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Zhai S, Yang Y, Wu Y, Li J, Li Y, Wu G, Liang J, Gao H. A visual CRISPR/dCas9-mediated enzyme-linked immunosorbent assay for nucleic acid detection with single-base specificity. Talanta 2023; 257:124318. [PMID: 36796171 DOI: 10.1016/j.talanta.2023.124318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/17/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Specific and economical nucleic acid detection is crucial for molecular diagnoses in resource-limited settings. Various facile readout approaches have been developed for nucleic acid detection, but they have limited specificity. Herein, nuclease-dead Cas9 (dCas9)/sgRNA was used as an excellent DNA recognition probe system to develop a visual clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated enzyme-linked immunosorbent assay (ELISA) for specific and sensitive detection of cauliflwer mosaic virus 35s (CaMV35S) promoter in genetically modified (GM) crops. In this work, the CaMV35S promoter was amplified with biotinylated primers, and then precisely bound with dCas9 in the presence of sgRNA. The formed complex was captured by antibody-coated microplate and bound to a streptavidin-labeled horseradish peroxidase probe for the visual detection. Under the optimal conditions, dCas9-ELISA could detect CaMV35s promoter as low as 12.5 copies μL-1. Moreover, the proposed method was capable to distinguish the target sequence with single-base specificity. Coupled with one-step extraction and recombinase polymerase amplification, dCas9-ELISA can identify actual GM rice seeds within 1.5 h from sampling to results without expensive equipment and technical expertise. Therefore, the proposed method offers a specific, sensitive, rapid and cost-effective detection platform for molecular diagnoses.
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Affiliation(s)
- Shanshan Zhai
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yao Yang
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yuhua Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jun Li
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yunjing Li
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Gang Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jingang Liang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100176, China.
| | - Hongfei Gao
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Wang J, Li J, Ge Q, Li J. A potential negative regulation of myostatin in muscle growth during the intermolt stage in Exopalaemon carinicauda. Gen Comp Endocrinol 2021; 314:113902. [PMID: 34529998 DOI: 10.1016/j.ygcen.2021.113902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Muscle growth in crustacean is a complicated process where the muscle grows and develops through muscle restoration, and the growth rate depends on the net muscle gain during molting. Myostatin (MSTN) is a conserved inhibitor of muscle growth in vertebrates, but until now solid evidence supporting a similar function of MSTN in invertebrates has been lacking. In this study, we identified and characterized MSTN from the shrimp Exopalaemon carinicauda (EcMSTN) to better understand its biological function. The full-length cDNA of EcMSTN was 1,518 bp, encoding 428 amino acid residues, and the genomic sequence was 1,851 bp, including three exons and two introns. EcMSTN was expressed in a wide range of tissues, but predominantly detected in the abdominal muscle (P < 0.05). Low expression was detected in the cleavage, blastula and gastrula stages in the early development stages, increasing after the nauplius stage. EcMSTN expression was negatively correlated with the growth traits. After EcMSTN knockdown using RNA interference, EcMSTN expression was down-regulated in the abdominal muscle and up-regulated the expression of growth-related genes, including fast myosin heavy chain and skeletal muscle actin 3. After inhibiting EcMSTN for 5 weeks, the RNAi-treated shrimp with reduced EcMSTN levels exhibited a dramatically higher body weight compared with that of the control group. Association analysis revealed that two SNP loci g.Mstn220 and g.Mstn567 were markedly associated with both body weight and body length. The results would clarify the negative role of EcMSTN in regulating muscle growth during the intermolt stage and provide growth-related markers for molecular marker assisted breeding of E. carinicauda.
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Affiliation(s)
- Jiajia Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jitao Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Qianqian Ge
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Wang J, Li M, Qin Z, Li J, Li J. Validation of growth-related quantitative trait loci markers in different Exopalaemon carinicauda families for marker-assisted selection. Anim Genet 2020; 51:324-329. [PMID: 31981462 DOI: 10.1111/age.12914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 01/08/2023]
Abstract
We detected growth-related QTL and associated markers from the backcross population of Exopalaemon carinicauda in the previous study. Based on our previous study, the 47 SNP markers associated with candidate growth trait QTL were selected to analyze the association between these markers and body weight (BW), body length and abdominal segment length traits in four different populations including wild population, a full-sib family, a half-sib family and a backcross population for evaluating their potential application of marker-assisted selection in E. carinicauda. The general linear model (GLM) and mixed linear model were applied and the associations between SNP loci and three growth-related traits verified. The results showed that the Marker79268 and Marker100644 were significantly associated with the BW trait in more than three populations by the GLM method. The Marker100644 was significantly associated with BW in the full-sib family, half-sib family and backcross populations by the GLM and mixed linear model methods. Our findings will provide useful SNP markers to go forward to improve growth performance through more refined marker-assisted selection in E. carinicauda.
