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Tan D, Han J, Sun Q, Cheng X, Liu J, Liu J, Li Q, Dai L. Application of Multiplex Fluorescence Polymerase Chain Reaction for Detecting Pathogenic Bacteria in Sputum Samples from Patients with Lower Respiratory Tract Infection. Infect Drug Resist 2023; 16:6999-7005. [PMID: 37933294 PMCID: PMC10625741 DOI: 10.2147/idr.s431425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Objective In this study, we conducted a multi-center research on six common lower respiratory tract pathogens using novel multiplex fluorescence quantitative polymerase chain reaction (PCR), and investigated the additional diagnostic value of this method, to provide a molecular diagnostic basis for clinical practice. Methods From March 2019 to October 2021, a total of 2047 respiratory sputum samples were collected from Hunan Provincial People's Hospital (the First Affiliated Hospital of Hunan Normal University), Hunan Provincial Children's Hospital, Jiangxi Provincial Children's Hospital, and Wuhan Infectious Disease Hospital. The samples were analyzed using a novel multiplex fluorescence quantitative PCR method for Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, Legionella pneumophila, and Staphylococcus aureus. The results were compared to the results of bacterial culture and sequencing, as well as the results of third-party kits. Results Compared to the bacterial culture method, 2047 samples were detected with a sensitivity of 100%, a specificity of 72.22%, and an overall compliance rate of 81.91%. Compared to the sequencing method, the positive agreement percentage was 99.88%, the negative agreement percentage was 97.72%, and the overall agreement rate was 98.84%. Compared to similar control reagents, the positive agreement percentage was 100%, negative agreement percentage was 79.79%, and overall compliance rate was 96.19%. Conclusion The multiplex fluorescence PCR method has the advantages of simultaneously detecting multiple pathogenic bacteria and reducing the duration of pathogen culture identification. Combined detection can increase the detection rate, which has favorable performance and application prospects.
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Affiliation(s)
- Deyong Tan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008People’s Republic of China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078People’s Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, 410078People’s Republic of China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, 410008People’s Republic of China
| | - Jianfeng Han
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Qingzhi Sun
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Xing Cheng
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Juan Liu
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Jia Liu
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
| | - Qing Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008People’s Republic of China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078People’s Republic of China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, 410078People’s Republic of China
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, 410008People’s Republic of China
| | - Lizhong Dai
- Sansure Biotech Inc, Changsha, Hunan Province, People’s Republic of China
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Kafi H, Emaneini M, Halimi S, Rahdar HA, Jabalameli F, Beigverdi R. Multiplex high-resolution melting assay for simultaneous detection of five key bacterial pathogens in urinary tract infections: A pilot study. Front Microbiol 2022; 13:1049178. [PMID: 36590389 PMCID: PMC9797728 DOI: 10.3389/fmicb.2022.1049178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
The diagnosis of urinary tract infections (UTIs) is usually based on the results of urine culture, but it is time-consuming, labor-intensive and has a low sensitivity. The aim of this study was to develop multiplex high-resolution melting assay (MHRM) for the simultaneous detection of five common bacterial pathogens (Escherichia coli, Klebsiella pneumoniae, Staphylococcus saprophyticus, Enterococcus faecalis, and group B streptococci (GBS)) directly from urine samples. A total of 287 urine specimens were evaluated by HRM assay and the results were compared with the conventional culture method. Five different melt curves generated and differentiated five bacterial pathogens. The detection limit of the MHRM assay was 1.5 × 103 CFU/ml for E. coli and K. pneumoniae and 1.5 × 102 CFU/ml for S. saprophyticus, E. faecalis and GBS. Compared to culture, the specificity of the MHRM assay ranged from 99.3 to 100%, and sensitivity 100% for all test pathogens. The MHRM assay developed in the current study might be functional tool for the diagnosis of UTIs and has the potential for direct detection of the organism in the clinical samples. Additionally, it creates results in less than 5 h, helping clinicians to start treatment with appropriate antimicrobial agents. This method could be a useful supplement to urine culture.
