Relevant bibliographies by topics / Denaturing high performance liquid chromatography (DHPLC)

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Academic literature on the topic 'Denaturing high performance liquid chromatography (DHPLC)'

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Published: 21 February 2023

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Journal articles on the topic "Denaturing high performance liquid chromatography (DHPLC)"

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Cole, David E. C., Francisco H. J. Yun, Betty Y. L. Wong, Andrew Y. Shuen, Ronald A. Booth, Alfredo Scillitani, Svetlana Pidasheva, Xiang Zhou, Lucie Canaff, and Geoffrey N. Hendy. "Calcium-sensing receptor mutations and denaturing high performance liquid chromatography." Journal of Molecular Endocrinology 42, no. 4 (January 29, 2009): 331–39. http://dx.doi.org/10.1677/jme-08-0164.

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The calcium-sensing receptor (CASR), a plasma membrane G-protein-coupled receptor, is expressed in parathyroid gland and kidney, and controls systemic calcium homeostasis. Inactivating CASR mutations are associated with familial hypocalciuric hypercalcemia (FHH) and neonatal severe hyperparathyroidism, and activating mutations cause autosomal dominant hypocalcemia (ADH). CASR mutation identification plays an important role in the clinical management of mineral metabolism disorders. We describe here a high-throughput method using screening with denaturing high performance liquid chromatography (DHPLC) to initially interrogate 12 amplicons covering translated exons and exon/intron boundaries, followed by sequencing of any amplicon with a modified melting curve relative to wild type, and direct sequencing of a 13th amplicon encoding the COOH-terminal tail to distinguish causative mutations from three common missense single nucleotide polymorphisms. A blinded analysis of 32 positive controls representing mutations throughout the CASR sequence, as well as 22 negative controls, yielded a concordance rate of 100%. We report eight novel and five recurrent FHH mutations, along with six novel and two recurrent ADH mutations. Thus, DHPLC provides a rapid and effective means to screen for CASR mutations.
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Xu, Li, Jason Evans, Thomas Ling, Kathy Nye, and Peter Hawkey. "Rapid Genotyping of CTX-M Extended-Spectrum β-Lactamases by Denaturing High-Performance Liquid Chromatography." Antimicrobial Agents and Chemotherapy 51, no. 4 (January 8, 2007): 1446–54. http://dx.doi.org/10.1128/aac.01088-06.

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ABSTRACT Denaturing high-performance liquid chromatography (dHPLC) is a powerful technique which has been used extensively to detect genetic variation. This is the first report of the application of dHPLC for rapid genotyping of bacterial β-lactamase genes. The technique was specifically developed to genotype members of all bla CTX-M DNA homology groups. Thirteen well-defined bla CTX-M extended-spectrum β-lactamase (ESBL)-producing strains were used to develop and optimize the dHPLC genotyping assay. Further evaluation was carried out with a blinded panel of 62 clinical isolates. The results of bla CTX-M genotyping achieved by dHPLC were comparable to the typing results obtained by DNA sequencing. Applying the newly developed dHPLC-based genotyping method, we successfully genotyped all 73 bla CTX-M ESBL-producing strains from the 4-month survey study. Furthermore, we found the first reported cases in the United Kingdom of clinically significant disease caused by CTX-M-14- and CTX-M-1-producing Escherichia coli strains. We conclude that the novel dHPLC assay is highly accurate, rapid, and cost-effective for the genotyping of bla CTX-M-producing ESBLs and has great potential for determining the clinical relevance of different and new bla CTX-M genotypes, as well as for epidemiological studies and surveillance programs.
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Crépin, Michel, Pascal Pigny, Fabienne Escande, Catherine Cardot Bauters, Alain Calender, Sylvain Lefevre, Marie-Pierre Buisine, Nicole Porchet, and Marie-Françoise Odou. "Evaluation of denaturing high performance liquid chromatography for the mutational analysis of the MEN1 gene." Journal of Molecular Endocrinology 36, no. 2 (April 2006): 369–76. http://dx.doi.org/10.1677/jme.1.01903.

