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Li H, Fang Y, Chen Y, Lin Y, Fang Z, Lin Z, Xie H, Zhang Z. A novel AllGlo probe-quantitative PCR method for detecting single nucleotide polymorphism in CYP2C19 to evaluate the antiplatelet activity of clopidogrel. Sci Rep 2024; 14:2358. [PMID: 38286794 PMCID: PMC10825217 DOI: 10.1038/s41598-024-52540-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
CYP2C19 gene has multiple single nucleotide polymorphism (SNP), which is the major determinant for clopidogrel treatment responses. Therefore, CYP2C19 SNP detection is essential for predicting clopidogrel efficacy. Currently, there is still no quick and effective method for routine detection of common CYP2C19 SNPs in clinical laboratories, which is critically needed prior to clopidogrel treatment. AllGlo™ based quantitative PCR was used to develop a novel genotyping method for CYP2C19 SNP detection, termed CyPAllGlo. The performance of CyPAllGlo was compared with that of the commonly used fluorescence in situ hybridization (FISH) method, and the data was verified by DNA sequencing. CyPallGlo was used to identify CYP2C19 polymorphisms in 363 patients with coronary heart disease. The univariate analysis was used to access the antiplatelet efficacy of clopidogrel in patients. The associations between CYP2C19 polymorphisms and clopidogrel efficacy were analyzed. Using CyPAllGlo to detect CYP2C19*2 and CYP2C19*3 alleles was highly specific and fast. The detection limit was approximately 0.07 µg/µl and 0.7 µg/µl for CYP2C19*2 and CYP2C19*3, respectively. The consistency between FISH and CyPAllGlo were 98.07% for CYP2C19*2 and 99.17% for CYP2C19*3. DNA sequencing showed that the accuracy of CyPAllGlo was 100%. The analysis time for the whole CyPAllGlo procedure was approximately 60 min. Univariate analysis showed that the anticoagulation efficacy of clopidogrel was related to patient age, CYP2C19 genotype, metabolic phenotype, and LDL level. The logistic regression analysis showed that the genotype of CYP2C19 and metabolic phenotype was the two risk factors for clopidogrel antiplatelet ineffectiveness. This novel CyPAllGlo is a rapid and accurate method for detection of CYP2C19 SNP. The specificity and consistency of CyPAllGlo are comparable with that of widely used DNA sequencing. These findings provide valuable rapid method for predicting clopidogrel efficacy, which can be quickly translated to improve personalized precision medicine for coronary heart disease treatment.
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Affiliation(s)
- Hongwei Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Zhengzhou Key Laboratory for In Vitro Diagnosis of Hypertensive Disorders of Pregnancy, Zhengzhou, 450052, China
| | - Yizhen Fang
- Department of Clinical Laboratory, Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Precision Medicine for Cardiovascular Disease, Xiamen, 361009, China
| | - Yongquan Chen
- Medical Laboratory Center, Xiamen Humanity Hospital, Fujian Medical University, No. 3777, Xianyue Road, Huli District, Xiamen, 361009, Fujian, China
- Xiamen Key Laboratory for Biomarkers and Translational Medicine, Xiamen, 361009, China
| | - Yuning Lin
- Medical Laboratory Center, Xiamen Humanity Hospital, Fujian Medical University, No. 3777, Xianyue Road, Huli District, Xiamen, 361009, Fujian, China
- Xiamen Key Laboratory for Biomarkers and Translational Medicine, Xiamen, 361009, China
| | - Zanxi Fang
- Department of Medical Laboratory Center, Xiamen University Affiliated Zhongshan Hospital, Xiamen, 361004, China
| | - Zhiyuan Lin
- Department of Clinical Laboratory, Xiamen Hospital of Traditional Chinese Medicine, Xiamen, 361001, China
| | - Huabin Xie
- Department of Clinical Laboratory, Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
- Xiamen Key Laboratory of Precision Medicine for Cardiovascular Disease, Xiamen, 361009, China.
| | - Zhongying Zhang
- Medical Laboratory Center, Xiamen Humanity Hospital, Fujian Medical University, No. 3777, Xianyue Road, Huli District, Xiamen, 361009, Fujian, China.
- Xiamen Key Laboratory for Biomarkers and Translational Medicine, Xiamen, 361009, China.
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2
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [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: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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3
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Okumura S, Ohsato Y. A novel rapid detection method for a single-nucleotide substitution mutation derived from canine urothelial and prostatic carcinoma cells present in small amounts in urine sediments. PLoS One 2023; 18:e0286229. [PMID: 37733700 PMCID: PMC10513316 DOI: 10.1371/journal.pone.0286229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
For early detection of canine urothelial and prostatic carcinoma, we intend to develop and commercialize a simple and rapid detection method for the BRAF V595E mutation, a known mutation in this cancer. Detection of the single-nucleotide substitution in cancer cells contained in urine sediments is effective for early cancer diagnosis. However, urine sediment also contains many normal cells, and when there is a small relative composition of cancer cells, the mutation is difficult to detect by conventional methods other than next-generation sequencing. Our new detection method enables reliable discrimination with the same labor and cost as the PCR method. We compared the results of our new method with the results of the conventional Sanger method for 38 canine urine sediment samples, and the results of 34 samples were consistent between both methods. The remaining four results were all determined to be negative by the Sanger method and positive by our new method. For these four samples, the ratio of the mutated gene to the wild-type gene was estimated using a third-generation sequencer, and the ratio of the mutated gene was 0.1%-1.4%. We postulate that the Sanger method gave a negative result because of the low abundance of the mutated gene in these samples, proving the high sensitivity of our new method.