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Affiliation(s)
- Hossein Kafi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahnaz Halimi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Ali Rahdar
- Department of Microbiology, School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran,*Correspondence: Reza Beigverdi,
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Vardevanyan PO, Parsadanyan MA, Antonyan AP, Shahinyan MA. Study of complexes of Hoechst 33258 with poly(rA)-poly(rU) depending on various ionic strengths in the water-saline solution. J Biomol Struct Dyn 2022; 40:1182-1188. [PMID: 32954957 DOI: 10.1080/07391102.2020.1823883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Comparative study of the complexes of groove-binding ligand Hoechst 33258 (H33258) with synthetic homopolynucleotides poly(rA)-poly(rU) and poly(dA)-poly(dT) has been carried out at various concentration ratios of r = ligand/nucleic acids (NA) and different ionic strengths of the water-saline solution 0.02, 0.04 and 0.1 M, using the method of UV-melting. It was revealed that the melting curves of the complexes of poly(dA)-poly(dT) with H33258 at the low concentrations of ligand are biphasic, which actually does not depend on the solution ionic strength. In the case of the complexes of poly(rA)-poly(rU)-H33258, the melting curves become quasi-biphasic only at the ionic strength 0.02 M and relatively high concentrations of the ligand. Differential melting curves (DMC) of the mentioned polynucleotides and their complexes with H33258 were obtained as well. DMC of poly(rA)-poly(rU) were found to be significantly wide at the ionic strengths of the solution 0.02 and 0.04 M and to show an intrinsic heterogeneity of double-stranded structure of this polynucleotide.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Poghos O Vardevanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Marine A Parsadanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Ara P Antonyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Mariam A Shahinyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
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Niba ETE, Wijaya YOS, Awano H, Taniguchi N, Takeshima Y, Nishio H, Shinohara M. DBS Screening for Glycogen Storage Disease Type 1a: Detection of c.648G>T Mutation in G6PC by Combination of Modified Competitive Oligonucleotide Priming-PCR and Melting Curve Analysis. Int J Neonatal Screen 2021; 7. [PMID: 34842616 DOI: 10.3390/ijns7040079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/26/2022] Open
Abstract
Glycogen storage disease type Ia (GSDIa) is an autosomal recessive disorder caused by glucose-6-phosphatase (G6PC) deficiency. GSDIa causes not only life-threatening hypoglycemia in infancy, but also hepatocellular adenoma as a long-term complication. Hepatocellular adenoma may undergo malignant transformation to hepatocellular carcinoma. New treatment approaches are keenly anticipated for the prevention of hepatic tumors. Gene replacement therapy (GRT) is a promising approach, although early treatment in infancy is essential for its safety and efficiency. Thus, GRT requires screening systems for early disease detection. In this study, we developed a screening system for GSDIa using dried blood spots (DBS) on filter paper, which can detect the most common causative mutation in the East-Asian population, c.648G>T in the G6PC gene. Our system consisted of nested PCR analysis with modified competitive oligonucleotide priming (mCOP)-PCR in the second round and melting curve analysis of the amplified products. Here, we tested 54 DBS samples from 50 c.648G (wild type) controls and four c.648T (mutant) patients. This system, using DBS samples, specifically amplified and clearly detected wild-type and mutant alleles from controls and patients, respectively. In conclusion, our system will be applicable to newborn screening for GSDIa in the real world.
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Ezenwa IC, Yoshino T. Electrical Resistivity of Cu and Au at High Pressure above 5 GPa: Implications for the Constant Electrical Resistivity Theory along the Melting Curve of the Simple Metals. Materials (Basel) 2021; 14:5476. [PMID: 34639875 DOI: 10.3390/ma14195476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/18/2021] [Indexed: 11/17/2022]
Abstract
The electrical resistivity of solid and liquid Cu and Au were measured at high pressures from 6 up to 12 GPa and temperatures ∼150 K above melting. The resistivity of the metals was also measured as a function of pressure at room temperature. Their resistivity decreased and increased with increasing pressure and temperature, respectively. With increasing pressure at room temperature, we observed a sharp reduction in the magnitude of resistivity at ∼4 GPa in both metals. In comparison with 1 atm data and relatively lower pressure data from previous studies, our measured temperature-dependent resistivity in the solid and liquid states show a similar trend. The observed melting temperatures at various fixed pressure are in reasonable agreement with previous experimental and theoretical studies. Along the melting curve, the present study found the resistivity to be constant within the range of our investigated pressure (6–12 GPa) in agreement with the theoretical prediction. Our results indicate that the invariant resistivity theory could apply to the simple metals but at higher pressure above 5 GPa. These results were discussed in terms of the saturation of the dominant nuclear screening effect caused by the increasing difference in energy level between the Fermi level and the d-band with increasing pressure.