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The identification of mutations in the MEN1 gene causing MEN1 has represented a challenge since the cloning of the gene in 1997 because of the lack of mutation hot-spots in the gene and the lack of phenotype–genotype correlations. The use of denaturing high performance liquid chromatography (DHPLC), a high throughput, reliable and automated heteroduplex-based technique, is the ideal for mutation detection in MEN1. In this work, DHPLC was optimised for the screening of the nine coding exons and splice junctions of MEN1. Thanks to collaboration between two French laboratories recognised as reference centres for genotypic MEN1 diagnosis (Lyon and Lille), a blind retrospective study conducted in a cohort of 160 unrelated MEN1 probands with (or without) known germline mutations was undertaken to evaluate the sensitivity of DHPLC. We were able to detect 101 different sequence variations by DHPLC, distributed in the 10 analysed DNA fragments and corresponding to 100% of mutation detection compared with direct sequencing. 1·2% of samples were considered as false positive, exhibiting a heterogenous profile. DHPLC did not detect five cases of deletion or duplication of complete exons, neither did direct sequencing, showing the limits of the technique. Nevertheless, the method appeared to allow automated, rapid and low-cost mutation detection with high accuracy. Direct sequencing can be then applied to identify the sequence variations on the targeted DNA fragments showing heterozygous profile by DHPLC. In conclusion, genotypic diagnosis of MEN1 can benefit from DHPLC in terms of efficacy, rapidity and cost.
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Priha, Outi, Mari Nyyssönen, Malin Bomberg, Arja Laitila, Jaakko Simell, Anu Kapanen, and Riikka Juvonen. "Application of Denaturing High-Performance Liquid Chromatography for Monitoring Sulfate-Reducing Bacteria in Oil Fields." Applied and Environmental Microbiology 79, no. 17 (June 21, 2013): 5186–96. http://dx.doi.org/10.1128/aem.01015-13.

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ABSTRACTSulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H2S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (dsrB) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 101to 6 × 105dsrBgene copies ml−1. DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and differentdsrBcompositions were detected at different geographical locations. The identifieddsrBgene sequences belonged to several phylogenetic groups, such asDesulfovibrio,Desulfococcus,Desulfomicrobium,Desulfobulbus,Desulfotignum,Desulfonatronovibrio, andDesulfonauticus. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.
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Kota, Raja, Markus Wolf, Wolfgang Michalek, and Andreas Graner. "Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.)." Genome 44, no. 4 (August 1, 2001): 523–28. http://dx.doi.org/10.1139/g01-053.

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Recent advances in DNA sequence analysis and the establishment of high-throughput assays have provided the framework for large-scale discovery and analysis of DNA sequence variation. In this context, single nucleotide polymorphisms (SNPs) are of particular interest. To initiate a systematic approach to develop an SNP map of barley (Hordeum vulgare L.), we have employed denaturing high-performance liquid chromatography (DHPLC) to analyse segregating SNP patterns in a doubled-haploid (DH) mapping population. To this end, SNPs between the parental genotypes were identified using a direct sequencing approach. Once a SNP was established between the parents, the optimal melting temperature of the PCR fragment containing the SNP was predicted for its analysis by DHPLC. Following the detection of the optimal temperature, the DH lines were analysed for the presence of either of the alleles. To test the utility of the analysis, data from previously mapped RFLP markers from which these SNPs were derived were compared. Results from these experiments indicate that DHPLC can be efficiently employed in analysing SNPs on a high-throughput scale.Key words: denaturing high performance liquid chromatography, doubled-haploid lines, restriction fragment length polymorphism, genetic mapping, molecular markers.
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Wagner, Andreas Otto, Cornelia Malin, and Paul Illmer. "Application of Denaturing High-Performance Liquid Chromatography in Microbial Ecology: Fermentor Sludge, Compost, and Soil Community Profiling." Applied and Environmental Microbiology 75, no. 4 (December 16, 2008): 956–64. http://dx.doi.org/10.1128/aem.01411-08.

