. Des Weiteren konnte eine Rückläufigkeit der Werte mit abnehmendem Aspergillose-Verdacht, sowie nach erfolgter antimykotischer Therapie beobachtet werden. Die diagnostische Sensitivität der Methode beträgt 81,3%, die Spezifität liegt bei 93,7%. Der positive prädiktive Wert ist 72,2%, der negative prädiktive Wert beträgt 96,1%. Als zusätzlicher Baustein in einer umfangreichen Gesamtdiagnostik, kann diese Methode einen Beitrag zur Verbesserung molekularer Nachweisverfahren leisten.
Invasive aspergillosis (IA), often caused by Aspergillus fumigatus, is an important cause of death of immunocompromised patients. Several DNA-extraction methods and PCR assays are available for detecting Aspergillus fumigatus DNA in bronchoalveolar lavage (BAL) samples of patients with invasive aspergillosis. These methods are often time consuming and emphasize the need to develop a clinical relevant rapid DNA isolation assay that gives reliable results in a short time. We have developed a new and rapid method which yields results within six hours.This was achieved by combining high-speed cell disruption using a mechanical extraction procedure (FastPrep), with a real-time PCR assay based on TaqMan technology.A newly designed Aspergillus-fumigatus-specific probe and Aspergillus-fumigatus-specific primers were established. This combination also produces quantitative results by comparing the results with a DNA serial dilution used in the real-time PCR. BAL fluids and other material from 204 patients were analyzed. According to the risk for an IA, the patients were devided in different groups, using specific criteria published by the EORTC. The results were related to these groups. For all 8 patients with proven IA, the detection of Aspergillus-fumigatus-DNA succeeded. In this group, the highest amount of Aspergillus-fumigatus-DNA was detected. A decraesing quantitiy of Aspergillus-fumigatus-DNA could be detected after antifungal treatment and connected with the decreasing suspicion of an IA in the other groups. The diagnostic sensitivity of this method is 81,3%, the specifity is 93,7%. The positive predictive value is 72,2%, the negative predicitive value 96,1%. Adjunctive use of these method may be helpful in the diagnosis of IA.
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Herrmann, Ilka [Verfasser]. "Quantifizierung frühbesiedelnder oraler Actinomyces spp. mittels neu etablierter TaqMan-PCRs / Ilka Herrmann." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2016. http://d-nb.info/1111038759/34.

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Simecek, Nikol. "Development of a database with web-based user interface for taqman assay design." Thesis, Cranfield University, 2007. http://hdl.handle.net/1826/1773.

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TaqMan RT-PCR (reverse transcription-polymerase chain reaction) is a technique used to measure the relative gene expression in a biological sample and is one of the core technologies used by the Molecular Pathology and Toxicology (MPT) Group at GlaxoSmithKline. Conducting TaqMan experiments is a complex process which involves the design of a TaqMan assay specific to a gene of interest. A wealth of data has been generated during assay design, but systems are not currently available to readily share this data within the MPT group. There is a need for a central data storage repository so that data associated with assay design can be organised efficiently and rapidly accessed. Experiments are conducted within limited timeframes and resource is often limited so this would be of great benefit to the MPT group. This thesis describes the development of a database to house data associated with TaqMan assay design, software to populate the database with minimal user interaction and a web based CGI application for members of the MPT group to query and submit data to the database. Finally, the output from testing the software is provided and discussed.
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Camarão, António Alexandre Riachos. "Development and optimisation of a group-specific real-time RT-PCR assay for the broad detection of the Simbu serogroup orthobunyaviruses." Master's thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2018. http://hdl.handle.net/10400.5/15823.

