1
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Jun CS, Lee W. Development of Lasing Silica Microsphere for High-Speed DNA Molecular Detection. SENSORS (BASEL, SWITZERLAND) 2024; 24:6088. [PMID: 39338832 PMCID: PMC11435820 DOI: 10.3390/s24186088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 09/06/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024]
Abstract
Laser and molecular detection techniques that have been used to overcome the limitations of fluorescent DNA labeling have presented new challenges. To address some of these challenges, we developed a DNA laser that uses a solid-state silica microsphere as a ring resonator and a site for DNA-binding reactions, as well as a platform to detect and sequence target DNA molecules. We detected target DNA using laser emission from a DNA-labeling dye and a developed solid-state silica microsphere ring resonator. The microsphere was sensitive; a single base mismatch in the DNA resulted in the absence of an optical signal. As each individual microsphere can be utilized as a parallel DNA analysis chamber, this optical digital detection scheme allows for high-throughput and rapid analysis. More importantly, the solid-state DNA laser is free from deformation, which guarantees stable lasing characteristics, and can be manipulated freely outside the solution. Thus, this promising advanced DNA laser scheme can be implemented on platforms other than optofluidic chips.
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Affiliation(s)
- Chan Seok Jun
- Department of Material Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonsuk Lee
- Nanophotonics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
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2
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Wittwer CT, Hemmert AC, Kent JO, Rejali NA. DNA melting analysis. Mol Aspects Med 2024; 97:101268. [PMID: 38489863 DOI: 10.1016/j.mam.2024.101268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.
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Affiliation(s)
- Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | | | - Jana O Kent
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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3
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Hong R, Yan Y, Zhu C, Zuo F, Zhang GW. Rapid genotyping of bovine MC1R gene c.296T>C and c.310delG haplotypes using high-resolution melting analysis. Anim Genet 2024; 55:173-174. [PMID: 37873887 DOI: 10.1111/age.13373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Affiliation(s)
- Rui Hong
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yi Yan
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Changhong Zhu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Chongqing, China
| | - Gong-Wei Zhang
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Chongqing, China
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4
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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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5
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Santhanam P, Labbé C, Tremblay V, Bélanger RR. A rapid molecular diagnostic tool to discriminate alleles of avirulence genes and haplotypes of Phytophthora sojae using high-resolution melting analysis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13406. [PMID: 38009407 PMCID: PMC10799203 DOI: 10.1111/mpp.13406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Abstract
Effectors encoded by avirulence genes (Avr) interact with the Phytophthora sojae resistance gene (Rps) products to generate incompatible interactions. The virulence profile of P. sojae is rapidly evolving as a result of the large-scale deployment of Rps genes in soybean. For a successful exploitation of Rps genes, it is recommended that soybean growers use cultivars containing the Rps genes corresponding to Avr genes present in P. sojae populations present in their fields. Determination of the virulence profile of P. sojae isolates is critical for the selection of soybean cultivars. High-resolution melting curve (HRM) analysis is a powerful tool, first applied in medicine, for detecting mutations with potential applications in different biological fields. Here, we report the development of an HRM protocol, as an original approach to discriminate effectors, to differentiate P. sojae haplotypes for six Avr genes. An HRM assay was performed on 24 P. sojae isolates with different haplotypes collected from soybean fields across Canada. The results clearly confirmed that the HRM assay discriminated different virulence genotypes. Moreover, the HRM assay was able to differentiate multiple haplotypes representing small allelic variations. HRM-based prediction was validated by phenotyping assays. This HRM assay provides a unique, cost-effective and efficient tool to predict virulence pathotypes associated with six different Avr (1b, 1c, 1d, 1k, 3a and 6) genes from P. sojae, which can be applied in the deployment of appropriate Rps genes in soybean fields.
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Affiliation(s)
- Parthasarathy Santhanam
- Département de PhytologieUniversité LavalQuebecQuebecCanada
- Present address:
Agriculture Agri‐Food Canada, MRDCMordenManitobaCanada
| | - Caroline Labbé
- Département de PhytologieUniversité LavalQuebecQuebecCanada
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6
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Kreitmann L, Miglietta L, Xu K, Malpartida-Cardenas K, D’Souza G, Kaforou M, Brengel-Pesce K, Drazek L, Holmes A, Rodriguez-Manzano J. Next-generation molecular diagnostics: Leveraging digital technologies to enhance multiplexing in real-time PCR. Trends Analyt Chem 2023; 160:116963. [PMID: 36968318 PMCID: PMC7614363 DOI: 10.1016/j.trac.2023.116963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Real-time polymerase chain reaction (qPCR) enables accurate detection and quantification of nucleic acids and has become a fundamental tool in biological sciences, bioengineering and medicine. By combining multiple primer sets in one reaction, it is possible to detect several DNA or RNA targets simultaneously, a process called multiplex PCR (mPCR) which is key to attaining optimal throughput, cost-effectiveness and efficiency in molecular diagnostics, particularly in infectious diseases. Multiple solutions have been devised to increase multiplexing in qPCR, including single-well techniques, using target-specific fluorescent oligonucleotide probes, and spatial multiplexing, where segregation of the sample enables parallel amplification of multiple targets. However, these solutions are mostly limited to three or four targets, or highly sophisticated and expensive instrumentation. There is a need for innovations that will push forward the multiplexing field in qPCR, enabling for a next generation of diagnostic tools which could accommodate high throughput in an affordable manner. To this end, the use of machine learning (ML) algorithms (data-driven solutions) has recently emerged to leverage information contained in amplification and melting curves (AC and MC, respectively) - two of the most standard bio-signals emitted during qPCR - for accurate classification of multiple nucleic acid targets in a single reaction. Therefore, this review aims to demonstrate and illustrate that data-driven solutions can be successfully coupled with state-of-the-art and common qPCR platforms using a variety of amplification chemistries to enhance multiplexing in qPCR. Further, because both ACs and MCs can be predicted from sequence data using thermodynamic databases, it has also become possible to use computer simulation to rationalize and optimize the design of mPCR assays where target detection is supported by data-driven technologies. Thus, this review also discusses recent work converging towards the development of an end-to-end framework where knowledge-based and data-driven software solutions are integrated to streamline assay design, and increase the accuracy of target detection and quantification in the multiplex setting. We envision that concerted efforts by academic and industry scientists will help advance these technologies, to a point where they become mature and robust enough to bring about major improvements in the detection of nucleic acids across many fields.
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Affiliation(s)
- Louis Kreitmann
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Research & Development, BioMérieux S.A, Marcy-l’Etoile, France
| | - Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London, UK
| | - Ke Xu
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College, London, UK
| | | | - Giselle D’Souza
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
| | | | - Laurent Drazek
- Research & Development, BioMérieux S.A, Marcy-l’Etoile, France
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, UK
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7
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Hemby SE, McIntosh S. Chronic haloperidol administration downregulates select BDNF transcript and protein levels in the dorsolateral prefrontal cortex of rhesus monkeys. Front Psychiatry 2023; 14:1054506. [PMID: 36816400 PMCID: PMC9932326 DOI: 10.3389/fpsyt.2023.1054506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Post-mortem studies in the prefrontal cortex and hippocampal formation from schizophrenia patients have revealed significant disruptions in the expression molecules associated with cytoarchitecture, synaptic structure, function, and plasticity, known to be regulated in part by brain derived neurotrophic factor (BDNF). Interestingly, several studies using postmortem brain tissue from individuals diagnosed with schizophrenia have revealed a significant reduction in BDNF mRNA and protein levels in the dorsolateral prefrontal cortex (DLPFC), hippocampus and related areas; however, differentiating the effects of illness from antipsychotic history has remained difficult. We hypothesized that chronic antipsychotic treatment may contribute to the altered BDNF mRNA and protein expression observed in post-mortem brains of individuals diagnosed with schizophrenia. To address the influence of antipsychotic administration on BDNF expression in the primate brain, rhesus monkeys orally administered haloperidol, clozapine, or vehicle twice daily for 180 days. We found BDNF splice variants 4 and 5 in the DLPFC and variant 2 in the EC were significantly down-regulated following chronic administration of haloperidol. In addition, proBDNF and mature BDNF expression in the DLPFC, but not the EC, were significantly reduced. Based on the known regulation of BDNF expression by BDNF-AS, we assessed the expression of this lncRNA and found expression was significantly upregulated in the DLPFC, but not EC. The results of the present study provide evidence of haloperidol-induced regulation of BDNF mRNA and protein expression in the DLFPC and suggest an important role for BDNF-AS in this regulation. Given the role of BDNF in synaptic plasticity, neuronal survival and maintenance, aberrant expression induced by haloperidol likely has significant ramifications for neuronal populations and circuits in primate cortex.