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ABSTRACT Genetic fingerprinting methods, such as denaturing gradient gel electrophoresis (DGGE), are used in microbial ecology for the analysis of mixed microbial communities but are associated with various problems. In the present study we used a new alternative method: denaturing high-performance liquid chromatography (dHPLC). This method was previously shown to work with samples from water and gut flora but had not yet been applied to complex environmental samples. In contrast to other publications dealing with dHPLC, we used a commonly available HPLC system. Samples from different origins (fermentor sludge, compost, and soil), all ecologically significant, were tested, and the 16S rRNA gene was amplified via PCR. After optimization of the HPLC elution conditions, amplicons of pure cultures and mixed microbial populations could be separated successfully. Systematic differentiation was carried out by a cloning approach, since fraction collection of the peaks did not result in satisfactory fragment separation. dHPLC was evaluated as a tool for microbial community analysis on a genetic level and demonstrated major improvements compared to gel-based fingerprinting methods, such as DGGE, that are commonly used in microbial ecology.
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Troedsson, Christofer, Richard F. Lee, Vivica Stokes, Tina L. Walters, Paolo Simonelli, and Marc E. Frischer. "Development of a Denaturing High-Performance Liquid Chromatography Method for Detection of Protist Parasites of Metazoans." Applied and Environmental Microbiology 74, no. 14 (May 23, 2008): 4336–45. http://dx.doi.org/10.1128/aem.02131-07.

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ABSTRACT Increasingly, diseases of marine organisms are recognized as significant biotic factors affecting ecosystem health. However, the responsible disease agents are often unknown and the discovery and description of novel parasites most often rely on morphological descriptions made by highly trained specialists. Here, we describe a new approach for parasite discovery, utilizing denaturing high-performance liquid chromatography (DHPLC) reverse-phase ion-paring technology. Systematic investigations of major DHPLC variables, including temperature, gradient conditions, and target amplicon characteristics were conducted to develop a mechanistic understanding of DNA fragment separation by DHPLC. As a model system, 18S rRNA genes from the blue crab (Callinectes sapidus) and a parasitic dinoflagellate Hematodinium sp. were used. Binding of 18S rRNA gene PCR amplicons to the DNA separation column in the presence of triethylammonium acetate (TEAA) was inversely correlated with temperature and could be predicted based on the estimated DNA helicity of the PCR amplicon. Amplicons of up to 498 bp were resolved as single chromatographic peaks if they had high (>95%) DNA helicity. Amplicons that differed by as few as 2 bp could be resolved. Separation of 18S rRNA gene PCR amplicons was optimized by simultaneous manipulation of both temperature and solvent gradients. The optimal conditions included targeting regions of high DNA helicity (>95%), temperatures in the range of 57 to 63°C, and a linear acetonitrile gradient from 13.75 to 17.5% acetonitrile in 0.1 M TEAA (55 to 70% buffer B) over a 9-min period. Under these conditions, amplicons from a variety of parasites and their hosts can be separated and detected by DHPLC.
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Kim, Il-Jin, Yong Shin, Hio Chung Kang, Jae-Hyun Park, Ja-Lok Ku, Hye-Won Park, Hye-Rin Park, et al. "Robust microsatellite instability (MSI) analysis by denaturing high-performance liquid chromatography (DHPLC)." Journal of Human Genetics 48, no. 10 (September 12, 2003): 525–30. http://dx.doi.org/10.1007/s10038-003-0070-y.

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Ray, Pierre F., Paule Benit, Jean Paul Bonnefont, and Arnold Munnich. "Chronology of reported denaturing high performance liquid chromatography (DHPLC)-based prenatal diagnoses." Prenatal Diagnosis 23, no. 1 (January 2003): 81. http://dx.doi.org/10.1002/pd.496.