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Wang D, Wang Y, Zhang M, Zhang Y, Sun J, Song C, Xiao F, Ping Y, Pan C, Hu Y, Wang C, Liu Y. Ladder-shape melting temperature isothermal amplification of nucleic acids. Biotechniques 2021; 71:358-69. [PMID: 34164991 DOI: 10.2144/btn-2020-0173] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A novel method, termed ladder-shape melting temperature isothermal amplification (LMTIA), was developed in this study. As a proof of concept, one pair of primers or two pairs of nested primers and a thermostable DNA polymerase were employed to amplify the internal transcribed spacer of Oryza sativa with the ladder-shape melting temperature curve. Our results demonstrated that the LMTIA assay with nested primers was 50-fold more sensitive than the LAMP assay with the same level of specificity. The LMTIA method has the potential to be used for the prevention and control of emerging epidemics caused by different types of pathogens.
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Zhong Z, Wang J, Zhang S. [Advances in multiple PCR technology studies]. Sheng Wu Gong Cheng Xue Bao 2020; 36:171-179. [PMID: 32147990 DOI: 10.13345/j.cjb.190206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Multiple PCR (Multiplex polymerase chain reaction, MPCR) is a technology to simultaneously amplify multiple targets through a single reaction and to detect the amplification products by reliable detection means so as to realize the diagnosis of multiple targets. MPCR has been well studied for its high efficiency, high throughput and low cost. At present, MPCR has been widely used in scientific research, disease diagnosis and other fields. Here, we summarize the development and application of MPCR from amplification and detection, and discuss the advantages and existing problems of MPCR. We propose that separate the reaction mixture into droplets or combined MPCR with the capillary convective PCR is expect to further improve the amplification efficiency of the surface of the solid phase carrier, so as to provide reference for the development of multiple PCR with high amplification efficiency, good consistency, good stability and multiplex detection.
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Affiliation(s)
- Zecheng Zhong
- School of Public Health, Xiamen University, Xiamen 361100, Fujian, China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361100, Fujian, China
| | - Jin Wang
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361100, Fujian, China
| | - Shiyin Zhang
- School of Public Health, Xiamen University, Xiamen 361100, Fujian, China.,National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361100, Fujian, China
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Torres-Corral Y, Fernández-Álvarez C, Santos Y. High-throughput identification and quantification of Vagococcus salmoninarum by SYBR Green I-based real-time PCR combined with melting curve analysis. J Fish Dis 2019; 42:1359-1368. [PMID: 31359457 DOI: 10.1111/jfd.13053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
This work describes a primer pair and a high-throughput SYBR Green I-based real-time PCR protocol combined with melting curve analysis for identification and quantification of Vagococcus salmoninarum in bacterial cultures and infected fish tissues. The 16S rRNA gene was selected for the design of the primer pair (SalF and SalR). The sensitivity and specificity of this primer pair were compared with other previously designed for conventional PCR. Although both primer pairs showed 100% specificity using pure bacterial cultures or DNA extracted from bacteria or fish tissues, the primer pairs designed in this study showed the highest sensitivity with a detection limit of 0.034 × 100 amplicon copies per assay (equivalent to 2 × 10-11 ng/µl, Cq value of 30.49 ± 1.71). The developed qPCR protocol allowed the detection of V. salmoninarum in non-lethal and lethal fish samples with detection levels of 0.17 × 100 gene copies in tissues artificially infected and 0.02 × 100 in tissues of fish experimentally infected with V. salmoninarum. The high sensitivity of the developed method suggests that it could be considered as a useful tool for diagnosis of vagococcosis and the detection of V. salmoninarum in asymptomatic or carrier fish.