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Affiliation(s)
- Scott E Hemby
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC, United States
| | - Scot McIntosh
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, High Point, NC, United States
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8
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Zoli M. Non-linear Hamiltonian models for DNA. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:431-447. [PMID: 35976412 DOI: 10.1007/s00249-022-01614-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Nucleic acids' physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse-grained models, e.g., the worm-like-chain, taken from polymer physics. In this review article, I discuss an intermediate (mesoscopic) approach and show how to build a three-dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also allows one to predict the thermodynamical and structural properties of molecules in solution. Relying on the idea that the base pair fluctuations can be conceived as trajectories, I have built over the past years a computational method based on the time-dependent path integral formalism to derive the partition function. While the main features of the method are presented, I focus here in particular on a newly developed statistical method to set the maximum amplitude of the base pair fluctuations, a key parameter of the theory. Some applications to the calculation of DNA flexibility properties are discussed together with the available experimental data.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology, University of Camerino, 62032, Camerino, Italy.
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9
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Rapid Detection of Antimicrobial Resistance in Mycoplasma genitalium by High-Resolution Melting Analysis with Unlabeled Probes. Microbiol Spectr 2022; 10:e0101422. [PMID: 35880894 PMCID: PMC9430336 DOI: 10.1128/spectrum.01014-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With looming resistance to fluoroquinolones in Mycoplasma genitalium, public health control strategies require effective antimicrobial resistance (AMR) diagnostic methods for clinical and phenotypic AMR surveillance. We developed a novel AMR detection method, MGparC-AsyHRM, based on the combination of asymmetric high-resolution melting (HRM) technology and unlabeled probes, which simultaneously performs M. genitalium identification and genotypes eight mutations in the parC gene that are responsible for most cases of fluoroquinolone resistance. These enhancements expand the traditional HRM from the conventional detection of single-position mutations to a method capable of detecting short fragments with closely located AMR positions with a high diversity of mutations. Based on the results of clinical sample testing, this method produces an accordance of 98.7% with the Sanger sequencing method. Furthermore, the specificity for detecting S83I, S83N, S83R, and D87Y variants, the most frequently detected mutations in fluoroquinolone resistance, was 100%. This method maintained a stable and accurate performance for genomic copies at rates of ≥20 copies per reaction, demonstrating high sensitivity. Additionally, no specific cross-reactions were observed when testing eight common sexually transmitted infection (STI)-related agents. Notably, this work highlights the significant potential of our method in the field of AMR testing, with the results suggesting that our method can be applied in a range of scenarios and to additional pathogens. In summary, our method enables high throughput, provides excellent specificity and sensitivity, and is cost-effective, suggesting that this method can be used to rapidly monitor the molecular AMR status and complement current AMR surveillance. IMPORTANCE Mycoplasma genitalium was recently added to the antimicrobial-resistant (AMR) threats "watch list" of the U.S. Centers for Disease Control and Prevention because this pathogen has become extremely difficult to treat as a result of increased resistance. M. genitalium is also difficult to culture, and therefore, molecule detection is the only method available for AMR testing. In this work, we developed a novel AMR detection method, MGparC-AsyHRM, based on the combination of asymmetrical HRM technology and unlabeled probes, and it simultaneously performs M. genitalium identification and genotypes eight mutations in the parC gene that are responsible for most cases of fluoroquinolone resistance. The MGparC-AsyHRM method is a high-throughput, low-cost, simple, and culture-free procedure that can enhance public health and management of M. genitalium infections and AMR control, providing a strong complement to phenotypic AMR surveillance to address the spread of fluoroquinolone resistance.
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10
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Huang Y, Shang M, Liu T, Wang K. High-throughput methods for genome editing: the more the better. PLANT PHYSIOLOGY 2022; 188:1731-1745. [PMID: 35134245 PMCID: PMC8968257 DOI: 10.1093/plphys/kiac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.
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Affiliation(s)
- Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Meiqi Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tingting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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11
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Development of a Gene-Based High Resolution Melting (HRM) Marker for Selecting the Gene ty-5 Conferring Resistance to Tomato Yellow Leaf Curl Virus. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tomato yellow leaf curl virus (TYLCV) causes serious yield reductions in China. The use of certain resistance genes in tomato varieties has alleviated the impact of the virus to a certain extent. Recently, varieties with the Ty-1, Ty-2, or Ty-3 genes lost their resistance to TYLCV in some areas in China. New genes should be introduced into tomato to maintain the resistance to TYLCV. Tomato line AVTO1227 has excellent resistance to disease due to the resistance gene ty-5. In this study, we screened different types of markers in a tomato F2 population to compare their accuracy and efficiency. The sequencing analysis results were consistent with the high resolution melting (HRM) marker genotype and field identification results. The result confirmed that the functional marker of ty-5 was accurate and reliable. The single nucleotide polymorphism-based HRM genotyping method established in this study can be used for the selection of breeding parent material, gene correlation analysis, and molecular marker-assisted breeding.
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12
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Lian X, Li Y, Li L, U K, Wang W, Shi Y, Ma J, Wang H. A novel single-tube multiplex real-time PCR assay for genotyping of thiopurine intolerance-causing variant NUDT15 c.415C>T. Exp Biol Med (Maywood) 2021; 246:1961-1967. [PMID: 34192970 DOI: 10.1177/15353702211026579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Thiopurines are commonly used in the treatment of acute lymphoblastic leukaemia and autoimmune conditions, can be limited by myelosuppression. The NUDT15 c.415C>T variant is strongly associated with thiopurine-induced myelosuppression, especially in Asians. The purpose of this study was to develop a fast and reliable genotyping method for NUDT15 c.415C>T and investigate the polymorphic distribution among different races in China. A single-tube multiplex real-time PCR assay for NUDT15 c.415C>T genotyping was established using allele-specific TaqMan probes. In 229 samples, the genotyping results obtained through the established method were completely concordant with those obtained by Sanger sequencing. The distributions of NUDT15 c.415C>T among 173 Han Chinese, 48 Miaos, 40 Kazakhs, and 40 Kirghiz were different, with allelic frequencies of 0.06, 0.02, 0.07, and 0, respectively. This method will provide a powerful tool for the implementation of the genotyping-based personalized prescription of thiopurines in clinical settings.
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Affiliation(s)
- Xiaoyun Lian
- Department of Hematology, Shaanxi Provincial Peoples' Hospital, Xi'an 710068, China
| | - Yanwei Li
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an 710069, China
| | - Lan Li
- Department of Hematology, Shaanxi Provincial Peoples' Hospital, Xi'an 710068, China
| | - Kaicheng U
- American Heritage School, Plantation, FL 33325, USA
| | - Wenxia Wang
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an 710069, China
| | - Yinmin Shi
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an 710069, China
| | - Jiying Ma
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an 710069, China
| | - Huijuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an 710069, China
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13
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Tiedemann RL, Eden HE, Huang Z, Robertson KD, Rothbart SB. Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays. Methods Mol Biol 2021; 2272:97-140. [PMID: 34009611 DOI: 10.1007/978-1-0716-1294-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.
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Affiliation(s)
| | - Hope E Eden
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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14
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Liu X, Qiu S, Mei L, Jing H, Lin X, Wang Q. A High-Resolution Melting Analysis with an Unlabeled Probe for CRISPR/Cas9-Induced ZBED6 Knockout Pigs Detection. J AOAC Int 2021; 104:541-545. [PMID: 33295625 DOI: 10.1093/jaoacint/qsaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND The zinc finger BED-type containing six knockout (ZBED6-KO) pigs were created to improve economic traits by increasing the expression of insulin-like growth factor 2. They were generated by CRISPR/CRISPR-associated protein 9 (Cas9) technology and a single-base deletion of ZBED6 was found. An efficient and rapid method was needed to detect this type of pig. OBJECTIVE This study aimed to develop a high-resolution melting (HRM) method to detect ZBED6-KO pigs. METHODS An unlabeled probe and two primers were designed to develop the HRM method. The limit of detection, specificity, and accuracy of the established method were tested by the constructed plasmid and DNA extracts of tissue specimens. RESULTS The limit of detection by the established method was 102 copies/µL. The HRM method with an unlabeled probe showed good specificity and high accuracy. CONCLUSIONS The established HRM analysis with an unlabeled probe showed it to be a highly effective, rapid, and reliable method to distinguish ZBED6-KO pigs from wild-type pigs. HIGHLIGHTS It is the first time that HRM analysis with an unlabeled probe has been used in the detection of genome editing pigs by the CRISPR/Cas9 technology.