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The Simbu serogroup within the genus Orthobunyavirus belongs to the family Peribunyaviridae and comprises 32 recognised three-segmented negative-sense single-stranded RNA viruses, divided into two phylogenetic clades. Some members of this group of arthropod-borne viruses, cosmopolitan distributed, cause neurologic disease in humans as well as reproductive and neurologic disease in domestic animals, however, definitive diagnosis always requires laboratorial confirmation. Few real-time RT-PCR assays have been developed for the molecular diagnosis of Simbu serogroup orthobunyaviruses. There are two published methods with broad detection capacity, utilising either a SYBR Green based chemistry able to recognise viruses from both clades, which is not absolutely specific, or a TaqMan based chemistry that recognises only clade B viruses. A novel group-specific TaqMan-based real-time RT-PCR assay was developed, optimised and laboratory validated for the broad detection of the Simbu serogroup orthobunyaviruses. The published genomic data of the Simbu serogroup members were evaluated, and a conserved region, situated in the segment encoding the nucleocapsid protein, was selected to design a universal primer set and a pair of differently labelled hydrolysis probes, which allowed for the distinction between the two phylogenetic clades of the Simbu serogroup. Seven prototype Simbu serogroup isolates were used for the development of the assay, namely Akabane orthobunyavirus, Simbu orthobunyavirus, Shuni orthobunyavirus, Sathuperi orthobunyavirus, Shamonda orthobunyavirus, Ingwavuma virus and Sabo virus. The primer and probe concentrations in the reaction were optimised. Amplification efficiency was determined for each one of the viruses: AKAV (99%), SIMV (96%), SHUV (96%), SATV (97%), SHAV (84%), INGV (93%) and SABOV (110%). A panel constituted of genetically related, causative agents of abortion in ruminants and arthropod-borne viruses was selected for in vitro specificity analysis, and in silico analysis was also performed. The assay was shown to be specific, as no cross-reactions were observed either in vitro or in silico, and sensitive, with a 95% limit of detection ranging from 10-0,39 to 10-3,61 TCID50/reaction, for the detection of Simbu serogroup viruses. The repeatability of the assay was evaluated for both probes detection, using the intra- and inter-run standard deviations and coefficient of variation. This work resulted in a manuscript in submission process to a peer-reviewed journal. In addition, a comprehensive review of the viruses of the Simbu serogroup was carried out, including sites of viral isolation and seroconversion, and a map was generated using a geographic information system tool.
RESUMO - O serogrupo Simbu pertence ao género Orthobunyavirus, família Peribunyaviridae, e é constituído por 32 vírus de RNA tri-segmentado de cadeia simples e polaridade negativa, divididos em duas clades filogenéticas. Alguns membros deste grupo de vírus transmitidos por artrópodes, com distribuição cosmopolita, causam doença neurológica em humanos bem como doença reprodutiva e neurológica em animais domésticos, no entanto, o diagnóstico definitivo requer sempre confirmação laboratorial. Poucos ensaios de RT-PCR em tempo real têm sido desenvolvidos para o diagnóstico molecular destes vírus, ainda assim, existem dois que se destacam pela capacidade de detecção em largo espectro. Um deles, com sistema de detecção de fluorescência baseado na utilização de SYBR Green, é capaz de detectar vírus das duas clades, mas não é absolutamente específico, e o outro, baseando-se na utilização de sondas TaqMan, só detecta vírus de uma das clades. Um ensaio de RT-PCR em tempo real grupo-específico, inédito, com sondas TaqMan, foi desenvolvido, optimizado e caracterizado em termos laboratoriais, para a detecção em largo espectro dos orthobunyavirus do serogrupo Simbu. Os dados publicados referentes ao genoma dos membros do serogrupo foram analisados, e uma região conservada, situada no segmento codificante da proteína da nucleocápdise, foi eleita para o desenho de um par de primers específicos universal, bem como de duas sondas de hidrólise específicas, distintamente marcadas, e que, portanto, permitem a diferenciação entre as clades filogenéticas. Sete isolados de referência foram utilizados no desenvolvimento do ensaio, nomeadamente Akabane orthobunyavirus, Simbu orthobunyavirus, Shuni orthobunyavirus, Sathuperi orthobunyavirus, Shamonda orthobunyavirus, Ingwavuma virus e Sabo virus e, consequentemente, as concentrações dos primers e sondas na reação foram optimizadas. A eficiência de amplificação foi determinada para cada um dos vírus: AKAV (99%), SIMV (96%), SHUV (96%), SATV (97%), SHAV (84%), INGV (93%) e SABOV (110%). Um painel constituído por vírus geneticamente relacionados, agentes causais de aborto em ruminantes e transmitidos por artrópodes foi seleccionado no sentido de avaliar a especificidade do ensaio in vitro, tendo sido também efectuada uma análise in silico. O ensaio é específico, visto que não foram observadas reacções cruzadas quer in vitro quer in silico, e sensível, com um limite de detecção de 95% entre 10-0,39 a 10-3,61 TCID50/reacção, para a detecção de vírus do serogrupo Simbu. A repetibilidade foi avaliada para a detecção com ambas as sondas, pelo cálculo do desvio padrão intra- e inter-corridas bem como do coeficiente de variação. Este trabalho originou um manuscrito em processo de submissão para uma revista cientifíca. Além disso, foi levada a cabo uma revisão bibliográfica do serogrupo Simbu, incluindo locais de isolamento viral e seroconversão, e um mapa inédito desta distribuição foi gerado.
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Cunty, Amandine. "Caractérisation de Pseudomonas syringae pv. actinidiae l’agent responsable de l’émergence d’une épidémie de chancre bactérien du kiwi en France et description de Pseudomonas syringae pv. actinidifoliorum, agent causal de taches foliaires sur kiwi." Thesis, Angers, 2015. http://www.theses.fr/2015ANGE0018/document.