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Bénit, Paule, Jean-Paul Bonnefont, Ali Kara Mostefa, Christine Francannet, Arnold Munnich, and Pierre F. Ray. "Denaturing high-performance liquid chromatography (DHPLC)-based prenatal diagnosis for tuberous sclerosis." Prenatal Diagnosis 21, no. 4 (March 7, 2001): 279–83. http://dx.doi.org/10.1002/pd.55.

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Dissertations / Theses on the topic "Denaturing high performance liquid chromatography (DHPLC)"

1

Junge, Cornelia. "Molekulargenetische Diagnostik des ATRX-Syndroms mittels Denaturing High-Performance Liquid Chromatography (DHPLC)." Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-147264.

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Die DNA-Sequenzierung nimmt in der molekulargenetischen Diagnostik seit vielen Jahren einen großen Stellenwert ein. Zeit- und kosteneffektivere Methoden wie die DHPLC wurden seither für verschiedene Gene etabliert. Ziel dieser Arbeit war die Etablierung der DHPLC für das ATRX-Gen bei Patienten mit Verdacht auf das ATRX-Syndrom. Nach erfolgreicher Etablierung der DHPLC sollten im Rahmen dieser Arbeit 38 Patientenproben des Instituts für Humangenetik der Universität Leipzig mit Verdacht auf das ATRX-Syndrom mittels DHPLC und Sequenzierung untersucht werden. Die Etablierung der DHPLC gelang in der vorliegenden Arbeit für alle - das ATRX-Gen vollständig umspannenden - 42 Fragmente. Jede der vorliegenden Sequenzvariationen konnte nach Abschluss der Arbeit detektiert werden. Unter Verwendung von Maxima® stellten sich initial 22 von 24 verschiedenen Sequenzvariationen zum Wildtyp different dar. Die verbleibenden zwei Mutationen p.R246C und p.A238P im Fragment 9 wurden unter Verwendung höherer Temperaturen, eines kürzeren Fragmentes oder anderer Polymeraseenzyme (AmpliTaq Gold® bzw. HighFidelity) detektiert. Nach Abschluss der Etablierung der DHPLC konnte eine Sensitivität und Spezifität von 100% erreicht werden. In den Patientenuntersuchungen des Instituts für Humangenetik der Universität Leipzig fanden sich bei 38 Patientenproben vier verschiedene als benigne beschriebene Polymorphismen bei insgesamt 19 Patienten, ein noch nicht veröffentlichter Polymorphismus im Intron 26 sowie eine bis dato nicht beschriebene und als pathogen einzustufende Mutation im Exon 34. In 100 Kontrollen der DNA-Bank des Instituts für Humangenetik der Universität Leipzig konnte der bisher nicht publizierte Polymorphismus im Intron 26 sieben Mal gefunden werden. Die bis dato nicht beschriebene Deletion p.2385_2395del im Exon 34 führt zu einem vorzeitigen Abbruch des ATRX-Proteins und ist somit als sicher pathogen einzustufen. Die Untersuchung der Mutter des Patienten konnte den Konduktorenstatus nachweisen. Für die Familie des betroffenen Patienten konnte mit der vorliegenden Arbeit die Diagnose des ATRX-Syndroms gesichert werden. Die DNA-Proben der Patienten bei denen keine Mutation nachgewiesen werden konnte, sollten bei weiterhin dringendem Verdacht auf das ATRX-Syndrom mittels qRT-PCR bzw. MLPA untersucht werden, um große Deletionen, Insertionen oder Duplikationen auszuschließen. Mithilfe dieser Arbeit gelang die Etablierung der DHPLC für das ATRX-Gen als ökonomische, sehr sensitive und effiziente Methode zur Diagnostik des ATRX-Syndroms. Die Entscheidung, in welcher Form und mit welcher Methode DNA-Proben bei Verdacht auf ATRX-Syndrom untersucht werden, bleibt jedoch eine individuelle Entscheidung jedes Instituts unter Betrachtung der jeweiligen Gegebenheiten vor Ort.
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Junge, Cornelia [Verfasser], Eberhard [Akademischer Betreuer] Passarge, Ursula [Akademischer Betreuer] Froster, Torsten [Gutachter] Schöneberg, and Evelin [Gutachter] Schröck. "Molekulargenetische Diagnostik des ATRX-Syndroms mittels Denaturing High-Performance Liquid Chromatography (DHPLC) / Cornelia Junge ; Gutachter: Torsten Schöneberg, Evelin Schröck ; Eberhard Passarge, Ursula Froster." Leipzig : Universitätsbibliothek Leipzig, 2014. http://d-nb.info/1238692419/34.