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Affiliation(s)
- Xiaofei Liu
- The Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Songyin Qiu
- The Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Lin Mei
- The Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Hongli Jing
- The Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xiangmei Lin
- The Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Qin Wang
- The Institute of Animal Inspection and Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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15
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GİRGİN ÖZGÜMÜŞ G, GÜNEY İ. BRCA1 ve BRCA2 Mutasyonlarının Tespitine Yönelik Yeni Nesil Dizileme Temelli Kit Geliştirilmesi ve Rutinde Kullanılan Yöntemler ile Valide Edilmesi. İSTANBUL GELIŞIM ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2021. [DOI: 10.38079/igusabder.843199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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16
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Duplex high resolution melting analysis (dHRMA) to detect two hot spot CYP24A1 pathogenic variants (PVs) associated to idiopathic infantile hypercalcemia (IIH). Mol Biol Rep 2021; 48:3303-3311. [PMID: 33864587 PMCID: PMC8172411 DOI: 10.1007/s11033-021-06324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/27/2021] [Indexed: 11/06/2022]
Abstract
Pathogenic variants (PVs) in CYP24A1 gene are associated with Idiopathic Infantile Hypercalcemia disease (IIH). The identification of CYP24A1 PVs can be a useful tool for the improvement of target therapeutic strategies. Aim of this study is to set up a rapid and inexpensive High Resolution Melting Analysis (HRMA)-based method for the simultaneous genotyping of two hot spot PVs in CYP24A1 gene, involved in IIH. A duplex-HRMA (dHRMA) was designed in order to detect simultaneously CYP24A1 c.428_430delAAG, p.(Glu143del) (rs777676129) and c.1186C > T, p.(Arg396Trp) (rs114368325), in peculiar cases addressed to our Laboratory. dHRMA was able to identify clearly and simultaneously both hot spot CYP24A1 PVs evaluating melting curve shape and melting temperature (Tm). This is the first dHRMA approach to rapidly screen the two most frequent CYP24A1 PVs in peculiar case, providing useful information for diagnosis and patient management in IIH disease.
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17
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Nishiike Y, Miyazoe D, Togawa R, Yokoyama K, Nakasone K, Miyata M, Kikuchi Y, Kamei Y, Todo T, Ishikawa-Fujiwara T, Ohno K, Usami T, Nagahama Y, Okubo K. Estrogen receptor 2b is the major determinant of sex-typical mating behavior and sexual preference in medaka. Curr Biol 2021; 31:1699-1710.e6. [PMID: 33639108 DOI: 10.1016/j.cub.2021.01.089] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/07/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023]
Abstract
Male and female animals typically display innate sex-specific mating behaviors, which, in vertebrates, are highly dependent on sex steroid signaling. While estradiol-17β (E2) signaling through estrogen receptor 2 (ESR2) serves to defeminize male mating behavior in rodents, the available evidence suggests that E2 signaling is not required in teleosts for either male or female mating behavior. Here, we report that female medaka deficient for Esr2b, a teleost ortholog of ESR2, are not receptive to males but rather court females, despite retaining normal ovarian function with an unaltered sex steroid milieu. Thus, contrary to both prevailing views in rodents and teleosts, E2/Esr2b signaling in the brain plays a decisive role in feminization and demasculinization of female mating behavior and sexual preference in medaka. Further behavioral testing showed that mutual antagonism between E2/Esr2b signaling and androgen receptor-mediated androgen signaling in adulthood induces and actively maintains sex-typical mating behaviors and preference. Our results also revealed that the female-biased sexual dimorphism in esr2b expression in the telencephalic and preoptic nuclei implicated in mating behavior can be reversed between males and females by altering the sex steroid milieu in adulthood, likely via mechanisms involving direct E2-induced transcriptional activation. In addition, Npba, a neuropeptide mediating female sexual receptivity, was found to act downstream of E2/Esr2b signaling in these brain nuclei. Collectively, these functional and regulatory mechanisms of E2/Esr2b signaling presumably underpin the neural mechanism for induction, maintenance, and reversal of sex-typical mating behaviors and sexual preference in teleosts, at least in medaka.
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Affiliation(s)
- Yuji Nishiike
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Daichi Miyazoe
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Rie Togawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Keiko Yokoyama
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Kiyoshi Nakasone
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Masayoshi Miyata
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Yukiko Kikuchi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Yasuhiro Kamei
- Spectrography and Bioimaging Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takeshi Todo
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoko Ishikawa-Fujiwara
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kaoru Ohno
- Division of Reproductive Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takeshi Usami
- Division of Reproductive Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Yoshitaka Nagahama
- Division of Reproductive Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kataaki Okubo
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
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18
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CRISPR/Cas9-Mediated Knockout of HOS1 Reveals Its Role in the Regulation of Secondary Metabolism in Arabidopsis thaliana. PLANTS 2021; 10:plants10010104. [PMID: 33419060 PMCID: PMC7825447 DOI: 10.3390/plants10010104] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 11/17/2022]
Abstract
In Arabidopsis, the RING finger-containing E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) functions as a main regulator of the cold signaling. In this study, CRISPR/Cas9-mediated targeted mutagenesis of the HOS1 gene in the first exon was performed. DNA sequencing showed that frameshift indels introduced by genome editing of HOS1 resulted in the appearance of premature stop codons, disrupting the open reading frame. Obtained hos1Cas9 mutant plants were compared with the SALK T-DNA insertion mutant, line hos1-3, in terms of their tolerance to abiotic stresses, accumulation of secondary metabolites and expression levels of genes participating in these processes. Upon exposure to cold stress, enhanced tolerance and expression of cold-responsive genes were observed in both hos1-3 and hos1Cas9 plants. The hos1 mutation caused changes in the synthesis of phytoalexins in transformed cells. The content of glucosinolates (GSLs) was down-regulated by 1.5-times, while flavonol glycosides were up-regulated by 1.2 to 4.2 times in transgenic plants. The transcript abundance of the corresponding MYB and bHLH transcription factors, which are responsible for the regulation of secondary metabolism in Arabidopsis, were also altered. Our data suggest a relationship between HOS1-regulated downstream signaling and phytoalexin biosynthesis.
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19
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Arbabi M, Hooshyar H, Delavari M, Pestechian N. Genotypes Identification of echinococcus granulosus isolated from iranian dogs and camels using three polymerase Chain reaction-based methods of cox1 gene. INTERNATIONAL ARCHIVES OF HEALTH SCIENCES 2021. [DOI: 10.4103/iahs.iahs_91_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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20
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Bidla G, Rosenblatt DS, Gilfix BM. Identification of Variants in Alpha-1-Antitrypsin by High Resolution Melting. J Appl Lab Med 2020; 6:715-728. [PMID: 33331634 DOI: 10.1093/jalm/jfaa191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/28/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Alpha-1-antitrypsin deficiency (AATD) is one of the most common hereditary disorders occurring in populations of European origin and is due to variants in SERPINA1, which encodes a protease inhibitor of neutrophil elastase, limiting lung damage from this enzyme. The World Health Organization has recommended that individuals with chronic obstructive pulmonary disease and asthma be tested for AATD. The development of inexpensive and simple genetic testing will help to meet this goal. METHODS Primers and synthetic SERPINA1 gene fragments (gBlocks) were designed for 5 AATD-associated variants. PCR was run on a CFX96 Thermal Cycler with High Resolution Melting (HRM) capacity and data analyzed using the supplied HRM-analysis software. Genomic DNA from individuals (n = 86) genotyped for the S and Z variants were used for validation. HRM-analysis was performed on 3 additional samples with low alpha-1-antitrypsin levels inconsistent with the genotype determined in our clinical laboratory. RESULTS Unique normalized melt curve and difference curve patterns were identified for the AAT variants Z, S, I, F, and MMalton using gBlocks. Similar curve shapes were seen when these primers were used to analyze the gDNA samples. HRM identified the genotypes of the gDNA correctly with 100% concordance. The curve shapes of some samples did not match the melting patterns of the targeted variant. Sequencing was used to identify the variants, including rare AATD variants c.1108_1115delinsAAAAACA (p.Glu370Lysfs*31) and c.1130dup (p.Leu377fs). CONCLUSION We developed a rapid and inexpensive HRM-analysis method for genotyping of Z, S, MMalton, I, and F variants that was also capable of detecting other variants.
