Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
Keywords: Mutation detection, SNP, Genotyping, Isothermal amplification, Polymerase chain reaction, LAMP.
[1]
Hsu TM, Law SM, Duan S, Neri BP, Kwok PY. Genotyping single-nucleotide polymorphisms by the invader assay with dual-color fluorescence polarization detection. Clin Chem 2001; 47(8): 1373-7.
[2]
Doria G, Franco R, Baptista P. Nanodiagnostics: fast colorimetric method for single nucleotide polymorphism/ mutation detection. IET Nanobiotechnol 2007; 1(4): 53-7.
[3]
Heidari Sharafdarkolaei S, Motovali-Bashi M, Gill P. Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes. RSC Advances 2017; 7: 25665-72.
[4]
Song Y, Zhang Y, Wang TH. Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction. Small 2013; 9(7): 1096-105.
[5]
Mitsunaga S, Shimizu S, Okudaira Y, et al. Improved loop-mediated isothermal amplification for HLA-DRB1 genotyping using RecA and a restriction enzyme for enhanced amplification specificity. Immunogenetics 2013; 65(6): 405-15.
[6]
Kim J, Easley CJ. Isothermal DNA amplification in bioanalysis: strategies and applications. Bioanalysis 2011; 3(2): 227-39.
[7]
Notomi T, Mori Y, Tomita N, Kanda H. Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects. J Microbiol 2015; 53(1): 1-5.
[8]
Parida M, Sannarangaiah S, Dash PK, Rao PV, Morita K. Loop mediated isothermal amplification (LAMP): a new generation of innovative gene amplification technique; perspectives in clinical diagnosis of infectious diseases. Rev Med Virol 2008; 18(6): 407-21.
[9]
Higashimoto Y, Ihira M, Ohta A, et al. Discriminating between varicella-zoster virus vaccine and wild-type strains by loop-mediated isothermal amplification. J Clin Microbiol 2008; 46(8): 2665-70.
[10]
Veigas B, Pedrosa P, Couto I, Viveiros M, Baptista PV. Isothermal DNA amplification coupled to Au-nanoprobes for detection of mutations associated to Rifampicin resistance in Mycobacterium tuberculosis. J Nanobiotechnology 2013; 11: 38.
[11]
Mori Y, Nagamine K, Tomita N, Notomi T. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 2001; 289(1): 150-4.
[12]
Mori Y, Kitao M, Tomita N, Notomi T. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J Biochem Biophys Methods 2004; 59(2): 145-57.
[13]
Mori Y, Hirano T, Notomi T. Sequence specific visual detection of LAMP reactions by addition of cationic polymers. BMC Biotechnol 2006; 6: 3.
[14]
Njiru ZK, Mikosza AS, Armstrong T, Enyaru JC, Ndung’u JM, Thompson AR. Loop-mediated isothermal amplification (LAMP) method for rapid detection of Trypanosoma brucei rhodesiense. PLoS Negl Trop Dis 2008; 2(1): e147.
[15]
Cai Z, Lou G, Cai T, Yang J, Wu N. Development of a novel genotype-specific loop-mediated isothermal amplification technique for Hepatitis B virus genotypes B and C genotyping and quantification. J Clin Virol 2011; 52(4): 288-94.
[16]
Zhang C, Zhu J, Yang J, Wan Y, Ma T, Cui Y. Determination of ABO blood group genotypes using the realtime loopmediated isothermal amplification method. Mol Med Rep 2015; 12(4): 5963-6.
[17]
Mitani Y, Lezhava A, Kawai Y, et al. Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology. Nat Methods 2007 Mar; 4(3): 257-62.
[18]
Tatsumi K, Mitani Y, Watanabe J, et al. Rapid screening assay for KRAS mutations by the modified smart amplification process. J Mol Diagn 2008; 10(6): 520-6.
[19]
Aomori T, Yamamoto K, Oguchi-Katayama A, et al. Rapid single-nucleotide polymorphism detection of cytochrome P450 (CYP2C9) and vitamin K epoxide reductase (VKORC1) genes for the warfarin dose adjustment by the SMart-amplification process version 2. Clin Chem 2009; 55(4): 804-12.
[20]
Watanabe J, Mitani Y, Kawai Y, et al. Use of a competitive probe in assay design for genotyping of the UGT1A1 *28 microsatellite polymorphism by the smart amplification process. Biotechniques 2007; 43(4): 479-84.
[21]
Conze T, Shetye A, Tanaka Y, et al. Analysis of genes, transcripts, and proteins via DNA ligation. Annu Rev Anal Chem 2009; 2: 215-39.
[22]
Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001; 11: 1095-9.
[23]
Zhao W, Ali MM, Brook MA, Li Y. Rolling circle amplification: Applications in nanotechnology and biodetection with functional nucleic acids. Angew Chem Int Ed 2008; 47: 6330-7.