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Affiliation(s)
- Yolanda Torres-Corral
- Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Clara Fernández-Álvarez
- Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ysabel Santos
- Departamento de Microbiología y Parasitología, Instituto de Investigación y Análisis Alimentario, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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Motta FC, Born PS, Resende PC, Brown D, Siqueira MM. An Inexpensive and Accurate Reverse Transcription-PCR-Melting Temperature Analysis Assay for Real-Time Influenza Virus B Lineage Discrimination. J Clin Microbiol 2019; 57:e00602-19. [PMID: 31554673 DOI: 10.1128/JCM.00602-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/09/2019] [Indexed: 11/20/2022] Open
Abstract
In this work, we describe a SYBR-Green one-step reverse transcription-PCR protocol coupled with a melting temperature analysis (RT-PCR-Tm ), which allows the discrimination of influenza B lineages Yamagata and Victoria. The assay is performed using a regular real-time thermocycler and is based on differences in melting temperature (Tm ) of a 131-bp amplicon, obtained from a conserved region of hemagglutinin gene. A total of 410 samples collected during the 2004, 2008, and 2010-2017 influenza seasons in Brazil were tested, and the lineages were correctly characterized using their melting profiles. The temperature range is significantly different between both lineages throughout the time (Mann-Whitney test; P < 0.0001, confidence interval = 95%), and the Tm is not affected by viral load (Spearman correlation test; r = 0.287, P = 2.245 × 10-9). The simplicity and cost-effectiveness of this protocol make it an option for influenza B lineage surveillance worldwide.
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Strunk A, Abbes A, Stuitje AR, Hettinga C, Sepers EM, Snetselaar R, Schouten J, Asselman FL, Cuppen I, Lemmink H, van der Pol WL, Engel H. Validation of a Fast, Robust, Inexpensive, Two-Tiered Neonatal Screening Test algorithm on Dried Blood Spots for Spinal Muscular Atrophy. Int J Neonatal Screen 2019; 5:21. [PMID: 33072980 PMCID: PMC7510214 DOI: 10.3390/ijns5020021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant mortality with an incidence of 1:10,000. The recently-introduced antisense oligonucleotide treatment improves the outcome of this disease, in particular when applied at an early stage of progression. The genetic cause of SMA is, in >95% of cases, a homozygous deletion of the survival motor neuron 1 (SMN1) gene, which makes the low-cost detection of SMA cases as part of newborn screening programs feasible. We developed and validated a new SALSA MC002 melting curve assay that detects the absence of the SMN1 exon 7 DNA sequence without detecting asymptomatic carriers and reliably discriminates SMN1 from its genetic homolog SMN2 using crude extracts from newborn screening cards. Melting curve analysis shows peaks specific for both the SMN1 gene and the disease modifying SMN2 homolog. The detection of the SMN2 homolog, of which the only clinically relevant difference from the SMN1 gene is a single nucleotide in exon 7, was only used to confirm a correct reaction in samples that lacked the SMN1 gene, and not for SMN2 quantification. We retrieved 47 DBS samples from children with genetically-confirmed SMA, after informed consent from parents, and 375 controls from the national archive of the Dutch National Institute for Public Health and the Environment (RIVM). The assay correctly identified all anonymized and randomized SMA and control samples (i.e., sensitivity and specificity of 100%), without the detection of carriers, on the three most commonly-used PCR platforms with melting curve analysis. This test's concordance with the second-tier 'golden standard' P021 SMA MLPA test was 100%. Using the new P021-B1 version, crude extracts from DBS cards could also be used to determine the SMN2 copy number of SMA patients with a high level of accuracy. The MC002 test showed the feasibility and accuracy of SMA screening in a neonatal screening program.