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Affiliation(s)
- Gawa Bidla
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Divisions of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada.,Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
| | - Brian M Gilfix
- Medical Biochemistry, Department of Specialized Medicine, McGill University Health Centre, Montreal, Quebec, Canada
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21
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England AD, Kheravii SK, Musigwa S, Kumar A, Daneshmand A, Sharma NK, Gharib-Naseri K, Wu SB. Sexing chickens (Gallus gallus domesticus) with high-resolution melting analysis using feather crude DNA. Poult Sci 2020; 100:100924. [PMID: 33652540 PMCID: PMC7936197 DOI: 10.1016/j.psj.2020.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/13/2020] [Accepted: 12/08/2020] [Indexed: 10/25/2022] Open
Abstract
Identification of sex in broiler chickens allows researchers to reduce the level of variation in an experiment caused by the sex effect. Broiler breeds commonly used in research are no longer feather sexable because of the change in their genetics. Other alternate sexing methods are costly and difficult to apply on a large scale. Therefore, a sexing method is required that is both cost effective and highly sensitive as well as having the ability to offer high throughput genotyping. In this study, high-resolution melting (HRM) analysis was used to detect DNA variations present in the gene chromodomain helicase DNA binding 1 protein (CHD1) on the Z and W chromosomes (CHD1Z and CHD1W, respectively) of chickens. In addition, a simplified DNA extraction protocol, which made use of the basal part of chicken feathers, was developed to speed up the sexing procedure. Three pairs of primers, that is, CHD1UNEHRM1F/R, CHD1UNEHRM2F/R, and CHD1UNEHRM3F/R, flanking the polymorphic regions between CHD1Z and CHD1W were used to differentiate male and female chickens via distinct melting curves, typical of homozygous or heterozygous genotypes. The assay was validated by the HRM-sexing of 1,318 broiler chicks and verified by examining the sex of the birds after dissection. This method allows for the sexing of birds within a couple of days, which makes it applicable for use on a large scale such as in nutritional experiments.
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Affiliation(s)
- A D England
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - S K Kheravii
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - S Musigwa
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - A Kumar
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - A Daneshmand
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - N K Sharma
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - K Gharib-Naseri
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia
| | - S B Wu
- School of Environmental and Rural Science, University of New England, Armidale 2351, NSW, Australia.
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22
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Wang F, Fu S, Lei J, Wu H, Shi S, Chen K, Hu J, Xu X. Identification of novel FUS and TARDBP gene mutations in Chinese amyotrophic lateral sclerosis patients with HRM analysis. Aging (Albany NY) 2020; 12:22859-22868. [PMID: 33159016 PMCID: PMC7746354 DOI: 10.18632/aging.103967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/30/2020] [Indexed: 11/25/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive loss of motor neurons. More than 30 genes have been linked to ALS to date, including FUS and TARDBP, which exhibit similar roles in RNA metabolism. This study explored the use of high-resolution melting (HRM) analysis to screen for FUS and TARDBP mutation hotspot regions in 146 Chinese ALS patients, which achieved 100% detection. Two FUS mutations were observed in two different familial ALS probands, a missense mutation (p.R521H) and a novel splicing mutation (c.1541+1G>A). Five TARDBP mutations were identified in six ALS patients, including a novel 3'UTR mutation (c.*731A>G) and four missense mutations (p.G294V, p.M337V, p.G348V, and p.I383V). We found that FUS mutations were present in 1.4% of Chinese ALS patients, whereas TARDBP mutations were responsible for 4.1% of Chinese ALS cases. Here, we describe the accuracy of using highly sensitive HRM analysis to identify two novel FUS and TARDBP mutations in Chinese sporadic and familial ALS cases. Our study contributes to the further understanding of the genetic and phenotypic diversity of ALS.
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Affiliation(s)
- Feng Wang
- Department of Clinical Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Shengyu Fu
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Jiafan Lei
- Department of Clinical Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Hongchen Wu
- Department of Neurology, Chunking General Hospital, Chongqing, China
| | - Shugui Shi
- Department of Neurology, Chunking General Hospital, Chongqing, China
| | - Kangning Chen
- Department of Neurology, First Affiliated Hospital of Army Medical University, Army Medical University, Chongqing, China
| | - Jun Hu
- Department of Neurology, First Affiliated Hospital of Army Medical University, Army Medical University, Chongqing, China
| | - Xueqing Xu
- Department of Clinical Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
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23
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Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms. Talanta 2020; 218:121141. [PMID: 32797898 DOI: 10.1016/j.talanta.2020.121141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.
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24
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Mosawi SH, Dalimi A, Safi N, Fotouhi-Ardakani R, Ghaffarifar F, Sadraei J. An unlabelled probe-based real time PCR and modified semi-nested PCR as molecular tools for analysis of chloroquine resistant Plasmodium vivax isolates from Afghanistan. Malar J 2020; 19:253. [PMID: 32664942 PMCID: PMC7362495 DOI: 10.1186/s12936-020-03323-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/07/2020] [Indexed: 11/27/2022] Open
Abstract
Background Plasmodium vivax resistance to chloroquine (CQ) has been reported from many endemic regions in the world. Plasmodium vivax is responsible for 95% of malaria cases in Afghanistan and CQ is the first-line treatment given for vivax malaria. The pvmdr-1 and pvcrt-o (K10 insertion) genes are possible markers for CQ-resistance in P. vivax isolates. There have been no studies done on the presence or absence of molecular markers for CQ-resistance P. vivax in Afghanistan. The present work aimed to evaluate the frequency of mutations in the pvmdr-1 and K10 insertion in the pvcrt-o genes of P. vivax. Methods Plasmodium vivax isolates were collected from Laghman, Baghlan and Khost provinces. For investigation of polymorphisms of desired regions in pvmdr-1 and pvcrt-o genes, sequencing was applied on the PCR products. A new asymmetric qPCR and melting analysis assay based on unlabelled probe developed for scanning of K10 insertion in pvcrt-o gene. Results The analysis of sequencing data of the pvmdr-1 gene showed wild type Y976 and K997 and mutant M958 and L1076 in 33 isolates from three provinces. Of the 36 samples evaluated for K10 insertion in pvcrt-o, 2/18(11%), 0/10(0%) and 0/8(0%) isolates from Laghman, Baghlan and Khost province, respectively, possessed K10 insertion, confirmed by either sequencing and unlabelled probes. Conclusion Two samples with K10 insertion and 33 samples with pvmdr1 polymorphism, indicating on the possibility of CQ resistance in P. vivax populations in Afghanistan. Furthermore, unlabelled probes are simple and inexpensive alternative tools for screening of P. vivax mutations.
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Affiliation(s)
- Sayed Hussain Mosawi
- Department of Medical Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.,Medical Sciences Research Center, Ghalib University, Kabul, Afghanistan
| | - Abdolhossein Dalimi
- Department of Medical Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Najibullah Safi
- World Health Organization Country Office, Kabul, Afghanistan
| | - Reza Fotouhi-Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Fatemeh Ghaffarifar
- Department of Medical Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javid Sadraei
- Department of Medical Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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25
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Ma L, Huang Y, Zhang H, Ning W, Qi R, Yuan H, Lv F, Liu L, Yu C, Wang S. Sensitive Detection and Conjoint Analysis of Promoter Methylation by Conjugated Polymers for Differential Diagnosis and Prognosis of Glioma. ACS APPLIED MATERIALS & INTERFACES 2020; 13:9291-9299. [PMID: 32436715 DOI: 10.1021/acsami.0c03218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glioma is the most common primary tumor in the central nervous system (CNS) with the worst prognosis. Accurate pathological diagnosis has always been a challenge for optimal management of glioma. Promoter methylation is an important mechanism of epigenetic silencing tumor-suppressor genes and a potential biomarker for differential diagnosis and prognosis. Herein, using the cationic conjugated polymer (CCP)-based fluorescence resonance energy transfer (FRET) technique, we realized a highly sensitive detection of promoter methylation in clinical samples of minimal methylation degree (1.25%) and trace DNA quantity (10 ng/μL). Results for three glioma-related genes (MGMT, CDKN2A, and TERT) were combined in a diagnostic classifier to analyze the glioma-CpG island methylator phenotype (G-CIMP), which achieved a sensitivity of 80% at a maximum specificity of 100% for a glioma diagnosis. Kaplan-Meier survival curves and Pearson correlation analysis revealed that the prognosis of glioma patients with high G-CIMP scores (>5) was significantly better than those with low G-CIMP scores, especially in diffuse midline glioma and astrocytoma. This CCP-based FRET technique for determining G-CIMP status could provide patients with rapid and reasonably accurate diagnosis of glioma, as well as a valuable prognostic prediction that can guide individual treatment.