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Affiliation(s)
- J Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - M Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,College of Fishery and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Z Qin
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - J Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - J Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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Isolation and characterization of three skeletal troponin genes and association with growth-related traits in Exopalaemon carinicauda. Mol Biol Rep 2018; 46:705-718. [DOI: 10.1007/s11033-018-4526-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022]
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Shi S, Yoon DY, Hodge-Bell K, Huerta-Yepez S, Hankinson O. Aryl hydrocarbon nuclear translocator (hypoxia inducible factor 1beta) activity is required more during early than late tumor growth. Mol Carcinog 2010; 49:157-65. [PMID: 19824022 DOI: 10.1002/mc.20585] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
c4 is a derivative of the mouse hepatoma cell line, Hepa-1, that harbors a mutation in the aryl hydrocarbon receptor nuclear translocator gene (Arnt, or hypoxia inducible factor 1beta [HIF-1beta]) leading to loss of activity. Clone 3 cells were generated by introducing a doxycycline-repressible Arnt expression vector into c4 cells. Clone 3 cells were injected subcutaneously into immunosuppressed mice, which were treated with doxycyline (a) throughout the growth of the subsequent tumor xenografts, or (b) from day 7 through to the end of the experiment (day 30), or not treated (c). Tumors in all groups grew exponentially between days 14 and 30, and at rates that were indistinguishable from each other. However, tumors in group a were smaller than those of the other two groups throughout the measurable growth period, while tumor volumes in groups b and c were not significantly different from each other. The degrees of vascularity and apoptosis did not correlate with the differences in degrees of growth between the different groups. Thus, Arnt is required during the early stages of growth of the tumors but less in later stages. Since Arnt does not detectably effect the growth kinetics of Hepa-1 cells either during hypoxia or normoxia, this requirement is unlikely to reflect a direct effect of Arnt on cell proliferation, and is therefore probably a consequence of altered interaction(s) between the tumor cells and the host. These studies suggest that Arnt (and HIF-1alpha/HIF-2alpha) inhibitors will be particularly effective against smaller tumors, including micrometastases.
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Affiliation(s)
- S Shi
- Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095-1732, USA
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Ye X, Tan Z, Zhang Y, Li K. Single Nucleotide Polymorphisms in the Chicken Mx gene at Position 2032 by Real-time Allele-specific PCR Melting-curve Analysis. J Poult Sci 2010; 47:133-138. [DOI: 10.2141/jpsa.009070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Xiangqun Ye
- Department of Microbiology and Immunology, Shantou University Medical College, China
| | - Zongcheng Tan
- Department of Microbiology and Immunology, Shantou University Medical College, China
- Department of Biology, Shantou University, China
| | | | - Kangsheng Li
- Department of Microbiology and Immunology, Shantou University Medical College, China
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Tan SW, Ideris A, Omar AR, Yusoff K, Hair-Bejo M. Detection and differentiation of velogenic and lentogenic Newcastle disease viruses using SYBR Green I real-time PCR with nucleocapsid gene-specific primers. J Virol Methods 2009; 160:149-56. [PMID: 19447142 DOI: 10.1016/j.jviromet.2009.05.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 05/05/2009] [Accepted: 05/07/2009] [Indexed: 10/20/2022]
Abstract
SYBR Green I real-time PCR was developed for detection and differentiation of Newcastle disease virus (NDV). Primers based on the nucleocapsid (NP) gene were designed to detect specific sequence of velogenic strains and lentogenic/vaccine strains, respectively. The assay was developed and tested with NDV strains which were characterized previously. The velogenic strains were detected only by using velogenic-specific primers with a threshold cycle (C(t)) 18.19+/-3.63 and a melting temperature (T(m)) 86.0+/-0.28 degrees C. All the lentogenic/vaccine strains, in contrast, were detected only when lentogenic-specific primers were used, with the C(t) value 14.70+/-2.32 and T(m) 87.4+/-0.21 degrees C. The assay had a dynamic detection range which spans over a 5log(10) concentration range, 10(9)-10(5) copies of DNA plasmid/reaction. The velogenic and lentogenic amplifications showed high PCR efficiency of 100% and 104%, respectively. The velogenic and lentogenic amplifications were highly reproducible with assay variability 0.45+/-0.31% and 1.30+/-0.65%, respectively. The SYBR Green I real-time PCR assay detected successfully the virus from tissue samples and oral swabs collected from the velogenic and lentogenic NDV experimental infection, respectively. In addition, the assay detected and differentiated accurately NDV pathotypes from suspected field samples where the results were in good agreement with both virus isolation and analysis of the fusion (F) cleavage site sequence. The assay offers an attractive alternative method for the diagnosis of NDV.
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Affiliation(s)
- Sheau Wei Tan
- Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
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A novel PCR-RFLP assay for the detection of the single nucleotide polymorphism at position +1440 in the human CXCR2 gene. Biochem Genet 2007; 45:737-41. [PMID: 17939034 DOI: 10.1007/s10528-007-9111-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 05/23/2007] [Indexed: 10/22/2022]
Abstract
We designed a novel PCR-RFLP assay to genotype for the CXCR2 +1440 (G/A) single nucleotide polymorphism, which provides a simple, low-cost, practical, and reproducible method. Allele frequencies in healthy Brazilian individuals were found to be 0.65% for allele A and 0.35% for allele G.