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Affiliation(s)
- Shiro Okumura
- Biotechnology and Food Research Institute, Fukuoka Industrial Technology Center, Kurume, Fukuoka, Japan
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4
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Chumworathayee W, Munkongdee T, Buasuwan N, Chaichompoo P, Svasti S. Diagnosis of α-thalassaemia by colorimetric gap loop mediated isothermal amplification. Sci Rep 2023; 13:9612. [PMID: 37311778 DOI: 10.1038/s41598-023-36676-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
α-Thalassaemia is an inherited haemoglobin disorder that results from the defective synthesis of α-globin protein. Couples whom both carry the α-thalassaemia 1 gene are at risk of having a foetus with the most severe thalassaemia, Hb Bart's hydrops fetalis, with a risk of maternal mortality. However, haematological parameters alone cannot distinguish between a α-thalassaemia 1 carrier and a homozygous α-thalassaemia 2, in which one α-globin gene has been deleted on each chromosome. A rapid and accurate molecular detection assay is essential for prevention of the disease in populations where α-thalassaemia 1 is common. Multiplex Gap-PCR analysis is widely used for diagnosis of α-thalassaemia. However, the technique requires a thermocycler and post-amplification processing, which limits its application in primary care or in rural areas in developing countries. Loop mediated isothermal amplification (LAMP) amplifies target DNA at a constant temperature and does not require a thermocycler. This study developed a colorimetric Gap-LAMP using malachite green to allow naked eye visualization of two deletional α-thalassaemia 1 commonly found in Asian populations, the Southeast Asian type (--SEA) and the Thai type (--THAI) deletions. The Gap-LAMP was performed on DNA samples from 410 individuals carrying various α-thalassaemia gene defects with 100% concordance with conventional Gap-PCR analysis. This method eliminates post-amplification processing or the use of expensive sophisticated equipment and allows screening large populations for the prevention and control of α-thalassaemia.
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Affiliation(s)
- Worakawee Chumworathayee
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology, Thanyaburi, Pathumthani, Thailand
| | - Thongperm Munkongdee
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Nattrika Buasuwan
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Pornthip Chaichompoo
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand.
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
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5
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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Liang J, Zeng J, Huang X, Zhu T, Gong Y, Dong C, Wang X, Zhao L, Xie L, Liang K, Tan Q, Cui Y, Kong B, Hui W. Super-assembly of integrated gold magnetic assay with loop-mediated isothermal amplification for point-of-care testing. NANO RESEARCH 2022; 16:1242-1251. [PMID: 35966151 PMCID: PMC9362447 DOI: 10.1007/s12274-022-4692-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED With the increasing global threat of various diseases and infections, it is essential to develop a fast, low-cost, and easy-to-use point-of-care testing (POCT) system for inspections at all levels of medical institutions and self-examination at home. In this work, gold magnetic nanoparticles (GMNPs) are used as the key material, and a rapid visual detection method is designed through integrating loop-mediated isothermal amplification (LAMP) and lateral flow assay (LFA) biosensor for detecting a variety of analytes which includes whole blood, buccal swabs, and DNA. It is worth to note that the proposed method does not need DNA extraction. Furthermore, uracil DNA glycosylase (UDG) is employed to eliminate carrier contamination for preventing false positive results. The whole detection process can be finished within 25 min. The accuracy of detection is measured by assessing the polymorphisms of the methylenetetrahydrofolate reductase (MTHFR) C677T. The detection limit of the newly developed extraction-free detection system for MTHFR C677T is 0.16 ng/μL. A preliminary clinical study of the proposed method is carried out by analyzing 600 clinical samples (including 200 whole blood samples, 100 buccal swabs, and 300 genomic DNA samples). The results indicate that the proposed method is 100% consistent with the sequencing results which provides a new choice for POCT and shows a broad application prospect in all levels of medical clinics and at home. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (details for MTHFR C677T primer sequences, the cell count results of samples at different dilution ratios, genotyping results and frequency samples, a Hardy-Weinberg equilibrium test, the sensitivity of the system, detection results of multiple samples, and optimization of the system) is available in the online version of this article at 10.1007/s12274-022-4692-9.