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Affiliation(s)
- Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Yiming Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Ruilian Qi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Haitao Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Chunjiang Yu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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26
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Martínez-Saucedo M, Ornelas-Fuentes C, Dedden M, Sánchez-Urbina R, Díaz-García H, Aquino-Jarquin G, Moreno-Salgado R, Granados-Riveron JT. Implementation of high-resolution melting analysis of the porcupine (PORCN) gene for molecular diagnosis of focal dermal hypoplasia: Identification of a novel mutation. J Gene Med 2020; 22:e3165. [PMID: 31984575 DOI: 10.1002/jgm.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/18/2020] [Accepted: 01/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Focal dermal hypoplasia (FDH) is rare X-linked dominant disease characterized by atrophy and linear pigmentation of the skin, split hand/foot deformities and ocular anomalies. FDH is caused by mutations of the Porcupine (PORCN) gene, which encodes an enzyme that catalyzes the palmitoylation of Wnt ligands required for their secretion. High resolution melting analysis (HRM) is a technique that allows rapid, labor-efficient, low-cost detection of genomic variants. In the present study, we report the successful implementation of HRM in the molecular diagnosis of FDH. METHODS Polymerase chain reaction and HRM assays were designed and optimized for each of the coding exons of the PORCN gene, processing genomic DNA samples form a non-affected control and a patient complying with the FDH diagnostic criteria. The causal mutation was characterized by Sanger sequencing from an amplicon showing a HRM trace suggesting heterozygous variation and was validated using an amplification-refractory mutation system (ARMS) assay. RESULTS The melting profiles suggested the presence of a variant in the patient within exon 1. Sanger sequencing revealed a previously unknown C to T transition replacing a glutamine codon for a premature stop codon at position 28, which was validated using ARMS. CONCLUSIONS Next-generation sequencing facilitates the molecular diagnosis of monogenic disorders; however, its cost-benefit ratio is not optimal when a single, small or medium size causal gene is already identified and the clinical diagnostic presumption is strong. Under those conditions, as it is the case for FDH, HRM represents a cost- and labor-effective approach.
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Affiliation(s)
- Mirna Martínez-Saucedo
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Carolina Ornelas-Fuentes
- Department of Medical Genetics and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Mark Dedden
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rocío Sánchez-Urbina
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez,, Mexico City, México
| | - Héctor Díaz-García
- Laboratory of Developmental Biology and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez,, Mexico City, México
| | - Guillermo Aquino-Jarquin
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Rodrigo Moreno-Salgado
- Department of Medical Genetics and Experimental Teratogenesis, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Javier T Granados-Riveron
- Laboratory of Research in Genomics, Genetics and Bioinformatics, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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A High Resolution DNA Melting Curve Analysis for the Rapid and Efficient Molecular Diagnostics of Extended Spectrum β-Lactamase Determinants from Foodborne Escherichia coli. Microorganisms 2020; 8:microorganisms8010090. [PMID: 31936584 PMCID: PMC7023082 DOI: 10.3390/microorganisms8010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/03/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
The accurate identification of Extended-Spectrum β-Lactamase (ESBL) genes in Gram-negative bacteria is necessary for surveillance and epidemiological studies of transmission through foods. We report a novel rapid, cheap, and accurate closed tube molecular diagnostic tool based on two multiplex HRM protocols for analysis of the predominant ESBL families encountered in foods. The first multiplex PCR assay targeted blaCTX-M including phylogenetic groups 1 (CTX-M-1-15, including CTX-M-1, CTX-M-3 and CTX-M-15), 2 (CTX-M-2), and 9 (CTX-M-9-14, including CTX-M-9 and CTX-M-14). The second assay involved blaTEM /bla CTX-M /blaSHV, including TEM variants (TEM-1 and TEM-2), SHV-1-56 (SHV-1, SHV-2 and SHV-56), and CTX-M-8-41 (CTX-M-8, CTX-M-25, CTX-M-26 and CTX-M-39 to CTX-M-41). The individual melting curves were differentiated by a temperature shift according to the type of ESBL gene. The specificity and sensitivity of the first assay were 100% and 98%, respectively. For the second assay, the specificity and sensitivity were 87% and 89%, respectively. The detection of ESBL variants or mutations in existing genes was also demonstrated by the subtyping of a variant of the CTXM-1-15. The HRM is a potential tool for the rapid detection of present β-lactamase genes and their characterization in a highly sensitive, closed-tube, inexpensive method that is applicable in high throughput studies.
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Zoli M. First-passage probability: a test for DNA Hamiltonian parameters. Phys Chem Chem Phys 2020; 22:26901-26909. [DOI: 10.1039/d0cp04046k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A method is developed to chose the set of input parameters for DNA mesoscopic Hamiltonian models.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology
- University of Camerino
- I-62032 Camerino
- Italy
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29
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Mohammad Rahimi H, Pourhosseingholi MA, Yadegar A, Mirjalali H, Zali MR. High-resolution melt curve analysis: A real-time based multipurpose approach for diagnosis and epidemiological investigations of parasitic infections. Comp Immunol Microbiol Infect Dis 2019; 67:101364. [PMID: 31590033 DOI: 10.1016/j.cimid.2019.101364] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Real-time PCR coupled with high resolution melting curve analysis is a practical technique that could be employed in multipurpose studies. During the recent decade, this technique has been practiced for different targets, worldwide. METHODS In the current study three major database centers consisted of PubMed, Scopus and Web of Science were searched until Aug 2019 for applications of HRM real-time PCR in parasitology studies using terms: "Parasite" AND "HRM real-time PCR" OR "High Resolution Melting curve analysis" OR "Real-time PCR", "Protozoan parasites" AND "HRM real-time PCR" OR "High Resolution Melting curve analysis" OR "Real-time PCR", "Helminth" AND "HRM real-time PCR" OR "High Resolution Melting curve analysis" OR "Real-time PCR". RESULTS Totally, 83 papers met our criteria and were included in our study. This method was more frequently used for protozoan parasites (52/83; 62.65%), while lower (31/83; 37.35%) studies were incorporated on helminths parasites. Furthermore, Plasmodium spp., and Leishmania spp., were the most prevalent protozoan parasites, and Taenia spp., and filers were the most frequent helminths that were studied by HRM real-time PCR. CONCLUSION HRM real-time PCR is a sensitive, flexible and cost-effective method that could be used for multipurpose studies.
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Affiliation(s)
- Hanieh Mohammad Rahimi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Pourhosseingholi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Mirjalali
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Fons NR, Sundaram RK, Breuer GA, Peng S, McLean RL, Kalathil AN, Schmidt MS, Carvalho DM, Mackay A, Jones C, Carcaboso ÁM, Nazarian J, Berens ME, Brenner C, Bindra RS. PPM1D mutations silence NAPRT gene expression and confer NAMPT inhibitor sensitivity in glioma. Nat Commun 2019; 10:3790. [PMID: 31439867 PMCID: PMC6706443 DOI: 10.1038/s41467-019-11732-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Pediatric high-grade gliomas are among the deadliest of childhood cancers due to limited knowledge of early driving events in their gliomagenesis and the lack of effective therapies available. In this study, we investigate the oncogenic role of PPM1D, a protein phosphatase often found truncated in pediatric gliomas such as DIPG, and uncover a synthetic lethal interaction between PPM1D mutations and nicotinamide phosphoribosyltransferase (NAMPT) inhibition. Specifically, we show that mutant PPM1D drives hypermethylation of CpG islands throughout the genome and promotes epigenetic silencing of nicotinic acid phosphoribosyltransferase (NAPRT), a key gene involved in NAD biosynthesis. Notably, PPM1D mutant cells are shown to be sensitive to NAMPT inhibitors in vitro and in vivo, within both engineered isogenic astrocytes and primary patient-derived model systems, suggesting the possible application of NAMPT inhibitors for the treatment of pediatric gliomas. Overall, our results reveal a promising approach for the targeting of PPM1D mutant tumors, and define a critical link between oncogenic driver mutations and NAD metabolism, which can be exploited for tumor-specific cell killing.