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La bactérie responsable de chancre sur bois, Pseudomonas syringae pv. actinidiae (Psa), a causé trois épidémies depuis les années 1980 et se décline en trois biovars. La plus récente et dévastatrice (causée par Psa biovar 3), a été détectée pour la première fois en 2008 en Italie et s’est rapidement répandue dans la majorité des pays producteurs de kiwi, dont en France en 2010. Nous avons analysé la diversité de 280 souches de P. syringae isolées de kiwi en France. La caractérisation biologique et l’analyse phylogénétique des souches par MLSA ont révélé que les biovars 1, 2 et 3 appartenaient à une même lignée génétique, groupant également P. s. pv. theae. Les souches de biovar 4 constituent un ensemble de 4 lignées génétiques distinctes qui ont été rassemblées au sein d’un nouveau pathovar (Pseudomonas syringae pv. actinidifoliorum (Psaf)). Ces souches sont caractérisées par une pathogénie réduite (taches foliaires mais pas de chancre). Cette nouvelle classification permet une meilleure gestion des épidémies de chancre bactérien du kiwi. Le développement d’un schéma MLVA composé de 11 VNTRs a permis d’étudier la structuration génétique de populations de Psa biovar 3, de révéler de la diversité au sein de ce pathovar et d’identifier l’origine italienne de l’épidémie en France. Le séquençage du génome de cinq souches de Psaf et la comparaison de ces séquences avec celles d’autres génomes de Psa et Psaf, disponibles sur NCBI, a permis le développement d’un nouvel outil de détection par PCR temps réel, plus spécifique de chaque biovar de Psa et de Psaf. La MLVA et la PCR temps réel développées ici contribueront à l’amélioration de la surveillance de Psa dans le monde
The causal agent of bacterial canker, Pseudomonas syringae pv. actinidiae (Psa),has been responsible ofthree epidemics since 1980’s.Psa is divided in three biovars. The most recent and severe outbreak (causedby Psa biovar 3) was detected for the first time in Italy in 2008. It has spread very quickly in the main kiwifruit producing countries, as in France in 2010. We analyzed the diversity of 280 strains of P. syringae isolated fromkiwifruit in France. The biological characterization and the phylogenetic analysis of the strains by MLSArevealed that the biovars 1, 2 and 3 belong to the same genetic lineage, which include P. s. pv. theae, as well.The biovar 4 strains, which are structured in 4 distinct genetic lineages, have been grouped in a new pathovar(Pseudomonas syringae pv. actinidifoliorum (Psaf)). These strains are characterized by a low virulence (onlyspots on leaves and no canker on wood). This new classification help with the management of the bacterialkiwifruit canker outbreaks. The development of an MLVA scheme composed of 11 VNTRs allowed to studythe genetic structuration of Psa biovar 3 populations, to reveal the diversity within this pathovar and to identifythe Italian origin of the epidemic in France. The genome sequencing of five Psaf strains and the comparisonbetween these sequences and those of Psa and Psaf genomes already available on NCBI, allowed thedevelopment of a new detection tool by real-time PCR, specific of each Psa biovar and of Psaf. The MLVA andthe real-time PCR based detection technique developed here will contribute to the improvement of the monitoringof kiwifruit bacterial canker around the world
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Kessler, Yvonne. "Quantitative TaqMan® real-time PCR assays for gene expression normalisation in feline tissues /." [S.l.] : [s.n.], 2009. http://opac.nebis.ch/cgi-bin/showAbstract.pl?sys=000292626.