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Affiliation(s)
- Jianping Liang
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Jie Zeng
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200438 China
| | - Xiaojuan Huang
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Tengteng Zhu
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Yonglong Gong
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Chen Dong
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Xiangrong Wang
- The College of life science, Northwest University, Xi’an, 710069 China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi’an, 710069 China
| | - Lingzhi Zhao
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Lei Xie
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200438 China
| | - Kang Liang
- School of Chemical Engineering, Graduate School of Biomedical Engineering, and Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052 Australia
| | - Qiongxiang Tan
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Yali Cui
- The College of life science, Northwest University, Xi’an, 710069 China
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi’an, 710077 China
| | - Biao Kong
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200438 China
| | - Wenli Hui
- The College of life science, Northwest University, Xi’an, 710069 China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, 710069 China
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7
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Zhang T, Zhao W, Zhao W, Si Y, Chen N, Chen X, Zhang X, Fan L, Sui G. Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Anal Chem 2021; 93:16184-16193. [PMID: 34818890 PMCID: PMC8672426 DOI: 10.1021/acs.analchem.1c04065] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022]
Abstract
Nowadays, rapid and accurate diagnosis of respiratory tract viruses is an urgent need to prevent another epidemic outbreak. To overcome this problem, we have developed a clustered, regularly interspaced short palindromic repeats (CRISPR) loop mediated amplification (LAMP) technology to detect influenza A virus, influenza B virus, respiratory syncytial A virus, respiratory syncytial B virus, and severe acute respiratory syndrome coronavirus 2, including variants of concern (B.1.1.7), which utilized CRISPR-associated protein 12a (Cas12a) to advance LAMP technology with the sensitivity increased 10 times. To reduce aerosol contamination in CRISPR-LAMP technology, an uracil-DNA-glycosylase-reverse transcription-LAMP system was also developed which can effectively remove dUTP-incorporated LAMP amplicons. In vitro Cas12a cleavage reaction with 28 crRNAs showed that there were no position constraints for Cas12a/CRISPR RNA (crRNA) recognition and cleavage in LAMP amplicons, and even the looped position of LAMP amplicons could be effectively recognized and cleaved. Wild-type or spike N501Y can be detected with a limit of detection of 10 copies/μL (wild-type) even at a 1% ratio level on the background (spike N501Y). Combining UDG-RT-LAMP technology, CRISPR-LAMP design, and mutation detection design, we developed a CRISPR-LAMP detection platform that can precisely diagnose pathogens with better stability and significantly improved point mutation detection efficiency.
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Affiliation(s)
- Tong Zhang
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Wei Zhao
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Wang Zhao
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Yuying Si
- Department
of Clinical Laboratory, Shanghai East Hospital, School of Medicine, Tong Ji University, 150 Ji Mo Road, Shanghai 200120, P. R. China
| | - Nianzhen Chen
- Department
of Clinical Laboratory, Shanghai East Hospital, School of Medicine, Tong Ji University, 150 Ji Mo Road, Shanghai 200120, P. R. China
| | - Xi Chen
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Xinlian Zhang
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
| | - Lieying Fan
- Department
of Clinical Laboratory, Shanghai East Hospital, School of Medicine, Tong Ji University, 150 Ji Mo Road, Shanghai 200120, P. R. China
| | - Guodong Sui
- Shanghai
Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3),
Department of Environmental Science and Engineering, Fudan University, 2205 Songhu Road, Shanghai 200433, P. R. China
- Department
of Medical Microbiology and Parasitology, School of Basic Medical
Sciences, Fudan University, Shanghai 200032, P. R. China
- Jiangsu
Collaborative Innovation Center of Atmospheric Environment and Equipment
Technology (CICAEET), Nanjing University
of Information Science & Technology, Nanjing 210044, PR China
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8
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Higgins O, Smith TJ. Loop-Primer Endonuclease Cleavage-Loop-Mediated Isothermal Amplification Technology for Multiplex Pathogen Detection and Single-Nucleotide Polymorphism Identification. J Mol Diagn 2021; 22:640-651. [PMID: 32409120 DOI: 10.1016/j.jmoldx.2020.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/15/2019] [Accepted: 02/03/2020] [Indexed: 12/27/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) provides effective diagnostic technology for infectious disease pathogen identification and is compatible with inexpensive instrumentation for use in disease-prevalent developing regions. However, simultaneous multiple-target detection and single-nucleotide polymorphism (SNP) identification, essential properties of nucleic acid diagnostics, are difficult to achieve using LAMP. This study introduces loop-primer endonuclease cleavage (LEC)-LAMP, a singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification. We developed a singleplex LEC-LAMP Neisseria meningitidis assay that demonstrated complete analytical specificity and a limit of detection of 3.1 genome copies per reaction. Small-scale clinical testing of this assay demonstrated 100% diagnostic specificity and sensitivity when assessed with anonymized DNA extracts from confirmed cases of bacterial meningitis infection. The single-base specificity of this assay indicated effective SNP identification properties when challenged with DNA templates containing SNPs located within a specific six-base region. This assay was modified to generate an allele-specific LEC-LAMP N. meningitidis assay that successfully demonstrated single-tube differentiation of wild-type and mutant allele templates. The singleplex assay was further modified to generate a multiplex LEC-LAMP assay that successfully demonstrated simultaneous multiple-target detection of three bacterial targets, N. meningitidis, Streptococcus pneumonia, and Hemophilus influenzae. LEC-LAMP is the first report of single-tube, real-time, singleplex or multiplex LAMP technology with single-base specificity for variable SNP identification.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | - Terry J Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland
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9
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Zhang C, Zheng T, Wang H, Chen W, Huang X, Liang J, Qiu L, Han D, Tan W. Rapid One-Pot Detection of SARS-CoV-2 Based on a Lateral Flow Assay in Clinical Samples. Anal Chem 2021; 93:3325-3330. [PMID: 33570399 PMCID: PMC7885334 DOI: 10.1021/acs.analchem.0c05059] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/05/2021] [Indexed: 01/01/2023]
Abstract
Rapid tests for pathogen identification and spread assessment are critical for infectious disease control and prevention. The control of viral outbreaks requires a nucleic acid diagnostic test that is sensitive and simple and delivers fast and reliable results. Here, we report a one-pot direct reverse transcript loop-mediated isothermal amplification (RT-LAMP) assay of SARS-CoV-2 based on a lateral flow assay in clinical samples. The entire contiguous sample-to-answer workflow takes less than 40 min from a clinical swab sample to a diagnostic result without professional instruments and technicians. The assay achieved an accuracy of 100% in 12 synthetic and 12 clinical samples compared to the data from PCR-based assays. We anticipate that our method will provide a universal platform for rapid and point-of-care detection of emerging infectious diseases.