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Affiliation(s)
- Nathan R Fons
- Department of Pathology, Yale University, New Haven, CT, 06520, USA.,Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Ranjini K Sundaram
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Gregory A Breuer
- Department of Pathology, Yale University, New Haven, CT, 06520, USA.,Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Sen Peng
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, 85004, USA
| | - Ryan L McLean
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Aravind N Kalathil
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Mark S Schmidt
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Diana M Carvalho
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Alan Mackay
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Chris Jones
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | | | - Javad Nazarian
- Children's National Health System, Washington, DC, 20010, USA
| | - Michael E Berens
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, 85004, USA.
| | - Charles Brenner
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.
| | - Ranjit S Bindra
- Department of Pathology, Yale University, New Haven, CT, 06520, USA. .,Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA.
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Darvishi FZ, Boroumand F, Saadat M. Genotyping of a 50 bp insertion/deletion genetic variation at promoter region of the superoxide dismutase 1 (SOD1) using high resolution melting analysis. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019; 222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).
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Affiliation(s)
- Alex M Zimmer
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yihang K Pan
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | | | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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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] [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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Xiang Z, Wan R, Zou B, Qi X, Huang Q, Kumar S, Pitman JL, Zhou G, Song Q. Highly sensitive and specific real-time PCR by employing serial invasive reaction as a sequence identifier for quantifying EGFR mutation abundance in cfDNA. Anal Bioanal Chem 2018; 410:6751-6759. [DOI: 10.1007/s00216-018-1316-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/26/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
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35
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Zhang Y, Qu S, Zhao J, Yu T, Guo L, Yin S, Hu X, Chen W, Lai W, Huang J. A novel RFLP-ARMS TaqMan PCR-based method for detecting the BRAF V600E mutation in melanoma. Oncol Lett 2018; 16:1615-1621. [PMID: 30008844 PMCID: PMC6036452 DOI: 10.3892/ol.2018.8844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 01/19/2018] [Indexed: 01/07/2023] Open
Abstract
To enable the rapid and sensitive screening of the BRAF V600E mutation in clinical samples, a novel method combining restriction fragment length polymorphism (RFLP) analysis with the popular amplification refractory mutation system (ARMS) TaqMan quantitative (qPCR) genotyping method in a single reaction tube was developed. A total of 2 primer pairs were designed to enrich for and genotype the BRAF mutational hotspot (RFLP primers and ARMS primers) and a restriction enzyme was used to remove the wild-type alleles. The analysis revealed that this method detected mutant alleles in mixed samples containing >0.1% mutant sequences. In a survey of 53 melanoma samples, this method detected 21 mutation-positive samples. This novel RFLP-ARMS TaqMan qPCR protocol may prove useful for detecting mutations in clinical samples containing only a small proportion of mutant alleles.
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Affiliation(s)
- Yunqing Zhang
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Shoufang Qu
- Division of In Vitro Diagnostic Reagents, National Institutes for Food and Drug Control, Beijing 100050, P.R. China
| | - Jinyin Zhao
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Ting Yu
- Division of In Vitro Diagnostic Reagents, National Institutes for Food and Drug Control, Beijing 100050, P.R. China
| | - Liping Guo
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Songchao Yin
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Xiaoxu Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Weijun Chen
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China.,Beijing BGI-GBI Biotech Co., Ltd, Beijing 101300, P.R. China
| | - Wei Lai
- Department of Dermatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, P.R. China
| | - Jie Huang
- Division of In Vitro Diagnostic Reagents, National Institutes for Food and Drug Control, Beijing 100050, P.R. China
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Susanti S, Fadhil W, Ebili HO, Asiri A, Nestarenkaite A, Hadjimichael E, Ham-Karim HA, Field J, Stafford K, Matharoo-Ball B, Hassall JC, Sharif A, Oniscu A, Ilyas M. N_LyST: a simple and rapid screening test for Lynch syndrome. J Clin Pathol 2018; 71:713-720. [DOI: 10.1136/jclinpath-2018-205013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 01/13/2023]
Abstract
AimsWe sought to use PCR followed by high-resolution melting analysis to develop a single closed-tube screening panel to screen for Lynch syndrome. This comprises tests for microsatellite instability (MSI), MLH1 methylation promoter and BRAF mutation.MethodsFor MSI testing, five mononucleotide markers (BAT25, BAT26, BCAT25, MYB, EWSR1) were developed. In addition, primers were designed to interrogate Region C of the MLH1 promoter for methylation (using bisulphite-modified DNA) and to test for mutations in codon 600 of BRAF. Two separate cohorts from Nottingham (n=99, 46 with MSI, 53 being microsatellite stable (MSS)) and Edinburgh (n=88, 45 MSI, 43 MSS) were tested.ResultsAll the cases (n=187) were blind tested for MSI and all were correctly characterised by our panel. The MLH1 promoter and BRAF were tested only in the Nottingham cohort. Successful blinded analysis was performed on the MLH1 promoter in 97 cases. All MSS cases showed a pattern of non-methylation while 41/44 cases with MSI showed full methylation. The three cases with MSI and a non-methylated pattern had aberrations in MSH2 and MSH6 expression. BRAF mutation was detected in 61% of MSI cases and 11% of MSS cases.Finally, 12 cases were blind screened by using the whole panel as a single test. Of these, five were identified as MSS, four as MSI/non-LS and three as MSI/possible LS. These results were concordant with the previous data.ConclusionWe describe the Nottingham Lynch Syndrome Test (N_LyST). This is a quick, simple and cheap method for screening for Lynch syndrome.
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Guo J, Li K, Jin L, Xu R, Miao K, Yang F, Qi C, Zhang L, Botella JR, Wang R, Miao Y. A simple and cost-effective method for screening of CRISPR/Cas9-induced homozygous/biallelic mutants. PLANT METHODS 2018; 14:40. [PMID: 29872452 PMCID: PMC5972395 DOI: 10.1186/s13007-018-0305-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND The CRISPR/Cas9 system is being used for genome editing purposes by many research groups in multiple plant species. Traditional sequencing methods to identify homozygous mutants are time-consuming, laborious and expensive. RESULTS We have developed a method to screen CRISPR/Cas9-induced mutants through Mutation Sites Based Specific Primers Polymerase Chain Reaction (MSBSP-PCR). The MSBSP-PCR method was successfully used to identify homozygous/biallelic mutants in Nicotiana tabacum and Arabidopsis thaliana, and we speculate that it can be used for the identification of CRISPR/Cas9-induced mutants in other plant species. Compared to traditional sequencing methods, MSBSP-PCR is simpler, faster and cheaper. CONCLUSIONS The MSBSP-PCR method is simple to implement and can save time and cost in the screening of CRISPR/Cas9-induced homozygous/biallelic mutants.
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Affiliation(s)
- Jinggong Guo
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Kun Li
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Lifeng Jin
- Zhengzhou Tabacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou, 450001 Henan China
| | - Rui Xu
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Kaiting Miao
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
- School of Life Science, Southwest University, No. 1, Tiansheng Road, Beibei, 400715 Chongqing China
| | - Fengbo Yang
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
| | - Chaoya Qi
- Zhengzhou Tabacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou, 450001 Henan China
| | - Lin Zhang
- Zhengzhou Tabacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou, 450001 Henan China
- College of Tobacco Science, Henan Agricultural University, No.63 Agriculture Road, Zhengzhou, 450002 Henan China
| | - Jose R. Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD Australia
| | - Ran Wang
- Zhengzhou Tabacco Research Institute of CNTC, No. 2 Fengyang Street, Zhengzhou, 450001 Henan China
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, 85 Minglun Street, Kaifeng, 475001 China
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Słomka M, Sobalska-Kwapis M, Wachulec M, Bartosz G, Strapagiel D. High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies. Int J Mol Sci 2017; 18:ijms18112316. [PMID: 29099791 PMCID: PMC5713285 DOI: 10.3390/ijms18112316] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023] Open
Abstract
High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.