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Affiliation(s)
- Annuska Strunk
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Andre Abbes
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Antoine R. Stuitje
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Chris Hettinga
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Eline M. Sepers
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Reinier Snetselaar
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Jan Schouten
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Fay-Lynn Asselman
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Inge Cuppen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - W. Ludo van der Pol
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Henk Engel
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
- Correspondence: ; Tel.: +31-38-424-7190
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Liu Z, Bingga G, Zhang C, Shao J, Shen H, Sun J, Zhang J. Application of Duplex Fluorescence Melting Curve Analysis (FMCA) to Identify Canine Parvovirus Type 2 Variants. Front Microbiol 2019; 10:419. [PMID: 30891024 PMCID: PMC6411689 DOI: 10.3389/fmicb.2019.00419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/18/2019] [Indexed: 11/15/2022] Open
Abstract
Canine parvovirus (CPV-2) is an enteric virus causing morbidity and mortality in dogs worldwide. Since CPV-2 emerged as canine pathogen, the original CPV-2 strain has constantly evolved, and its primary variants (CPV-2a, CPV-2b, and CPV-2c) co-circulate to varying extents in canine populations worldwide. Thus, rapid and accurate laboratory diagnoses of CPV-2 variants are crucial to monitor CPV-2 evolution. Conventional methods for CPV-2 genotyping are laborious, time consuming, and determining the genotype of a CPV-2 variant often requires two or more reaction tubes. The present study developed a probe-based fluorescence melting curve analysis (FMCA) for genotyping six different CPV-2 variants (original CPV-2, CPV-2a, CPV-2b, CPV-2c, and vaccine strains of CPVpf and CPVint) in a single reaction tube using only two TaqMan probes. One of the TaqMan probes (FAM labeled) was designed to perfectly match with the target sequence of CPV-2a, this probe allows a 1-bp mismatched hybridization with the CPV-2b VP2 gene region (A4062G), and a 2-bp mismatched hybridization for CPV-2c (A4062G and T4064A); Another TaqMan probe (HEX labeled) was produced to perfectly match with the target sequence of original CPV-2, this probe enables 1-bp mismatched hybridization with the other CPV-2 variants (A3045T). Using the two TaqMan probes, all six CPV-2 variants were readily distinguished by their respective melting temperature values in a single reaction tube. The detection limits of this assay were 1–10 copies per reaction for six CPV-2 construction plasmids and no cross reactions were observed with several other common canine viruses. In this assay, co-infected samples were also directly identified via probe-based FMCA without using a mixing control; only a pure control is required. The clinical evaluation of this assay was demonstrated by analyzing 83 clinical fecal samples, among which 41 (49.39%), 8 (9.63%), and 14 (16.87%) samples were found to be positive for CPV-2a, CPV-2b, and CPV-2c, respectively. The concordance rate between probe-based FMCA and Sanger sequencing was 100%. Thus, the duplex FMCA is effective, rapid, simple, high-throughput, and straightforward for genotyping CPV-2 variants, and is useful to effectively diagnose and monitor CPV-2 epidemiology.
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Affiliation(s)
- Zhicheng Liu
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gali Bingga
- Vocational and Technical College of Inner Mongolia Agricultural University, Baotou, China
| | - Chunhong Zhang
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junjie Shao
- Changzhou Wumu Animal Hospital, Changzhou, China
| | - Haiyan Shen
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Junying Sun
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jianfeng Zhang
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Khosravi AD, Hashemzadeh M, Hashemi Shahraki A, Teimoori A. Differential Identification of Mycobacterial Species Using High-Resolution Melting Analysis. Front Microbiol 2017; 8:2045. [PMID: 29109708 PMCID: PMC5660063 DOI: 10.3389/fmicb.2017.02045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/06/2017] [Indexed: 01/20/2023] Open
Abstract
Infections caused by non-tuberculous mycobacteria (NTM) is increasing wordwide. Due to the difference in treatment of NTM infections and tuberculosis, rapid species identification of mycobacterial clinical isolates is necessary for the effective management of mycobacterial diseases treatment and their control strategy. In this study, a cost-effective technique, real-time PCR coupled with high-resolution melting (HRM) analysis, was developed for the differentiation of Mycobacterial species using a novel rpoBC sequence. A total of 107 mycobacterial isolates (nine references and 98 clinical isolates) were subjected to differentiation using rpoBC locus sequence in a real-time PCR-HRM assay scheme. From 98 Mycobacterium clinical isolates, 88 species (89.7%), were identified at the species level by rpoBC locus sequence analysis as a gold standard method. M. simiae was the most frequently encountered species (41 isolates), followed by M. fortuitum (20 isolates), M. tuberculosis (15 isolates), M. kansassi (10 isolates), M. abscessus group (5 isolates), M. avium (5 isolates), and M. chelonae and M. intracellulare one isolate each. The HRM analysis generated six unique specific groups representing M. tuberculosis complex, M. kansasii, M. simiae, M. fortuitum, M. abscessus–M. chelonae group, and M. avium complex. In conclusion, this study showed that the rpoBC-based real-time PCR followed by HRM analysis could differentiate the majority of mycobacterial species that are commonly encountered in clinical specimens.