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Affiliation(s)
- Chao Zhang
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Tingting Zheng
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hua Wang
- Department
of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei Chen
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Xiaoye Huang
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Jianqi Liang
- Clinical
Laboratory, Central Hospital of Loudi, Loudi, Hunan 417099, China
| | - Liping Qiu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Da Han
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Weihong Tan
- Institute
of Molecular Medicine (IMM), Shanghai Key Laboratory for Nucleic Acid
Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and
Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute
of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy
of Sciences, Hangzhou, Zhejiang 310018, China
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10
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Varona M, Anderson JL. Advances in Mutation Detection Using Loop-Mediated Isothermal Amplification. ACS OMEGA 2021; 6:3463-3469. [PMID: 33585732 PMCID: PMC7876693 DOI: 10.1021/acsomega.0c06093] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 05/25/2023]
Abstract
Detection of mutations and single-nucleotide polymorphisms is highly important for diagnostic applications. Loop-mediated isothermal amplification (LAMP) is a powerful technique for the rapid and sensitive detection of nucleic acids. However, LAMP traditionally does not possess the ability to resolve single-nucleotide differences within the target sequence. Because of its speed and isothermal nature, LAMP is ideally suited for point-of-care applications in resource-limited settings. Recently, different approaches have been developed and applied to enable single-nucleotide differentiation within target sequences. This Mini-Review highlights advancements in mutation detection using LAMP. Methods involving primer design and modification to enable sequence differentiation are discussed. In addition, the development of probe-based detection methods for mutation detection are also covered.
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11
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Arjuna S, Venkataram R, Dechamma PN, Chakraborty G, Babu N, D'Cruz A, Hosmane GB, Chakraborty A. Non-invasive detection of EGFR mutations by cell-free loop-mediated isothermal amplification (CF-LAMP). Sci Rep 2020; 10:17559. [PMID: 33067539 PMCID: PMC7568567 DOI: 10.1038/s41598-020-74689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022] Open
Abstract
Targeting epidermal growth factor receptor (EGFR) through tyrosine kinase inhibitors (TKI) is a successful therapeutic strategy in non-small cell lung cancer. However, the response to TKI therapy depends on specific activating and acquired mutations in the tyrosine kinase domain of the EGFR gene. Therefore, confirming the EGFR status of patients is crucial, not only for determining the eligibility, but also for monitoring the emergence of mutations in patients under TKI therapy. In this study, our aim was to develop a cost effective, yet sensitive, technique that allows the detection of therapeutically-relevant EGFR hotspot mutations at isothermal conditions in a non-invasive manner. Previously, we developed an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for screening germline and somatic de novo T790M EGFR mutation in lung cancer patients. In this study, we used cell free DNA as a template in AS-LAMP assay (CF-LAMP) for non-invasive detection of two hotspot EGFR mutations (T790M, and L858R) and compared its efficiency with ultrasensitive droplet digital PCR (ddPCR) assay. The results of CF-LAMP assay were consistent with those obtained in ddPCR assay, indicating the robustness of the method. CF-LAMP may serve as a valuable and cost-effective alternative for liquid biopsy techniques used in molecular diagnosis of non-small cell lung cancer.
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Affiliation(s)
- Srividya Arjuna
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Rajesh Venkataram
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Pandyanda Nanjappa Dechamma
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Gunimala Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Nishith Babu
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India
| | - Audrey D'Cruz
- Department of Health Dentistry, A B Shetty Memorial Institute of Dental Sciences, Nitte (Deemed to be University), Mangaluru, India
| | - Giridhar Belur Hosmane
- Department of Pulmonary Medicine, K S Hegde Medical Academy, Nitte (Deemed to be University), Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), Nitte (Deemed to be University), Kotekar-Beeri Road, Deralakatte, Mangaluru, 575018, India.
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12
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Drogou C, Sauvet F, Erblang M, Detemmerman L, Derbois C, Erkel MC, Boland A, Deleuze JF, Gomez-Merino D, Chennaoui M. Genotyping on blood and buccal cells using loop-mediated isothermal amplification in healthy humans. ACTA ACUST UNITED AC 2020; 26:e00468. [PMID: 32461926 PMCID: PMC7240324 DOI: 10.1016/j.btre.2020.e00468] [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: 02/07/2020] [Revised: 03/23/2020] [Accepted: 05/10/2020] [Indexed: 12/11/2022]
Abstract
Genetic variations contribute to phenotypic individual vulnerabilities to sleep debt. LAMP-MC is a recently developed method to characterize Single Nucleotide Polymorphism. Detection is performed directly from whole blood or buccal cells. LAMP-MC method produced specific melting curves for 5 sleep debt-related SNPs. High concordance of results was observed between LAMP-MC and Taqman referent method.