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Affiliation(s)
- Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
| | - Monika Wachulec
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Grzegorz Bartosz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236 Łódź, Poland.
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Pilarskiego 14/16, 90-231 Łódź, Poland.
- BBMRI.pl Consortium, 54-066 Wrocław, Poland.
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Hua Y, Wang C, Huang J, Wang K. A simple and efficient method for CRISPR/Cas9-induced mutant screening. J Genet Genomics 2017; 44:207-213. [PMID: 28416245 DOI: 10.1016/j.jgg.2017.03.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/17/2017] [Accepted: 03/07/2017] [Indexed: 11/28/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system provides a technological breakthrough in mutant generation. Several methods such as the polymerase chain reaction (PCR)/restriction enzyme (RE) assay, T7 endonuclease I (T7EI) assay, Surveyor nuclease assay, PAGE-based genotyping assay, and high-resolution melting (HRM) analysis-based assay have been developed for screening CRISPR/Cas9-induced mutants. However, these methods are time- and labour-intensive and may also be sequence-limited or require very expensive equipment. Here, we described a cost-effective and sensitive screening technique based on conventional PCR, annealing at critical temperature PCR (ACT-PCR), for identifying mutants. ACT-PCR requires only a single PCR step followed by agarose gel electrophoresis. We demonstrated that ACT-PCR accurately distinguished CRISPR/Cas9-induced mutants from wild type in both rice and zebrafish. Moreover, the method can be adapted for accurately determining mutation frequency in cultured cells. The simplicity of ACT-PCR makes it particularly suitable for rapid, large-scale screening of CRISPR/Cas9-induced mutants in both plants and animals.
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Affiliation(s)
- Yufeng Hua
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Chun Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jian Huang
- School of Biology & Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
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Langaee T, Stauffer L, Galloway C, Solayman MH, Cavallari L. Cross-Validation of High-Resolution Melting Analysis-Based Genotyping Platform. Genet Test Mol Biomarkers 2017; 21:259-264. [DOI: 10.1089/gtmb.2016.0317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Taimour Langaee
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Lynda Stauffer
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Cheryl Galloway
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Mohamed H. Solayman
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Larisa Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
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Gobena D, Roig J, Galmarini C, Hulvey J, Lamour K. Genetic diversity ofPhytophthora capsiciisolates from pepper and pumpkin in Argentina. Mycologia 2017; 104:102-7. [DOI: 10.3852/11-147] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Gobena
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, Tennessee
| | | | | | - Jon Hulvey
- Department of Plant, Soil, and Insect Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville Tennessee
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Daems D, Knez K, Delport F, Spasic D, Lammertyn J. Real-time PCR melting analysis with fiber optic SPR enables multiplex DNA identification of bacteria. Analyst 2017; 141:1906-11. [PMID: 26881275 DOI: 10.1039/c5an02342d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fiber optic surface plasmon resonance (FO-SPR) technology was developed that enables simultaneous quantification and identification of multiple DNA targets on the same platform. The bioassay was based on the hybridization/melting of DNA-coated Au nanoparticles on the FO-SPR sensor when targets are present. The multiplex concept was successfully demonstrated on two related bacteria and for detection of multiple mutations in sequences. In conclusion, FO-SPR technology shows a great potential as a next generation in vitro diagnostics tool.
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Affiliation(s)
- D Daems
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - K Knez
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - F Delport
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - D Spasic
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
| | - J Lammertyn
- KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
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Xu JJ, Yao FR, Jiang M, Zhang YT, Guo F. High-resolution melting analysis for rapid and sensitive NOTCH1 screening in chronic lymphocytic leukemia. Int J Mol Med 2017; 39:415-422. [PMID: 28075457 DOI: 10.3892/ijmm.2017.2849] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/14/2016] [Indexed: 11/05/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a biological and clinical heterogeneous disease. Activating mutations of NOTCH1 have been implicated to be associated with adverse prognosis in CLL. The objective of the present study was to develop an effective high-resolution melting (HRM) assay for detecting NOTCH1 mutations. Genomic DNA (gDNA) extracted from 133 CLL patients was screened by HRM assay, and the results were compared with the data obtained using direct sequencing. The relative sensitivity of the HRM assay and direct sequencing was evaluated using diluted gDNA with different NOTCH1 mutational frequencies. The HRM assay was able to detect and discriminate samples with NOTCH1 mutations from the wild-type template in CLL. Eight of the 133 CLL patients (6.02%) were scored positively for NOTCH1 mutations in the HRM assay. The results of the NOTCH1 mutations detected by HRM analysis achieved 100% concordance with those determined from direct sequencing. HRM had a higher sensitivity (1%) and shorter turn-around time (TAT), compared to direct sequencing. In conclusion, the HRM assay developed by us was confirmed to be a rapid, sensitive, and promising approach for high-throughput prognostic NOTCH1 screening in CLL. It enables real-time NOTCH1 evaluation, which is of great significance in clinical practice and may facilitate the decision-making of clinicians in CLL.
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Affiliation(s)
- Jing-Jing Xu
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Fei-Rong Yao
- Department of Radiology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Min Jiang
- Department of Blood Transfusion, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - You-Tao Zhang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Feng Guo
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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PCR-Based Detection Methods for Single-Nucleotide Polymorphism or Mutation: Real-Time PCR and Its Substantial Contribution Toward Technological Refinement. Adv Clin Chem 2017; 80:45-72. [PMID: 28431642 DOI: 10.1016/bs.acc.2016.11.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) and single-nucleotide mutations result from the substitution of only a single base. The SNP or mutation can be relevant to disease susceptibility, pathogenesis of disease, and efficacy of specific drugs. It is important to detect SNPs or mutations clinically. Methods to distinguish/detect SNPs or mutations should be highly specific and sensitive. In this regard, polymerase chain reaction (PCR) has provided the necessary analytical performance for many molecular analyses. PCR-based methods for SNP/mutation detection are broadly categorized into two types-(1) polymorphic or mutant allele-directed specific analysis using primers matched with substituted nucleotide or using oligonucleotides to block or clamp the nontargeted template, and (2) melting curve analysis, which is combined with the real-time PCR techniques using hydrolysis probes, hybridization probes, or double-stranded DNA-binding fluorescent dyes. Innovative and novel approaches as well as technical improvements have made SNP- or mutation-detection methods increasingly more sophisticated. These advances include DNA/RNA preparation and subsequent amplification steps, and miniaturization of PCR instruments such that testing may be performed with relative ease in clinical laboratories or as a point-of-care test in clinical settings.
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Lee W, Chen Q, Fan X, Yoon DK. Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption. LAB ON A CHIP 2016; 16:4770-4776. [PMID: 27868127 PMCID: PMC5137248 DOI: 10.1039/c6lc01258b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
DNA lasers self-amplify optical signals from a DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target. In this work, we propose and demonstrate an optofluidic laser that has a single layer of DNA molecules as the gain material. A target DNA produces intensive laser emission comparable to existing DNA lasers, while any unnecessary fluorescence background is successfully suppressed. As a result, the target DNA can be detected with a single laser pulse, in a truly digital manner. Since the DNA molecules cover only a single layer on the surface of the laser microcavity, the DNA sample consumption is a few orders of magnitude lower than that of existing DNA lasers. Furthermore, the DNA molecules are stained by simply immersing the microcavity in the intercalating dye solution, and thus the proposed DNA laser is free of any complex dye-labelling process prior to analysis.
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Affiliation(s)
- Wonsuk Lee
- Graduate School of Nanoscience and Technology and KINC, KAIST, Daejeon, 305-701, Republic of Korea.
| | - Qiushu Chen
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave., Ann Arbor, MI 48109, USA.
| | - Xudong Fan
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave., Ann Arbor, MI 48109, USA.
| | - Dong Ki Yoon
- Graduate School of Nanoscience and Technology and KINC, KAIST, Daejeon, 305-701, Republic of Korea.