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Steyn, HC, A. Pretorius, and CME McCrindle. "A quantitative real-time PCR assay for Ehrlichia ruminantium using pCS20." Elsevier, 2008. http://encore.tut.ac.za/iii/cpro/DigitalItemViewPage.external?sp=1000379.

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Heartwater is a tick borne disease that affects ruminants and wild animals in Africa south of the Sahara. It is caused by Ehrlichia ruminantium and transmitted by the tick Amblyomma hebraeum. The protocols currently used to detect heartwater take several days to complete. Here, we describe the development of a pCS20 quantitative real-time PCRTaqMan probe assay to detect E. ruminantium in livestock blood and ticks from the field. The assay is based on the conserved pCS20 gene region of E. ruminantium that contains two overlapping genes, rnc and ctaG [Collins, N.E., Liebenberg, J., De Villiers, E.P., Brayton, K.A., Louw, E., Pretorius, A., Faber, F.E., Van Heerden, H., Josemans, A., Van Kleef, M., Steyn, H.C., Van Strijp, M.F., Zweygarth, E., Jongejan, F., Maillard, J.C., Berthier, D., Botha, M., Joubert, F., Corton, C.H., Thomson, N.R., Allsopp, M.T., Allsopp, B.A., 2005. The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. PNAS 102, 838–843]. The pCS20 quantitative real-time PCRTaqMan probe was compared to the currently used pCS20 PCR and PCR/32P-probe test with regards to sensitivity, specificity and the ability to detect DNA in field samples and in blood from experimentally infected sheep. This investigation showed that the pCS20 quantitative real-time PCRTaqMan probe was the most sensitive assay detecting seven copies of DNA/ml of cell culture. All three assays, however, cross react with Ehrlichia canis and Ehrlichia chaffeensis. The pCS20 real-time PCR detected significantly more positive field samples. Both the PCR and pCS20 real-time PCR could only detect E. ruminantium parasites in the blood of experimentally infected sheep during the febrile reaction. The PCR/32P-probe assay, however, detected the parasite DNA 1 day before and during the febrile reaction. Thus, because this new quantitative pCS20 real-time PCRTaqMan probe assay was the most sensitive and can be performed within 2 h it is an effective assay for epidemiological surveillance and monitoring of infected animals.
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Books on the topic "Taqman"

1

Pārsāyī: Taqvā. Tihrān: Payām-i Āzādī, 2002.

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Öğünç, Bıtrıs. Taqlab: 532. Augsburg: Maṭbaʻtā d-Ḥúyādā ʼAtorāyā b-ʼÚrípí Meṣʻāytā, 1988.

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Vrnjak, Hajrudin. Taqwa: Poezija. Sarajevo: Kaligraf, 2002.

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Şarî deste u taqmekan. Kurdistan, Iraq]: Saram Qewamî, 2008.

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Barsūm, ʻAwnī. al-Taqnīn al-kanasī: Taqnīn al-Kanīsah al-Qibṭīyah al- Urthūdhuksīyah. al-Jīzah: Kanīsat Mār Murqus bi-al-Jīzah, 1994.

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Sayyid, Kamāl. Wa-Kāna taqīyan: Riwāyah tārīkhīyah. Bayrūt: Dār al-Nubalāʾ, 2000.

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Aḥmad ibn ʻAwaḍ Allāh ibn Dākhīl al-Luhaybī Ḥarbī. al- Māturīdīyah: Dirāsatan wa-taqwīman. al-Riyāḍ: Dār al-ʻĀṣimah, 1992.

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Taqnīn al-ṣafaqāt al-ʻumūmīyah. al-Jazāʼir: Dār Hūmah lil-Ṭibāʻah wa-al-Nashr wa-al-Tawzīʻ, 2009.

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Taqnīn al-aḥkām al-qaḍāʼīyah. al-Riyāḍ: Muḥammad ʻAbd al-ʻAzīz al-Fāʼiz, 2010.

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Arifinsyah. Pedoman Puasa Menggapai Taqwa . JAKARTA: Al-Hijri Jakarta, 2004.

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Book chapters on the topic "Taqman"

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Arnemann, J. "Taqman-Sonden." In Springer Reference Medizin, 2260–61. Berlin, Heidelberg: Springer Berlin Heidelberg, 2019. http://dx.doi.org/10.1007/978-3-662-48986-4_3591.