Genetic variations contribute to phenotypic individual vulnerabilities to sleep debt, particularly for five single nucleotide polymorphisms (SNPs). Loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) is a recently developed method to characterize SNPs. The aim of present study was to evaluate the LAMP-MC method on blood and buccal cells for detection of five SNPs of interest in healthy humans. We first analyzed signals obtained from LAMP-MC method on 42 samples. Then we compared the results with those of referent TaqMan method. The LAMP-MC method produced specific melting curves for the five SNPs. A high concordance of genotyping results was observed between the two methods for rs5751876_ADORA2A, rs1800629_TNF-α, rs73598374_ADA and rs228697_PER3 in blood and saliva (Cohen’s kappa coefficient >0.80). A good agreement ( = 0.61) was observed for rs4680_COMT in blood only. LAMP-MC is a simple and reliable method to study genetic influences on health, sleep debt-related performance impairments and countermeasures.
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Affiliation(s)
- Catherine Drogou
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | - Fabien Sauvet
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | - Mégane Erblang
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | | | - Céline Derbois
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Marie Claire Erkel
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Jean François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Danielle Gomez-Merino
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
| | - Mounir Chennaoui
- Institut de Recherche Biomédicale des Armées (IRBA), Brétigny sur Orge, France.,Université de Paris, Equipe d'Accueil VIgilance FAtigue et SOmmeil (VIFASOM), EA 7330, Paris, France
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13
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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14
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Bui TT, Moi ML, Morita K, Hasebe F. Development of Universal and Lineage-Specific Primer Sets for Rapid Detection of the Zika Virus (ZIKV) in Blood and Urine Samples Using One-Step Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). Jpn J Infect Dis 2019; 73:153-156. [PMID: 31666491 DOI: 10.7883/yoken.jjid.2019.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Zika is a mosquito-borne disease that has been posing a significant threat to public health in recent years. The Zika virus (ZIKV), the causative agent of this disease, is classified into 2 distinct genetic lineages, namely Asian and African. While molecular nucleic acid analysis methods have been shown to be useful for the diagnosis of ZIKV infection, the development of assays based on one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) offers several advantages, such as shorter incubation times, ease of handling, and rapid detection. In this study, a universal LAMP primer set was developed to target conserved sequences of known ZIKV lineages. Additionally, the Af7462 and As1788 primer sets were designed based on LAMP-based single-nucleotide polymorphism (SNPs) typing for the specific detection of the African and Asian lineages. The developed RT-LAMP assays could specifically detect the African and Asian lineages of ZIKV, with a detection limit ranging from 0.17 FFU/mL to 2.3×102 FFU/mL. As ZIKV viremia ranges between 102 to 106 PFU/mL or 103 to 106 copies/mL, the data indicate that the viremia range of clinical samples is within the detection range of our assay. Due to the high specificity and sensitivity, as well as the ease of use of our assay, it could potentially be used for early clinical diagnosis applications.
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Affiliation(s)
- Thu Thuy Bui
- Department of Virology, Institute of Tropical Medicine, Nagasaki University
| | - Meng Ling Moi
- Department of Virology, Institute of Tropical Medicine, Nagasaki University
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University
| | - Futoshi Hasebe
- Vietnam Research station, Center for Infectious Disease Research in Asia and Africa, Institute of Tropical Medicine, Nagasaki University
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15
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Tu YK, Lin YC, Feng YW, Tseng YY, Chen HW. Visual, sensitive and rapid event-specific detection of genetically modified potato EH92-527-1 by loop-mediated isothermal amplification method. Biosci Biotechnol Biochem 2019; 84:43-52. [PMID: 31495297 DOI: 10.1080/09168451.2019.1661766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To date, studies on the application of loop-mediated isothermal amplification (LAMP) in the detection of genetically modified organisms (GMOs) are stably increasing and demonstrates LAMP is a potential and promising method for on spot identification of GMOs. However, little information is known for detection of GM potato events by LAMP. In this report, we developed an optimized and visual LAMP assay with high specificity and sensitivity to rapidly amplify genomic DNA of potato EH92-527-1 within 45 min. The limit of detection of LAMP in our study is 10-fold higher than the conventional PCR. Furthermore, LAMP products can be directly observed via naked eyes by addition of SYBR Green I without gel electrophoresis analysis and PCR-based equipment. Therefore, the LAMP assay developed in this paper provides an efficient, convenient and cost-effective tool for the detection of GM potato EH92-527-1.