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Namkung JH, Lee JE, Kim E, Cho HJ, Kim S, Shin ES, Cho EY, Yang JM. IL-5 and IL-5 receptor alpha polymorphisms are associated with atopic dermatitis in Koreans. Allergy 2007; 62:934-42. [PMID: 17620072 DOI: 10.1111/j.1398-9995.2007.01445.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Eosinophils are recruited into the affected tissue of asthma and atopic dermatitis (AD) patients. IL-5 and IL-5R are highly expressed in the AD skin lesions, yet the reported levels of IL-8 are controversial. METHOD We genotyped 17 singlenucleotide polymorphisms (SNPs) from five genes of the 1120 case-control samples (646 AD and 474 controls). We measured the serum IL-5 concentrations in 87 individuals [36 ADe (AD extrinsic), 18 ADi (AD intrinsic) and 33 controls] by ELISA, and compared the results among these groups. RESULT The rs2522411SNP and haplotype T-A in the IL-5 gene were significantly associated with the ADe. The serum IL-5 concentration was higher in the ADe than that in the ADi patients without any correlation with the rs2522411SNP. In the IL-5RA gene, the rs334809SNP showed a weak association with AD, and the rs6771148SNP and the haplotype T-C-T of the three adjacent tagged SNPs had an effect on the blood eosinophil counts and the serum ECP levels in the AD patients. However, we could not detect any relationship between AD and the SNPs in the IL-8 and IL-8R genes. CONCLUSION We found that the rs2522411SNP and the haplotype T-A in the IL-5 gene and the serum IL-5 levels were strongly associated with the allergic type of AD, but not with the nonallergic type of AD. The association of the rs6771148SNP and the haplotype T-C-T in the IL5RA gene with the blood eosinophil counts and the serum ECP levels indicates that the IL5RA gene has a role for controlling eosinophils in the peripheral blood.
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Affiliation(s)
- J-H Namkung
- Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Korea
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Gupta M, Yates CR, Meibohm B. SYBR Green-based real-time PCR allelic discrimination assay for beta2-adrenergic receptor polymorphisms. Anal Biochem 2006; 344:292-4. [PMID: 16026755 DOI: 10.1016/j.ab.2005.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Revised: 05/16/2005] [Accepted: 05/17/2005] [Indexed: 10/25/2022]
Affiliation(s)
- Manish Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Linzmeier RM, Ganz T. Human defensin gene copy number polymorphisms: comprehensive analysis of independent variation in alpha- and beta-defensin regions at 8p22-p23. Genomics 2006; 86:423-30. [PMID: 16039093 DOI: 10.1016/j.ygeno.2005.06.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 06/10/2005] [Accepted: 06/14/2005] [Indexed: 10/25/2022]
Abstract
To investigate defensin gene copy number polymorphisms, a quantitative real-time PCR assay was developed and used to study DNA from 27 unrelated individuals of diverse ethnic and racial backgrounds. The DEFB4 and DEFB103A genes varied in tandem, with copy numbers 2 to 8, with a mode of 6 per diploid genome (PDG). The combined copy numbers of the DEFA1 and DEFA3 genes ranged from 5 to 14, with a mode of 10 copies PDG. The copy numbers of the DEFA1/3 genes varied independently of those of the DEFB4 and DEFB103A genes. The amount of HNP-1 and HNP-3 peptides expressed in neutrophils was found to be proportional to the combined copy number of DEFA1 and DEFA3. The DEFA3 allele was absent in 7/27 subjects. The highly copy-number-variable DEFA1 and DEFA3 genes are flanked by other defensin genes present uniformly at 2 copies PDG. The remarkable variability in defensin gene copy numbers could contribute to differences in individual resistance to infections.
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Affiliation(s)
- Rose M Linzmeier
- Department of Medicine and Department of Pathology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1690, USA.
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Gibson NJ. The use of real-time PCR methods in DNA sequence variation analysis. Clin Chim Acta 2005; 363:32-47. [PMID: 16182268 DOI: 10.1016/j.cccn.2005.06.022] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 06/21/2005] [Accepted: 06/21/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND Real-time (RT) PCR methods for discovering and genotyping single nucleotide polymorphisms (SNPs) are becoming increasingly important in various fields of biological sciences. SNP genotyping is widely used to perform genetic association studies aimed at characterising the genetic factors underlying inherited traits. The detection and quantification of somatic mutations is an important tool for investigating the genetic causes of tumorigenesis. In infectious disease diagnostics there is an increasing emphasis placed on genotyping variation within the genomes of pathogenic organisms in order to distinguish between strains. METHODS There are several platforms and methods available to the researcher wishing to undertake SNP analysis using real-time PCR methods. These use fluorescent technologies for discriminating between the alternate alleles of a polymorphism. There are several real-time PCR platforms currently on the market. Two of the key technical challenges are allele discrimination and allele quantification. CONCLUSIONS Applications of this technology include SNP genotyping, the sensitive detection of somatic mutations and infectious disease subtyping.
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Affiliation(s)
- Neil J Gibson
- R&D Genetics, AstraZeneca Pharmaceuticals, 19G9 Mereside, Macclesfield, Cheshire, UK.
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