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Arnemann, J. "Taqman-Sonden." In Lexikon der Medizinischen Laboratoriumsdiagnostik, 1. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-662-49054-9_3591-1.

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Dötsch, Jörg, Ellen Schoof, and Wolfgang Rascher. "Quantitative TaqMan Real-Time PCR." In Medical Biomethods Handbook, 305–13. Totowa, NJ: Humana Press, 2005. http://dx.doi.org/10.1385/1-59259-870-6:305.

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Shen, Gong-Qing, Kalil G. Abdullah, and Qing Kenneth Wang. "The TaqMan Method for SNP Genotyping." In Methods in Molecular Biology, 293–306. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-411-1_19.

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Keys, David N., Janice K. Au-Young, and Richard A. Fekete. "TaqMan® Array Cards in Pharmaceutical Research." In Methods in Molecular Biology, 87–97. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-663-4_6.

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Schleinitz, Dorit, Johanna K. DiStefano, and Peter Kovacs. "Targeted SNP Genotyping Using the TaqMan® Assay." In Methods in Molecular Biology, 77–87. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-61737-954-3_6.

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Weller, S. A., J. G. Elphinstone, N. C. Smith, J. Hennessy, and D. E. Stead. "Detection of Plant Associated Bacteria by TaqMan™ PCR." In Plant Pathogenic Bacteria, 441–45. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0003-1_99.

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Woodward, John. "Bi-Allelic SNP Genotyping Using the TaqMan® Assay." In Methods in Molecular Biology, 67–74. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0446-4_6.

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Karpova, Yaroslava, and Alexei V. Tulin. "TaqMan Multiplex qPCR Method to Genotype PARG Knockout Mice." In Methods in Molecular Biology, 363–71. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2891-1_22.

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Stager, Charles E., and Tavat A. Buraruk. "COBAS® AmpliPrep/COBAS® TaqMan® HCV Test." In Modern Clinical Molecular Techniques, 153–70. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-2170-2_11.

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Conference papers on the topic "Taqman"

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Belgrader, P., W. Benett, R. Frattaroli, D. Hadley, R. Langlois, S. Lehew, R. Mariella, et al. "Multi-Chamber, Real-Time DNA Analysis in the Field Using Microfabricated Silicon Chambers." In ASME 1998 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1998. http://dx.doi.org/10.1115/imece1998-1255.

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Abstract During 1997, we designed and built a 10-chamber thermal cycling system which was capable of performing the polymerase chain reaction (PCR) using TaqMan® probes. Each chamber includes a thin-film resistive heater which was deposited directly on the microfabricated silicon chamber, for efficient heating, and the design of the silicon chambers permitted efficient, forced-convective cooling with air. Each silicon chamber contained etched holes for directly exciting the TaqMan® probes and monitoring their fluorescence emission. Our software, which controlled the thermal cycling, monitored the TaqMan® emission from each chamber on every thermal cycle, and performed automatic calling of positives for each chamber. We used this system at Dugway Proving Grounds in January, 1998, during the detector/identifier portion of the Joint Field Trials IV. With this system, we were able to detect and identify all three organisms that were used as simulants during JFT IV; this required the analysis of 32 unknowns per day for 10 days.
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Laig, Marion, Kamini Varma, and Vidya Venkatesh. "Abstract 746: TaqMan Rare Mutation Assays targeting the TERT promoter region." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-746.

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Laig, Marion, Frances Chan, Le Lac, Ted Straub, Kamini Varma, and David Keys. "Abstract 402: Multiplex TaqMan assays for rare mutation analysis using digital PCR." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-402.

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Gunay, Melih, and Mehmet Karakoc. "TaqMan array card data management system for epidemiologic surveillance and clinical study." In 2017 International Conference on Computer Science and Engineering (UBMK). IEEE, 2017. http://dx.doi.org/10.1109/ubmk.2017.8093533.

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Looijenga, Leendert HJ, Ton Van Agthoven, and Ad Gillis. "Abstract 1088: Efficient detection of germ cell cancer related miRNAs in serum using the TaqMan miRNA ABC purification bead kit in combination with the Taqman advanced miRNA assays." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-1088.