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Affiliation(s)
- Yuan-Kai Tu
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
| | - Yen-Chun Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
| | - Yu-Wei Feng
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
| | - Yeu-Yang Tseng
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Han-Wei Chen
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung City, Taiwan
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16
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Malpartida-Cardenas K, Rodriguez-Manzano J, Yu LS, Delves MJ, Nguon C, Chotivanich K, Baum J, Georgiou P. Allele-Specific Isothermal Amplification Method Using Unmodified Self-Stabilizing Competitive Primers. Anal Chem 2018; 90:11972-11980. [PMID: 30226760 PMCID: PMC6195307 DOI: 10.1021/acs.analchem.8b02416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022]
Abstract
Rapid and specific detection of single nucleotide polymorphisms (SNPs) related to drug resistance in infectious diseases is crucial for accurate prognostics, therapeutics and disease management at point-of-care. Here, we present a novel amplification method and provide universal guidelines for the detection of SNPs at isothermal conditions. This method, called USS-sbLAMP, consists of SNP-based loop-mediated isothermal amplification (sbLAMP) primers and unmodified self-stabilizing (USS) competitive primers that robustly delay or prevent unspecific amplification. Both sets of primers are incorporated into the same reaction mixture, but always targeting different alleles; one set specific to the wild type allele and the other to the mutant allele. The mechanism of action relies on thermodynamically favored hybridization of totally complementary primers, enabling allele-specific amplification. We successfully validate our method by detecting SNPs, C580Y and Y493H, in the Plasmodium falciparum kelch 13 gene that are responsible for resistance to artemisinin-based combination therapies currently used globally in the treatment of malaria. USS-sbLAMP primers can efficiently discriminate between SNPs with high sensitivity (limit of detection of 5 × 101 copies per reaction), efficiency, specificity and rapidness (<35 min) with the capability of quantitative measurements for point-of-care diagnosis, treatment guidance, and epidemiological reporting of drug-resistance.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jesus Rodriguez-Manzano
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Ling-Shan Yu
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Michael J. Delves
- Department
of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Chea Nguon
- National
Centre for Parasitology, Entomology and
Malaria Control, Phnom Penh 12302, Cambodia
| | - Kesinee Chotivanich
- Department
of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Jake Baum
- Department
of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Pantelis Georgiou
- Centre
for Bio-Inspired Technology, Department of Electrical and Electronic
Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
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17
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Zhang C, Liu X, Yao Y, Liu K, Hui W, Zhu J, Dou Y, Hua K, Peng M, Wang Z, Vermorken AJM, Cui Y. Genotyping of Multiple Clinical Samples with a Combined Direct PCR and Magnetic Lateral Flow Assay. iScience 2018; 7:170-179. [PMID: 30245369 PMCID: PMC6153416 DOI: 10.1016/j.isci.2018.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/19/2018] [Accepted: 09/05/2018] [Indexed: 02/09/2023] Open
Abstract
Developing a sensitive, low-cost, and easy-to-use point-of-care testing system for genotyping is important for informing treatment decisions and predicting the risk of underlying diseases. Conventional methods normally require complex operational procedures as well as expensive and sophisticated instruments. Here, we report a general approach that enables us to detect the genotype of multiple sample types directly without DNA purification. Moreover, the PCR results can be further quantitatively analyzed based on a magnetic lateral flow assay (MLFA) system, which avoids multiple steps needed for conventional nucleic acid biosensors. As a demonstration, we show that three genotypes of aldehyde dehydrogenase 2 (ALDH2) can be identified using a small volume of sample with an accuracy of 100% and a sensitivity of 1.0 × 102 cells/μL, which are better than those of the gold standard methods. We believe that the direct PCR-MLFA system represents a significant advance toward the development of portable, sensitive biomedical platforms.
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Affiliation(s)
- Chao Zhang
- College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaonan Liu
- College of Life Sciences, Northwest University, Xi'an, China
| | - Yao Yao
- Shaanxi Provincial Engineering Research Center of Nano-Biomedical Detection, Xi'an, China
| | - Kewu Liu
- College of Life Sciences, Northwest University, Xi'an, China
| | - Wenli Hui
- College of Life Sciences, Northwest University, Xi'an, China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center of Nano-Biomedical Detection, Xi'an, China
| | - Yaling Dou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Kai Hua
- College of Life Sciences, Northwest University, Xi'an, China
| | - Mingli Peng
- Shaanxi Provincial Engineering Research Center of Nano-Biomedical Detection, Xi'an, China
| | - Zuankai Wang
- Department of Mechanical Engineering, City University of Hong Kong, Hong Kong, China.
| | | | - Yali Cui
- College of Life Sciences, Northwest University, Xi'an, China; Shaanxi Provincial Engineering Research Center of Nano-Biomedical Detection, Xi'an, China.
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18
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Liu X, Zhang C, Zhao M, Liu K, Li H, Li N, Gao L, Yang X, Ma T, Zhu J, Hui W, Hua K, Cui Y. A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types. Biosens Bioelectron 2018; 115:70-76. [PMID: 29803102 PMCID: PMC7126597 DOI: 10.1016/j.bios.2018.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/06/2018] [Accepted: 05/10/2018] [Indexed: 01/10/2023]
Abstract
Genotyping of single nucleotide polymorphisms (SNPs) in point-of-care (POC) settings could be further improved through simplifying the treatment of samples. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on direct loop-mediated isothermal amplification (LAMP) without DNA extraction, known as Direct-LAMP. Samples from various sources (including whole blood, dried blood spot, buccal swab and saliva), treated with NaOH, can be used directly in amplification. The turnaround time was about 30 min from sample collection to provision of results. The accuracy was evaluated by assessing the polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and aldehyde dehydrogenase-2 (ALDH2) Glu504Lys, which are better known for their critical role in folate and ethanol metabolism, respectively. Completely consistent genotyping results reveal that Direct-LAMP is generally concordant with sequencing. This system can serve as a very promising platform in the fields of disease predisposition, drug metabolism and personalized medicine.
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Affiliation(s)
- Xiaonan Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Chao Zhang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mengye Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Kewu Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Hang Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ningning Li
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Linlin Gao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xuemin Yang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ting Ma
- Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi'an 710077, China
| | - Wenli Hui
- College of Life Sciences, Northwest University, Xi'an 710069, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China
| | - Kai Hua
- College of Life Sciences, Northwest University, Xi'an 710069, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China.
| | - Yali Cui
- College of Life Sciences, Northwest University, Xi'an 710069, China; Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi'an 710077, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China.