[24]
Yan L, Zhou J, Zheng Y, et al. Isothermal amplified detection of DNA and RNA. Mol Biosyst 2014; 10(5): 970-1003.
[25]
Cho EJ, Yang L, Levy M, Ellington AD. Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP. J Am Chem Soc 2005; 127(7): 2022-3.
[26]
Larsson C, Koch J, Nygren A, et al. In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nat Methods 2004; 1(3): 227-32.
[27]
Krzywkowski T, Hauling T, Nilsson M. In Situ Single-Molecule RNA Genotyping Using Padlock Probes and Rolling Circle Amplification. Methods Mol Biol 2017; 1492: 59-76.
[28]
Pavankumar AR, Engstrom A, Liu J, Herthnek D, Nilsson M. Proficient Detection of Multi-Drug-Resistant Mycobacterium tuberculosis by Padlock Probes and Lateral Flow Nucleic Acid Biosensors. Anal Chem 2016; 88(8): 4277-84.
[29]
Mezger A, Ohrmalm C, Herthnek D, Blomberg J, Nilsson M. Detection of rotavirus using padlock probes and rolling circle amplification. PLoS One 2014; 9(11): e111874.
[30]
Barisic I, Schoenthaler S, Ke R, Nilsson M, Noehammer C, Wiesinger-Mayr H. Multiplex detection of antibiotic resistance genes using padlock probes. Diagn Microbiol Infect Dis 2013; 77(2): 118-25.
[31]
Weibrecht I, Lundin E, Kiflemariam S, et al. In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay. Nat Protoc 2013; 8(2): 355-72.
[33]
Chen X, Sullivan PF. Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J 2003; 3(2): 77-96.
[34]
Hayashi K, Ishigami M, Ishizu Y, et al. A comparison of direct sequencing and Invader assay for Y93H mutation and response to interferon-free therapy in hepatitis C virus genotype 1b. J Gastroenterol Hepatol 2018; 33: 249-55.
[35]
Ono T, Miyawaki S, Kimura F, et al. BCR-ABL1 mutations in patients with imatinib-resistant Philadelphia chromosome-positive leukemia by use of the PCR-Invader assay. Leuk Res 2011; 35(5): 598-603.
[36]
Hosono N, Chantarangsu S, Kiyotani K, et al. Development of new HLA-B*3505 genotyping method using Invader assay. Pharmacogenet Genomics 2010; 20(10): 630-3.
[37]
Tadokoro K, Akutsu Y, Tanaka K, et al. Comparative quantitative analysis of 14 types of human papillomavirus by real-time polymerase chain reaction monitoring Invader reaction (Q-Invader assay). Diagn Microbiol Infect Dis 2010; 66(1): 58-64.
[38]
Murphy DG, Cote L, Fauvel M, Rene P, Vincelette J. Multicenter comparison of Roche COBAS AMPLICOR MONITOR version 1.5, Organon Teknika NucliSens QT with Extractor, and Bayer Quantiplex version 3.0 for quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 2000; 38(11): 4034-41.
[39]
Romano JW, Tetali S, Lee EM, et al. Genotyping of the CCR5 chemokine receptor by isothermal NASBA amplification and differential probe hybridization. Clin Diagn Lab Immunol 1999; 6(6): 959-65.
[40]
Jeantet D, Schwarzmann F, Tromp J, et al. NucliSENS EasyQ HPV v1 test - Testing for oncogenic activity of human papillomaviruses. J Clin Virol 2009; 45(Suppl. 1): 29-37.
[41]
Berard C, Cazalis MA, Leissner P, Mougin B. DNA nucleic acid sequence-based amplification-based genotyping for polymorphism analysis. Biotechniques 2004; 37(4): 680-2.
[42]
Mohammadi-Yeganeh S, Paryan M, Mirab Samiee S, Kia V, Rezvan H. Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV. Iran J Microbiol 2012; 4(2): 47-54.
[43]
Moore C, Telles JN, Corden S, et al. Development and validation of a commercial real-time NASBA assay for the rapid confirmation of influenza A H5N1 virus in clinical samples. J Virol Methods 2010; 170(1-2): 173-6.
[44]
Mollasalehi H, Yazdanparast R. An improved non-crosslinking gold nanoprobe-NASBA based on 16S rRNA for rapid discriminative bio-sensing of major salmonellosis pathogens. Biosens Bioelectron 2013; 47: 231-6.
[45]
Xu W, Xie X, Li D, Yang Z, Li T, Liu X. Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). Small 2012; 8(12): 1846-50.
[46]
Li J, Yao QH, Fu HE, Zhang XL, Yang HH. High sensitive and label-free colorimetric DNA detection based on nicking endonuclease-assisted activation of DNAzymes. Talanta 2011; 85(1): 91-6.