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Affiliation(s)
- Azar D Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Rizzi G, Lee JR, Dahl C, Guldberg P, Dufva M, Wang SX, Hansen MF. Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array. ACS Nano 2017; 11:8864-8870. [PMID: 28832112 PMCID: PMC5810360 DOI: 10.1021/acsnano.7b03053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.
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Affiliation(s)
- Giovanni Rizzi
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
| | - Jung-Rok Lee
- Division of Mechanical and Biomedical Engineering, ELTEC College of Engineering, Ewha Womans University, Seoul 03760, South Korea
- Department of Materials Science and Engineering, Stanford University, Stanford, California 93405, United States
| | - Christina Dahl
- Danish Cancer Society Research Center, Copenhagen, DK 2100, Denmark
| | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, DK 2100, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, Stanford, California 93405, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 93405, United States
- Corresponding Authors:.
| | - Mikkel F. Hansen
- Department of Micro- and Nanotechnology DTU Nanotech, Technical University of Denmark, Building 345B, Kongens Lyngby, DK 2800, Denmark
- Corresponding Authors:.
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Dos Santos Rocha A, de Amorim ISS, Simão TDA, da Fonseca ADS, Garrido RG, Mencalha AL. High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science. J Forensic Sci 2017; 63:536-540. [PMID: 28834547 DOI: 10.1111/1556-4029.13552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Abstract
Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics.
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Affiliation(s)
- Alípio Dos Santos Rocha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil.,Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Isis Salviano Soares de Amorim
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Tatiana de Almeida Simão
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Adenilson de Souza da Fonseca
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Rodrigo Grazinoli Garrido
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
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15
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Rubio MDS, Penha Filho RAC, Almeida AMD, Berchieri A. Development of a multiplex qPCR in real time for quantification and differential diagnosis of Salmonella Gallinarum and Salmonella Pullorum. Avian Pathol 2017; 46:644-651. [PMID: 28589774 DOI: 10.1080/03079457.2017.1339866] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently there are 2659 Salmonella serovars. The host-specific biovars Salmonella Pullorum and Salmonella Gallinarum cause systemic infections in food-producing and wild birds. Fast diagnosis is crucial to control the dissemination in avian environments. The present work describes the development of a multiplex qPCR in real time using a low-cost DNA dye (SYBr Green) to identify and quantify these biovars. Primers were chosen based on genomic regions of difference (RoD) and optimized to control dimers. Primers pSGP detect both host-specific biovars but not other serovars and pSG and pSP differentiate biovars. Three amplicons showed different melting temperatures (Tm), allowing differentiation. The pSGP amplicon (97 bp) showed Tm of 78°C for both biovars. The pSG amplicon (273 bp) showed a Tm of 86.2°C for S. Gallinarum and pSP amplicon (260 bp) dissociated at 84.8°C for S. Pullorum identification. The multiplex qPCR in real time showed high sensitivity and was capable of quantifying 108-101 CFU of these biovars.
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Affiliation(s)
- Marcela da Silva Rubio
- a School of Agricultural and Veterinary Sciences , São Paulo State University (FCAV/UNESP) , São Paulo , Brazil
| | | | - Adriana Maria de Almeida
- a School of Agricultural and Veterinary Sciences , São Paulo State University (FCAV/UNESP) , São Paulo , Brazil
| | - Angelo Berchieri
- a School of Agricultural and Veterinary Sciences , São Paulo State University (FCAV/UNESP) , São Paulo , Brazil
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16
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Wan Z, Zhang Y, He Z, Liu J, Lan K, Hu Y, Zhang C. A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses. Int J Mol Sci 2016; 17:E1880. [PMID: 27886052 DOI: 10.3390/ijms17111880] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023] Open
Abstract
Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 102 copies for HCoV-OC43, and 3 × 101 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples.