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Junge, Cornelia. "Molekulargenetische Diagnostik des ATRX-Syndroms mittels Denaturing High-Performance Liquid Chromatography (DHPLC)." Doctoral thesis, 2013. https://ul.qucosa.de/id/qucosa%3A12684.

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Die DNA-Sequenzierung nimmt in der molekulargenetischen Diagnostik seit vielen Jahren einen großen Stellenwert ein. Zeit- und kosteneffektivere Methoden wie die DHPLC wurden seither für verschiedene Gene etabliert. Ziel dieser Arbeit war die Etablierung der DHPLC für das ATRX-Gen bei Patienten mit Verdacht auf das ATRX-Syndrom. Nach erfolgreicher Etablierung der DHPLC sollten im Rahmen dieser Arbeit 38 Patientenproben des Instituts für Humangenetik der Universität Leipzig mit Verdacht auf das ATRX-Syndrom mittels DHPLC und Sequenzierung untersucht werden. Die Etablierung der DHPLC gelang in der vorliegenden Arbeit für alle - das ATRX-Gen vollständig umspannenden - 42 Fragmente. Jede der vorliegenden Sequenzvariationen konnte nach Abschluss der Arbeit detektiert werden. Unter Verwendung von Maxima® stellten sich initial 22 von 24 verschiedenen Sequenzvariationen zum Wildtyp different dar. Die verbleibenden zwei Mutationen p.R246C und p.A238P im Fragment 9 wurden unter Verwendung höherer Temperaturen, eines kürzeren Fragmentes oder anderer Polymeraseenzyme (AmpliTaq Gold® bzw. HighFidelity) detektiert. Nach Abschluss der Etablierung der DHPLC konnte eine Sensitivität und Spezifität von 100% erreicht werden. In den Patientenuntersuchungen des Instituts für Humangenetik der Universität Leipzig fanden sich bei 38 Patientenproben vier verschiedene als benigne beschriebene Polymorphismen bei insgesamt 19 Patienten, ein noch nicht veröffentlichter Polymorphismus im Intron 26 sowie eine bis dato nicht beschriebene und als pathogen einzustufende Mutation im Exon 34. In 100 Kontrollen der DNA-Bank des Instituts für Humangenetik der Universität Leipzig konnte der bisher nicht publizierte Polymorphismus im Intron 26 sieben Mal gefunden werden. Die bis dato nicht beschriebene Deletion p.2385_2395del im Exon 34 führt zu einem vorzeitigen Abbruch des ATRX-Proteins und ist somit als sicher pathogen einzustufen. Die Untersuchung der Mutter des Patienten konnte den Konduktorenstatus nachweisen. Für die Familie des betroffenen Patienten konnte mit der vorliegenden Arbeit die Diagnose des ATRX-Syndroms gesichert werden. Die DNA-Proben der Patienten bei denen keine Mutation nachgewiesen werden konnte, sollten bei weiterhin dringendem Verdacht auf das ATRX-Syndrom mittels qRT-PCR bzw. MLPA untersucht werden, um große Deletionen, Insertionen oder Duplikationen auszuschließen. Mithilfe dieser Arbeit gelang die Etablierung der DHPLC für das ATRX-Gen als ökonomische, sehr sensitive und effiziente Methode zur Diagnostik des ATRX-Syndroms. Die Entscheidung, in welcher Form und mit welcher Methode DNA-Proben bei Verdacht auf ATRX-Syndrom untersucht werden, bleibt jedoch eine individuelle Entscheidung jedes Instituts unter Betrachtung der jeweiligen Gegebenheiten vor Ort.
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Hung, Chia-Cheng, and 洪加政. "Rapid Genetic Screening of β-Thalassemia：Coupling Heteroduplex and Primer Extension Analysis by Denaturing High Performance Liquid Chromatography." Thesis, 2003. http://ndltd.ncl.edu.tw/handle/10258414248784031375.