[47]
Piepenburg O, Williams CH, Stemple DL, Armes NA. DNA detection using recombination proteins. PLoS Biol 2006; 4(7): e204.
[48]
Shin Y, Perera AP, Kim KW, Park MK. Real-time, label-free isothermal solid-phase amplification/detection (ISAD) device for rapid detection of genetic alteration in cancers. Lab Chip 2013; 13(11): 2106-14.
[49]
Kersting S, Rausch V, Bier FF, von Nickisch-Rosenegk M. Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens. Mikrochim Acta 2014; 181(13-14): 1715-23.
[50]
Yang Y, Qin X, Zhang X, et al. Development of real-time and lateral flow dipstick recombinase polymerase amplification assays for rapid detection of goatpox virus and sheeppox virus. Virol J 2017; 14(1): 131.
[51]
Wang JC, Liu LB, Han QA, Wang JF, Yuan WZ. An exo probe-based recombinase polymerase amplification assay for the rapid detection of porcine parvovirus. J Virol Methods 2017; 248: 145-7.
[52]
Ma B, Fang J, Wang Y, et al. Isothermal Method of a Recombinase Polymerase Amplification Assay for the Detection of Most Common High-Risk Human Papillomavirus Type 16 and Type 18 DNA. Clin Lab 2017; 63(1): 27-38.
[53]
Gill P, Amini M, Ghaemi A, et al. Detection of Helicobacter pylori by enzyme-linked immunosorbent assay of thermophilic helicase-dependent isothermal DNA amplification. Diagn Microbiol Infect Dis 2007; 59(3): 243-9.
[54]
Gill P, Abdul-Tehrani H, Ghaemi A, et al. Molecular detection of Mycobacterium tuberculosis by tHDA-ELISA DIG detection system. Int Jof Antimicrob Agents 2007; 29: 570-1.
[55]
Gill P, Abdul-Tehrani H, Ghaemi A, Hashempour T, Alvandi A, Noori-Daloii M. Thermophilic helicase-dependent isothermal DNA amplification for molecular detection of Helicobacter pylori. Int Jof Antimicrob Agents 2007; 29: 135-6.
[56]
Valentini P, Fiammengo R, Sabella S, et al. Gold-nanoparticle-based colorimetric discrimination of cancer-related point mutations with picomolar sensitivity. ACS Nano 2013; 7(6): 5530-8.
[57]
Gill P, Alvandi AH, Abdul-Tehrani H, Sadeghizadeh M. Colorimetric detection of Helicobacter pylori DNA using isothermal helicase-dependent amplification and gold nanoparticle probes. Diagn Microbiol Infect Dis 2008; 62(2): 119-24.
[58]
Wu X, Chen C, Xiao X, Deng MJ. Development of Reverse Transcription Thermostable Helicase-Dependent DNA Amplification for the Detection of Tomato Spotted Wilt Virus. J AOAC Int 2016; 99(6): 1596-9.
[59]
Chen X, Wu X, Gan M, et al. Rapid detection of Staphylococcus aureus in dairy and meat foods by combination of capture with silica-coated magnetic nanoparticles and thermophilic helicase-dependent isothermal amplification. J Dairy Sci 2015; 98(3): 1563-70.
[60]
Ma F, Liu M, Tang B, Zhang CY. Sensitive Quantification of MicroRNAs by Isothermal Helicase-Dependent Amplification. Anal Chem 2017; 89(11): 6182-7.
[61]
Yeh HC, Ho YP, Shih Ie M, Wang TH. Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis. Nucleic Acids Res 2006; 34(5): e35.
[62]
Chang CC, Chen CC, Wei SC, Lu HH, Liang YH, Lin CW. Diagnostic devices for isothermal nucleic acid amplification. Sensors (Basel) 2012; 12(6): 8319-37.
[63]
Tröger V, Niemann K, Gärtig C, Kuhlmeier D. Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems. Nanomedicine & Nanotechnology 2015; 6(3): 282-301.
[64]
Parida M, Posadas G, Inoue S, Hasebe F, Morita K. Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus. J Clin Microbiol 2004; 42(1): 257-63.
[65]
Enosawa M, Kageyama S, Sawai K, et al. Use of loop-mediated isothermal amplification of the IS900 sequence for rapid detection of cultured Mycobacterium avium subsp. paratuberculosis. J Clin Microbiol 2003; 41(9): 4359-65.
[66]
Parida M, Horioke K, Ishida H, et al. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay. J Clin Microbiol 2005; 43(6): 2895-903.
[67]
Neeraja M, Lakshmi V, Lavanya V, et al. Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India. J Virol Methods 2015; 211: 22-31.
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