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Zhong WL, Wang L, Wu X, Zhang J, Chen XF, Zhang W, Dou X, Yu B. Development of Unlabeled Probe Based High-Resolution Melting Analysis for Detection of Filaggrin Gene Mutation c.3321delA. J Clin Lab Anal 2016; 30:892-896. [PMID: 27040325 PMCID: PMC6806714 DOI: 10.1002/jcla.21953] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/11/2016] [Accepted: 01/16/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Filaggrin gene (FLG) plays an important role in skin barrier function, and loss-of-function mutations of FLG have been shown to be a predisposing factor for atopic dermatitis (AD). The c.3321delA mutation is the most common FLG mutation in Chinese population. We aim to develop a rapid, cost-efficiency, and reliable closed-tube method that has not been described for the detection of c.3321delA mutation. METHODS Recombinant wild-type and mutant plasmids of c.3321delA mutation were constructed, heterozygous mutant plasmids were prepared by mixing the mutant plasmids and wild-type plasmids at 1:1 ratio. High-resolution melting analysis (HRMA) coupled with an unlabeled DNA probe was employed to identify the shift in melting temperature of the probe-template complex, which reflects the presence of c.3321delA mutation. RESULTS Unlabeled probe based HRMA was able to distinguish all three genotypes (wild-type, heterozygote, and mutant) of c.3321delA mutation. Then, we applied this method to genotype 1,317 clinical samples. Genotyping results obtained from unlabeled probe HRMA were 100% concordant with the results from direct sequencing. CONCLUSION We developed a fast and high-throughput method to detect the c.3321delA mutation.
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Affiliation(s)
- Wei-Long Zhong
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, P.R. China
- Division of Clinical Medicine, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Luo Wang
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, P.R. China
| | - Xia Wu
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, P.R. China
- Division of Clinical Medicine, Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Jie Zhang
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, P.R. China
| | - Xiao-Fan Chen
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, P.R. China
| | - Wei Zhang
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, P.R. China.
| | - Xia Dou
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, P.R. China.
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, P.R. China.
| | - Bo Yu
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, P.R. China.
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, P.R. China.
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Castan M, Ben Ali SE, Hochegger R, Ruppitsch W, Haslberger AG, Brandes C. Analysis of the genetic stability of event NK603 in stacked corn varieties using high-resolution melting (HRM) analysis and Sanger sequencing. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2749-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Immune dysregulation in patients with PTEN hamartoma tumor syndrome: Analysis of FOXP3 regulatory T cells. J Allergy Clin Immunol 2016; 139:607-620.e15. [PMID: 27477328 PMCID: PMC5292998 DOI: 10.1016/j.jaci.2016.03.059] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 01/25/2016] [Accepted: 03/22/2016] [Indexed: 12/14/2022]
Abstract
Background Patients with heterozygous germline mutations in phosphatase and tensin homolog deleted on chromosome 10 (PTEN) experience autoimmunity and lymphoid hyperplasia. Objectives Because regulation of the phosphoinositide 3-kinase (PI3K) pathway is critical for maintaining regulatory T (Treg) cell functions, we investigate Treg cells in patients with heterozygous germline PTEN mutations (PTEN hamartoma tumor syndrome [PHTS]). Methods Patients with PHTS were assessed for immunologic conditions, lymphocyte subsets, forkhead box P3 (FOXP3)+ Treg cell levels, and phenotype. To determine the functional importance of phosphatases that control the PI3K pathway, we assessed Treg cell induction in vitro, mitochondrial depolarization, and recruitment of PTEN to the immunologic synapse. Results Autoimmunity and peripheral lymphoid hyperplasia were found in 43% of 79 patients with PHTS. Immune dysregulation in patients with PHTS included lymphopenia, CD4+ T-cell reduction, and changes in T- and B-cell subsets. Although total CD4+FOXP3+ Treg cell numbers are reduced, frequencies are maintained in the blood and intestine. Despite pathogenic PTEN mutations, the FOXP3+ T cells are phenotypically normal. We show that the phosphatase PH domain leucine-rich repeat protein phosphatase (PHLPP) downstream of PTEN is highly expressed in normal human Treg cells and provides complementary phosphatase activity. PHLPP is indispensable for the differentiation of induced Treg cells in vitro and Treg cell mitochondrial fitness. PTEN and PHLPP form a phosphatase network that is polarized at the immunologic synapse. Conclusion Heterozygous loss of function of PTEN in human subjects has a significant effect on T- and B-cell immunity. Assembly of the PTEN-PHLPP phosphatase network allows coordinated phosphatase activities at the site of T-cell receptor activation, which is important for limiting PI3K hyperactivation in Treg cells despite PTEN haploinsufficiency.
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Boroumand M, Ziaee S, Zarghami N, Anvari MS, Cheraghi S, Abbasi SH, Jalali A, Pourgholi L. The Kalirin Gene rs9289231 Polymorphism as a Novel Predisposing Marker for Coronary Artery Disease. Lab Med 2016; 45:302-8. [PMID: 25316661 DOI: 10.1309/lmls813zdphrfluu] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Atherosclerosis is the leading cause of death and disability worldwide. Genetic variations play a major role in the process of atherosclerosis. Recently, rs9289231 genetic variations of the Kalirin gene (KALRN) on chromosome 3q21.2 have been introduced as potential genetic markers for coronary artery disease (CAD). OBJECTIVE In this case-control study, we investigated the association between genetic susceptibility to CAD and rs9289231 G/T polymorphism, located on the KALRN gene, in an Iranian population. METHODS Our cohort consisted of 1486 individuals undergoing coronary angiography. Of these, we considered the 1007 patients with CAD to be case individuals and the 479 individuals with normal coronary conditions to be control individuals. We performed single-nucleotide polymorphism (SNP) genotyping via the high resolution melting (HRM) technique. RESULTS Our data showed that the minor allele (G) frequency of rs9289231 SNP was higher in our CAD group than that in our control group (odds ratio, 1:37; confidence interval, 1.07-1.74; P = .01). The results of our data analysis highlighted a genetic association between rs9289231 polymorphism and severity and development of CAD. CONCLUSIONS We consider the GG genotype and the G allele of rs9289231 polymorphism of KALRN to be genetic risk factors for CAD in an Iranian population, especially in early-stage atherosclerotic vascular disease.
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Affiliation(s)
- Mohammadali Boroumand
- Department of Pathology and Laboratory Medicine and Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shayan Ziaee
- Department of Molecular Pathology, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nosratollah Zarghami
- Department of Medical Biotechnology, Tabriz University of Medical Science, Tabriz, Iran
| | - Maryam Sotudeh Anvari
- Department of Pathology and Laboratory Medicine and Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Cheraghi
- Department of Molecular Pathology, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Arash Jalali
- Department of Molecular Pathology, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Pourgholi
- Department of Molecular Pathology, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
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Ramezanzadeh M, Salehi M, Salehi R. Assessment of high resolution melt analysis feasibility for evaluation of beta-globin gene mutations as a reproducible, cost-efficient and fast alternative to the present conventional method. Adv Biomed Res 2016; 5:71. [PMID: 27169102 PMCID: PMC4854030 DOI: 10.4103/2277-9175.180640] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022] Open
Abstract
Background: Beta-thalassemia is the most prevalent monogenic disease throughout the world. It was the first genetic disorder nominated for nation-wide prevention programs involving population screening for heterozygotes and prenatal diagnosis (PND) in Iran. Due to the high prevalence of beta-thalassemia, the shift from conventional mutation detection methods to more recently developed techniques based on novel innovative technologies are essential. We aimed to develop a real-time polymerase chain reaction (PCR) based protocol using high resolution melting (HRM) analysis for diagnosis of common beta-thalassemia mutations. Materials and Methods: Forty DNA samples extracted from peripheral blood of suspected beta-thalassemia carriers participated in this study were subjected to amplification refractory mutation system (ARMS). We then used 20 of these samples for HRM optimization. When 100% sensitivity and specificity was obtained with HRM procedure, we applied the technique for mutation detection on another remaining 20 samples as thalassemia cases with unknown mutations (detected mutations with ARMS-PCR kept confidential). Finally, the HRM procedure applied on 2 chorionic villous sample (CVS) biopsied from 12 weeks gestational age pregnant women for routine PND analysis. Results: In the first step of study, Fr 8/9 (+G), IVSI-1 (G > A), IVSI-5 (G > C), IVSI-110 (G > A), and CD44 (−C) mutations were diagnosed in samples under study using ARMS-PCR technique. Finally, the HRM procedure applied on 20 unknown samples and 2 CVS The results of HRM were in complete concordance with ARMS and confirmed by sequencing. Conclusions: The advantages of HRM analysis over conventional methods is high throughput, rapid, accurate, cost-effective, and reproducible.
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Affiliation(s)
- Mahboubeh Ramezanzadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansour Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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