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17
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Erdem M, Kesmen Z, Özbekar E, Çetin B, Yetim H. Application of high-resolution melting analysis for differentiation of spoilage yeasts. J Microbiol 2016; 54:618-25. [PMID: 27572511 DOI: 10.1007/s12275-016-6017-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 06/24/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
Abstract
A new method based on high resolution melting (HRM) analysis was developed for the differentiation and classification of the yeast species that cause food spoilage. A total 134 strains belonging to 21 different yeast species were examined to evaluate the discriminative power of HRM analysis. Two different highly variable DNA regions on the 26 rRNA gene were targeted to produce the HRM profiles of each strain. HRM-based grouping was compared and confirmed by (GTG)5 rep-PCR fingerprinting analysis. All of the yeast species belonging to the genera Pichia, Candida, Kazachstania, Kluyveromyces, Debaryomyces, Dekkera, Saccharomyces, Torulaspora, Ustilago, and Yarrowia, which were produced as species-specific HRM profiles, allowed discrimination at species and/or strain level. The HRM analysis of both target regions provided successful discrimination that correlated with rep-PCR fingerprinting analysis. Consequently, the HRM analysis has the potential for use in the rapid and accurate classification and typing of yeast species isolated from different foods to determine their sources and routes as well as to prevent contamination.
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18
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Chatzidimopoulos M, Ganopoulos I, Vellios E, Madesis P, Tsaftaris A, Pappas AC. Development of a two-step high-resolution melting (HRM) analysis for screening sequence variants associated with resistance to the QoIs, benzimidazoles and dicarboximides in airborne inoculum of Botrytis cinerea. FEMS Microbiol Lett 2014; 360:126-31. [PMID: 25196894 DOI: 10.1111/1574-6968.12594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/25/2014] [Accepted: 09/01/2014] [Indexed: 11/30/2022] Open
Abstract
A rapid, high-resolution melting (HRM) analysis protocol was developed to detect sequence variations associated with resistance to the QoIs, benzimidazoles and dicarboximides in Botrytis cinerea airborne inoculum. HRM analysis was applied directly in fungal DNA collected from air samplers with selective medium. Three and five different genotypes were detected and classified according to their melting profiles in BenA and bos1 genes associated with resistance to benzimidazoles and dicarboximides, respectively. The sensitivity of the methodology was evident in the case of the QoIs, where genotypes varying either by a single nucleotide polymorphism or an additional 1205-bp intron were separated accurately with a single pair of primers. The developed two-step protocol was completed in 82 min and showed reduced variation in the melting curves' formation. HRM analysis rapidly detected the major mutations found in greenhouse strains providing accurate data for successfully controlling grey mould.
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Affiliation(s)
- Michael Chatzidimopoulos
- Department of Agriculture, Crop Production and Rural Environment, Laboratory of Plant Pathology, University of Thessaly, Volos, Greece
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Lu Q, Huang X, Chen H, Zhao X. A novel melting curve-based method for detecting c-kit mutations in acute myeloid leukemia. Oncol Lett 2014; 8:99-104. [PMID: 24959227 PMCID: PMC4063585 DOI: 10.3892/ol.2014.2128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 04/03/2014] [Indexed: 01/30/2023] Open
Abstract
The c-kit gene encodes a class III tyrosine kinase receptor. Specific somatic mutations in c-kit have been associated with acute myeloid leukemia (AML) and are markers of a poor prognosis in AML. Various methods have been used to detect the c-kit gene mutation; however, the suitability of these methods in the clinical management of AML remains unclear. The current study developed a novel method, using modified hybridization probes and melting curve analysis, for detecting c-kit mutations in exon 17. Dual-labeled self-quenched oligonucleotide probes containing two segments, labeled with carboxyrhodamine or hexachlorofluorescein, were designed to detect sequences around the D816 or N820/N822 mutation hot spots in exon 17 of c-kit. The exon 17 region of c-kit was amplified by polymerase chain reaction using control plasmids carrying wild-type or mutant sequences, or genomic DNA derived from AML patients. Melting curve analysis of the amplification products was performed using a self-quenched probe. The results showed that the detection sensitivity, assayed using mutation-positive control plasmids, was 10% for the N820G mutation and 5% for the six other mutations; N822K(A), N822K(G), D816V, D816Y, D816H and D816F. In addition, c-kit mutations were identified in six of the 12 samples from the core-binding factor (CBF)-AML patients. This demonstrates that the novel method developed in the present study, is simple, rapid, specific and highly sensitive, and may facilitate the diagnosis and treatment of CBF-AML.