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19
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Cai S, Jung C, Bhadra S, Ellington AD. Phosphorothioated Primers Lead to Loop-Mediated Isothermal Amplification at Low Temperatures. Anal Chem 2018; 90:8290-8294. [PMID: 29968462 DOI: 10.1021/acs.analchem.8b02062] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an extremely powerful tool for the detection of nucleic acids with high sensitivity and specificity. However, LAMP shows optimal performance at around 65 °C, which limits applications in point-of-care-testing (POCT). Here, we have developed a version of LAMP that uses phosphorothioated primers (PS-LAMP) to enable more efficient hairpin formation and extension at the termini of growing concatamers, and that therefore works at much lower temperatures. By including additional factors such as chaotropes (urea) and single-stranded DNA binding protein (SSB), the sensitivities and selectivities for amplicon detection with PS-LAMP at 40 °C were comparable with a regular LAMP reaction at 65 °C.
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Affiliation(s)
- Sheng Cai
- Laboratory of Pharmaceutical Analysis and Drug Metabolism, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research , Zhejiang University , Hangzhou , Zhejiang 310058 , China
| | - Cheulhee Jung
- Division of Biotechnology , College of Life Sciences and Biotechnology, Korea University , Seoul 02841 , Republic of Korea
| | - Sanchita Bhadra
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas at Austin , Austin , Texas 78712 , United States
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20
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Erlichster M, Tye-Din JA, Varney MD, Skafidas E, Kwan P. Rapid, Loop-Mediated Isothermal Amplification Detection of Celiac Disease Risk Alleles. J Mol Diagn 2018; 20:307-315. [PMID: 29458095 DOI: 10.1016/j.jmoldx.2018.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 12/20/2017] [Accepted: 01/19/2018] [Indexed: 02/07/2023] Open
Abstract
Human leukocyte antigen (HLA) genotyping has become a useful investigation in the diagnostic work-up of celiac disease (CD), with utility in risk stratification and screening. However, broad application of this technology has been hindered by the cost and time burden of conventional laboratory-based assays. We have developed and validated CD-loop-mediated isothermal amplification (CD-LAMP), a LAMP assay, which enables rapid identification of the signature CD risk genotypes, HLA-DQ2.5, HLA-DQ8, HLA-DQ2.2, and HLA-DQA1*05. Sample-to-answer is achieved in approximately 65 minutes without DNA purification, thermal cycling, or specialized analytical equipment. CD-LAMP genotyping of samples was 100% concordant with accredited pathology genotyping on a panel of 40 blood and 20 saliva samples. In a panel of 100 purified DNA samples, genotyping of the high-risk DQ2.5 genotype was 100% concordant with accredited pathology genotyping, with slightly reduced sensitivity for the DQ8 genotype (97.1%) and reduced specificity for the DQ8 (93.9%) and DQ2.2 (95.1%) genotypes. CD-LAMP results are easily visualized and instrument free through the addition of a DNA intercalating dye after amplification. Combined with point-of-care antibody testing, CD-LAMP may enable immediate, confident CD diagnosis at a low cost in the clinical setting.
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Affiliation(s)
- Michael Erlichster
- Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Jason A Tye-Din
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia; Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Gastroenterology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Michael D Varney
- Victorian Transplantation and Immunogenetics Service, Australian Red Cross Blood Service, Melbourne, Victoria, Australia
| | - Efstratios Skafidas
- Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia; Department of Electrical and Electronic Engineering, University of Melbourne, Melbourne, Victoria, Australia; The Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
| | - Patrick Kwan
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia; Department of Electrical and Electronic Engineering, University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.
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21
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Carlos FF, Veigas B, Matias AS, Doria G, Flores O, Baptista PV. Allele specific LAMP- gold nanoparticle for characterization of single nucleotide polymorphisms. ACTA ACUST UNITED AC 2017; 16:21-25. [PMID: 29124021 PMCID: PMC5671399 DOI: 10.1016/j.btre.2017.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/27/2022]
Abstract
Allele-specific isothermal amplification method (AS-LAMP) for SNP characterization. Use of ssDNA-functionalized gold nanoparticles (AuNPs) for SNP full discrimination. A simple and low-cost strategy to provide fast results in medium throughput settings. AS-LAMP amplification products can be easily interpreted in less than 15 min.
Due to their relevance as disease biomarkers and for diagnostics, screening of single nucleotide polymorphism (SNPs) requires simple and straightforward strategies capable to provide results in medium throughput settings. Suitable approaches relying on isothermal amplification techniques have been evolving to substitute the cumbersome and highly specialized PCR amplification detection schemes. Nonetheless, identification of an individual’s genotype still requires sophisticated equipment and laborious methods. Here, we present a low-cost and reliable approach based on the allele specific loop-mediated isothermal amplification (AS-LAMP) coupled to ssDNA functionalized gold nanoparticle (Au-nanoprobe) colorimetric sequence discrimination. The Au-nanoprobe integration allows for the colorimetric detection of AS-LAMP amplification product that can be easily interpreted in less than 15 min. We targeted a clinical relevant SNP responsible for lactose intolerance (-13910C/T dbSNP rs#: 4988235) to demonstrate its proof of concept and full potential of this novel approach.
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Affiliation(s)
- Fábio Ferreira Carlos
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- i3N/CENIMAT, Departamento de Ciências de Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Ana S. Matias
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Gonçalo Doria
- STABVIDA, Investigação e Serviços em Ciências Biológicas, Lda. Madan Parque, 2825-182 Caparica, Portugal
| | - Orfeu Flores
- STABVIDA, Investigação e Serviços em Ciências Biológicas, Lda. Madan Parque, 2825-182 Caparica, Portugal
| | - Pedro V. Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- Corresponding author.