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Jackson, Stephen M., Harita Veereshlingham, and Kamini Varma. "Abstract 5201: Using Taqman assays to verify eQTL links arising from GWAS studies." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-5201.

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Laig, Marion, Brian Ho, Nivedita S. Majumdar, Le T. Lac, Frances Chan, Ramesh Sathiyaa, Iain Russel, et al. "Abstract 5251: TaqMan® rare mutation assays for QuantStudio® 3D digital PCR system." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-5251.

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Chandramouli, Gadisetti VR, G. Larry Maxwell, and John I. Risinger. "Abstract 4050: Normalization of TaqMan human microRNA array data using average expression of controls." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-4050.

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Cunha, Gabriela Quevedo, ALVARO LARGURA, ANGÉLICA REGINA CAPPELLARI, DIOGO MULLER LACERDA, and MARCO ANTÔNIO LARGURA. "IMPLANTAÇÃO DO TESTE DE SEXAGEM FETAL A PARTIR DA OITAVA SEMANA DE GESTAÇÃO PELA TÉCNICA DE PCR EM TEMPO REAL NO SISTEMA TAQMAN." In I Congresso Nacional de Pesquisas e Estudos Genéticos On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/geneticon/9121.

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Introdução: A análise do DNA fetal livre de células (cffDNA), encontrado circulante no sangue materno, é uma técnica não invasiva, que pode ser utilizada para determinação do sexo fetal em estágios iniciais da gravidez. O método baseia-se na análise da expressão de fragmentos genéticos associados ao cromossomo Y (DYS14 – alvo específico) pela técnica do PCR em tempo real. A amplificação desse gene exclusivamente caracteriza um fenótipo masculino e a não amplificação, um fenótipo feminino. Objetivo: Implantação da técnica de detecção do sexo fetal a partir da oitava semana de gestação em amostras de sangue total materno através da técnica de PCR (Reação em Cadeia da Polimerase) em tempo real no sistema Taqman. Material e Método: Foi aplicado um questionário a 47 gestantes referentes aos critérios de inclusão ou exclusão, assim como um Termo de Consentimento para a autorização do teste. As amostras de plasma foram então submetidas à extração de DNA e subsequente análise do material genético pelo método de PCR em tempo real no sistema Taqman, utilizando as sondas para os alvos DYS14, para identificação do cromossomo Y e da beta-globina (HBB) como controle interno e validação do protocolo. Resultados: Das 47 gestantes, foram identificados 21 fetos com o sexo feminino e 26 masculinos. Todas as amostras foram enviadas para um laboratório externo de referência para validação dos resultados onde foi obtido 100% de assertividade. Conclusão: A aplicação dessa nova metodologia traz agilidade e confiabilidade para a detecção do sexo fetal em idades gestacionais precoces, atreladas a uma metodologia não invasiva.
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Araujo, Irene, Alexandre Fialho, Rosane Assis, Ediuardo Volotão, Darwin Operario, Eric Houpt, Duncan Steele, Fatima Serhan, and Gloria Rey-Benito. "A laboratory-developed TaqMan Array Card for simultaneous detection and genotyping of Group A rotavirus." In III Seminário Anual Científico e Tecnológico de Bio-Manguinhos. Instituto de Tecnologia em Imunobiológicos, 2015. http://dx.doi.org/10.35259/isi.sact.2015_28499.

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Reports on the topic "Taqman"

1

Gardner, S., and C. Jaing. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees. Office of Scientific and Technical Information (OSTI), March 2012. http://dx.doi.org/10.2172/1047247.

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Jaing, C., A. Hinkley, S. Gardner, and J. Thissen. Report for Evaluation of Canonical SNP Taqman Assays to Detect Biothreat Agents and Environmental Samples for DHS. Office of Scientific and Technical Information (OSTI), May 2011. http://dx.doi.org/10.2172/1122226.

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Daniels, J. I., W. J. Wilson, T. Z. DeSantis, F. J. Gouveia, G. L. Anderson, J. H. Shinn, R. Pletcher, S. M. Johnson, and D. Pappagianis. Development of a Quantitative TaqMan{trademark}-PCR Assay and Feasibility of Atmosphoric Collection for Coccidioides Immits for Ecological Studies. Office of Scientific and Technical Information (OSTI), February 2002. http://dx.doi.org/10.2172/15002759.

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