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Affiliation(s)
- Quanyi Lu
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Xiao Huang
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Huaying Chen
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Xiaomin Zhao
- Department of Hematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
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Furugaki K, Yasuno H, Iwai T, Moriya Y, Harada N, Fujimoto-Ouchi K. Melting curve analysis for mutations of EGFR and KRAS. Anticancer Res 2014; 34:613-621. [PMID: 24510990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Epidermal growth factor receptor (EGFR) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations are common in non-small cell lung cancer (NSCLC) and colorectal cancer (CRC). The aim of the present study was to develop a simple and versatile tool to determine EGFR and KRAS mutations for pre-clinical research in the laboratory. We developed a melting curve analysis to detect exon 19 deletion, L858R mutation, and T790M mutation of EGFR, and codon 12/13 and codon 61 mutations of KRAS using LightCycler480 with mutation-specific sensor and anchor probes. The analytical method was applicable to determine the approximate rate of heterogeneity of mutation in the genomic DNA of cancer cell lines. In conclusion, our melting curve analysis is a rapid and semi-quantitative method to screen for exon 19 deletion, L858R or T790M mutations of EGFR and codon 12/13/61 mutations of KRAS in cancer cell lines.
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Affiliation(s)
- Koh Furugaki
- Product Research Department, Kamakura Research Laboratories, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa Japan.
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21
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Polak E, Ficek A, Radvanszky J, Soltysova A, Urge O, Cmelova E, Kantarska D, Kadasi L. Phenylalanine hydroxylase deficiency in the Slovak population: genotype-phenotype correlations and genotype-based predictions of BH4-responsiveness. Gene 2013; 526:347-55. [PMID: 23764561 DOI: 10.1016/j.gene.2013.05.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
We investigated the mutation spectrum of the phenylalanine hydroxylase gene (PAH) in a cohort of patients from 135 Slovak PKU families. Mutational screening of the known coding region, including conventional intron splice sites, was performed using high-resolution melting analysis, with subsequent sequencing analysis of the samples showing deviated melting profiles compared to control samples. The PAH gene was also screened for deletions and duplications using MLPA analysis. Forty-eight different disease causing mutations were identified in our patient group, including 30 missense, 8 splicing, 7 nonsense, 2 large deletions and 1 small deletion with frameshift; giving a detection rate of 97.6%. The most prevalent mutation was the p.R408W, occurring in 47% of all alleles, which concurs with results from neighboring and other Slavic countries. Other frequent mutations were: p.R158Q (5.3%), IVS12+1G>A (5.3%), p.R252W (5.1%), p.R261Q (3.9%) and p.A403V (3.6%). We also identified three novel missense mutations: p.F233I, p.R270I, p.F331S and one novel variant: c.-30A>T in the proximal part of the PAH gene promoter. A spectrum of 84 different genotypes was observed and a genotype based predictions of BH4-responsiveness were assessed. Among all genotypes, 36 were predicted to be BH4-responsive represented by 51 PKU families. In addition, genotype-phenotype correlations were performed.
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Affiliation(s)
- Emil Polak
- Comenius University, Faculty of Natural Sciences, Department of Molecular Biology, Mlynska Dolina, 842 15 Bratislava, Slovak Republic.
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Weber LA. P-V-T, Thermodynamic and Related Properties of Oxygen from the Triple Point to 300 K at Pressures to 33 MN/m 2. J Res Natl Bur Stand A Phys Chem 1970; 74A:93-129. [PMID: 32523174 PMCID: PMC6753035 DOI: 10.6028/jres.074a.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The results of new experimental pressure-volume-temperature measurements on oxygen are presented. The data range in temperature from 54 to 300 K and in pressure from 0.1 to about 33 MN/m2. The following properties are tabulated for selected isobars: molar volume, (∂P/∂ρ) T , (∂P/∂T)ρ, internal energy, enthalpy, entropy, specific heats at constant volume and at constant pressure, and the velocity of sound. Additional tables present the above properties for saturated liquid and vapor, the freezing liquid P-V-T relationship, and the derived Joule-Thomson inversion curve. New values for the critical density and triple point density are presented, and the second and third virial coefficients are tabulated.
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Affiliation(s)
- L A Weber
- Institute for Basic Standards, National Bureau of Standards, Boulder, Colorado 80302
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