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Mahittikorn A, Thammasonthijarern N, Roobthaisong A, Udonsom R, Popruk S, Siri S, Mori H, Sukthana Y. Development of a loop-mediated isothermal amplification technique and comparison with quantitative real-time PCR for the rapid visual detection of canine neosporosis. Parasit Vectors 2017; 10:394. [PMID: 28835287 PMCID: PMC5569544 DOI: 10.1186/s13071-017-2330-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 08/14/2017] [Indexed: 11/10/2022] Open
Abstract
Background Dogs are the definitive hosts of Neospora caninum and play an important role in the transmission of the parasite. Despite the high sensitivity of existing molecular tools such as quantitative real-time PCR (qPCR), these techniques are not suitable for use in many countries because of equipment costs and difficulties in implementing them for field diagnostics. Therefore, we developed a simplified technique, loop-mediated isothermal amplification (LAMP), for the rapid visual detection of N. caninum. Methods LAMP specificity was evaluated using a panel containing DNA from a range of different organisms. Sensitivity was evaluated by preparing 10-fold serial dilutions of N. caninum tachyzoites and comparing the results with those obtained using qPCR. Assessment of the LAMP results was determined by recognition of a colour change after amplification. The usefulness of the LAMP assay in the field was tested on 396 blood and 115 faecal samples from dogs, and one placenta from a heifer collected in Lopburi, Nakhon Pathom, Sa Kaeo, and Ratchaburi provinces, Thailand. Results Specificity of the LAMP technique was shown by its inability to amplify DNA from non-target pathogens or healthy dogs. The detection limit was the equivalent of one genome for both LAMP and qPCR. LAMP and qPCR detected positive N. caninum infection in 15 of 396 (3.8%) blood samples; LAMP detected 9/115 (7.8%) positive faecal samples, while qPCR detected 5/115 (4.3%) positive faecal samples. The placental tissue was shown to be positive by both techniques. Agreement between LAMP and qPCR was perfect in blood samples (kappa value, 1.00) and substantial in faecal samples (kappa value, 0.697). Conclusions This is the first known LAMP assay developed for the amplification of N. caninum. The technique effectively and rapidly detected the parasite with high sensitivity and specificity and was cost-effective. This assay could be used in the field to confirm the diagnosis of canine or bovine neosporosis. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2330-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aongart Mahittikorn
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nipa Thammasonthijarern
- Department of Tropical Pediatrics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Amonrattana Roobthaisong
- Section of Bacterial Infections, Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections, Nonthaburi, Thailand
| | - Ruenruetai Udonsom
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Supaluk Popruk
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sukhontha Siri
- Department of Epidemiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Hirotake Mori
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yaowalark Sukthana
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Ayukawa Y, Hanyuda S, Fujita N, Komatsu K, Arie T. Novel loop-mediated isothermal amplification (LAMP) assay with a universal QProbe can detect SNPs determining races in plant pathogenic fungi. Sci Rep 2017; 7:4253. [PMID: 28652587 PMCID: PMC5484703 DOI: 10.1038/s41598-017-04084-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is grouped into three races based on their pathogenicity to different host cultivars. Rapid detection and discrimination of Fol races in field soils is important to prevent tomato wilt disease. Although five types of point mutations in secreted in xylem 3 (SIX3) gene, which are characteristic of race 3, have been reported as a molecular marker for the race, detection of these point mutations is laborious. The aim of this study is to develop a rapid and accurate method for the detection of point mutations in SIX3 of Fol. Loop-mediated isothermal amplification (LAMP) of SIX3 gene with the universal QProbe as well as two joint DNAs followed by annealing curve analysis allowed us to specifically detect Fol and discriminate race 3 among other races in about one hour. Our developed method is applicable for detection of races of other plant pathogenic fungi as well as their pesticide-resistant mutants that arise through point mutations in a particular gene.
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Affiliation(s)
- Yu Ayukawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Saeri Hanyuda
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Naoko Fujita
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Ken Komatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
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Fang P, He JY, Han AX, Lan T, Dai DP, Cai JP, Hu GX. Effects of CYP2C19 Variants on Fluoxetine Metabolism in vitro. Pharmacology 2017; 100:91-97. [DOI: 10.1159/000475598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
Aims: CYP2C19 is an important member of the cytochrome P450 enzyme superfamily. We recently identified 31 CYP2C19 alleles in the Han Chinese population. The aim of this study was to assess the catalytic activities of these allelic isoforms and their effects on the metabolism of fluoxetine in vitro. Methods: The wild-type and 30 CYP2C19 variants were expressed in insect cells and each variant was characterized using fluoxetine as the substrate. Reactions were performed at 37°C with 20-1,000 µmol/L substrate for 30 min. By using ultra-high performance liquid chromatography-mass spectrometry to detect the products, the kinetic parameters Km, Vmax, and intrinsic clearance (Vmax/Km) of norfluoxetine were determined. Results: Among the CYP2C19 variants tested, T130M showed similar intrinsic clearance (Vmax/Km) values with CYP2C19*1, while the intrinsic clearance values of other variants were significantly decreased (from 9.56 to 77.77%). In addition, CYP2C19*3 and *35FS could not be detected because they have no detectable enzyme activity. Conclusion: In China, the assessment of CYP2C19 variants in vitro offers valuable information relevant to the personalized medicine for CYP2C19-metabolized drug.
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