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碩士
國立臺灣大學
醫學工程學研究所
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Beta-thalassemia is a common autosomal recessive hereditary disease in the Meditertanean, Asia and Africa area. It is a single gene inheritable disease resulting from single or few nucleotides mutations on the beta-globin gene. The purpose of this study is to develop a rapid, reliable and economic molecular diagnosis method for common mutational screening in beta-thalassemia. We did develop a rapid and highly specific mutation screening test for the diagnosis of beta-thalassemia by coupling heteroduplex and primer extension analysis based on the Denaturing High Performance Liquid Chromatography (DHPLC) system. The sensitivity and specificity of this method were evaluated in 161 Taiwan healthy heterozygous carriers with 10 different beta-globin mutations and 30 patients with 12 different compound heterozygous or homozygous beta-thalassemia mutations. By using heteroduplex analysis, all the sequence variants could be identified precisely. The sensitivity and the specificity reached up to 99%. Furthermore, we developed primer extension analysis coupled with DHPLC as a powerful tool for genotyping eight common mutations in the beta-globin gene. Compared to classic approaches of mutation screening, this method allows a rapid, highly sensitive, highly specific, cost effective and semi-automated mutational screening of a large number of samples. Therefore, mutational analysis of coupling heteroduplex analysis and primer extension by DHPLC is capable to be the first-line clinical screening and diagnosis tool for beta-thalassemia patients.
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徐光正. "Coupling CEL Nuclease Mutation Detection System and Denaturing High Performance Liquid Chromatography for Rapid Identification of the β-thalassemia Mutations." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/88285926503296349639.

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Book chapters on the topic "Denaturing high performance liquid chromatography (DHPLC)"

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Leung, Kim Hung, and Shea Ping Yip. "Denaturing High-Performance Liquid Chromatography (DHPLC) for Nucleic Acid Analysis." In Springer Protocols Handbooks, 89–106. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-375-6_7.

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Oldenburg, J., O. El-Maarri, V. Ivaskevicius, S. Rost, B. H. F. Weber, and R. Schwaab. "Evaluation of Denaturing High Performance Liquid Chromatography (DHPLC) in the Analysis of Hemophilia A." In 31st Hemophilia Symposium Hamburg 2000, 130–40. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-59383-3_15.

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Marsh, Deborah J., and Viive M. Howell. "The Use of Denaturing High Performance Liquid Chromatography (DHPLC) for Mutation Scanning of Hereditary Cancer Genes." In Methods in Molecular Biology, 133–45. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-759-4_8.

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Fackenthal, Donna Lee, Pei Xian Chen, Ted Howe, and Soma Das. "Denaturing High-Performance Liquid Chromatography for Mutation Detection and Genotyping." In Methods in Molecular Biology, 25–54. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-435-7_2.

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Rugg, Elizabeth L., and Gareth J. Magee. "Use of Denaturing High-Performance Liquid Chromatography in Molecular Medicine." In Medical Biomethods Handbook, 315–25. Totowa, NJ: Humana Press, 2005. http://dx.doi.org/10.1385/1-59259-870-6:315.

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Menegatti, E., M. Ferrone, S. Gallone, M. Mameli, E. Grosso, and N. Migone. "Molecular Genetic Analysis of von Hippel-Lindau Disease by Denaturing High-Performance Liquid Chromatography." In Contributions to Nephrology, 306–11. Basel: KARGER, 2001. http://dx.doi.org/10.1159/000060206.

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