The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases


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Abstract

Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.

About the authors

Mohamad Hesam Shahrajabian

National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute,, Chinese Academy of Agricultural Sciences,

Email: info@benthamscience.net

Wenli Sun

National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

Author for correspondence.
Email: info@benthamscience.net

References

  1. Shahrajabian MH, Sun W, Soleymani A, Cheng Q. Traditional herbal medicines to overcome stress, anxiety and improve mental health in outbreaks of human coronaviruses. Phytother Res 2020; 2020(1): 1-11. doi: 10.1002/ptr.6888 PMID: 33350538
  2. Shahrajabian MH, Sun W, Cheng Q. The importance of flavonoids and phytochemicals medicinal plants with antiviral activities. Mini Rev Org Chem 2021; 18: 1-26. doi: 10.2174/1570178618666210707161025
  3. Shahrajabian MH, Sun W, Cheng Q. Different methods for molecular and rapid detection of human novel coronavirus. Curr Pharm Des 2021; 27(25): 2893-903. doi: 10.2174/1381612827666210604114411 PMID: 34086547
  4. Shahrajabian MH, Sun W, Cheng Q. Molecular breeding and the impacts of some important genes families on agronomic traits, a review. Genet Resour Crop Evol 2021; 68(5): 1709-30. doi: 10.1007/s10722-021-01148-x
  5. Sun W, Shahrajabian MH, Cheng Q. Natural dietary and medicinal plants with anti-obesity therapeutics activities for treatment and prevention of obesity during lock down and in post- COVID-19 era. Appl Sci 2021; 11(17): 7889. doi: 10.3390/app11177889
  6. Espy MJ, Uhl JR, Sloan LM, et al. Real-time PCR in clinical microbiology: Applications for routine laboratory testing. Clin Microbiol Rev 2006; 19(1): 165-256. doi: 10.1128/CMR.19.1.165-256.2006 PMID: 16418529
  7. Paudel D, Jarman R, Limkittikul K, et al. Comparison of real-time SYBR green dengue assay with real-time taqman RT-PCR dengue assay and the conventional nested PCR for diagnosis of primary and secondary dengue infection. N Am J Med Sci 2011; 3(10): 478-85. doi: 10.4297/najms.2011.3478. PMID: 22363089
  8. Jakkul W, Chaisiri K, Saralamba N, et al. Newly developed SYBR Green-based quantitative real-time PCRs revealed coinfection evidence of Angiostrongylus cantonensis and A. malaysiensis in Achatina fulica existing in Bangkok Metropolitan, Thailand. Food Waterborne Parasitol 2021; 23: e00119. doi: 10.1016/j.fawpar.2021.e00119 PMID: 33817357
  9. Wang Y, Li Y, Cui Y, et al. Establishment of a duplex SYBR green I-based real-time polymerase chain reaction assay for the rapid detection of canine circovirus and canine astrovirus. Mol Cell Probes 2020; 54: 101666. doi: 10.1016/j.mcp.2020.101666 PMID: 32919029
  10. Wang Y, Cui Y, Li Y, et al. Simultaneous detection of duck circovirus and novel goose parvovirus via SYBR green I-based duplex real-time polymerase chain reaction analysis. Mol Cell Probes 2020; 53: 101648. doi: 10.1016/j.mcp.2020.101648 PMID: 32798710
  11. Zheng L, Chai L, Tian R, Zhao Y, Chen HY, Wang Z. Simultaneous detection of porcine reproductive and respiratory syndrome virus and porcine circovirus 3 by SYBR green І-based duplex real-time PCR. Mol Cell Probes 2020; 49: 101474. doi: 10.1016/j.mcp.2019.101474 PMID: 31655106
  12. Deprez L, Corbisier P, Kortekaas AM, et al. Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material. Biomol Detect Quantif 2016; 9: 29-39. doi: 10.1016/j.bdq.2016.08.002 PMID: 27617230
  13. Kahyo T, Iwaizumi M, Yamada H, Tao H, Kurachi K, Sugimura H. Application of digital PCR with chip-in-a-tube format to analyze Adenomatous polyposis coli (APC) somatic mosaicism. Clin Chim Acta 2017; 475: 91-6. doi: 10.1016/j.cca.2017.10.015 PMID: 29055690
  14. Abachin E, Convers S, Falque S, Esson R, Mallet L, Nougarede N. Comparison of reverse-transcriptase qPCR and droplet digital PCR for the quantification of dengue virus nucleic acid. Biologicals 2018; 52: 49-54. doi: 10.1016/j.biologicals.2018.01.001 PMID: 29398345
  15. Bai Y, Qu Y, Wu Z, et al. Absolute quantification and analysis of extracellular vesicle lncRNAs from the peripheral blood of patients with lung cancer based on multi-colour fluorescence chip-based digital PCR. Biosens Bioelectron 2019; 142: 111523. doi: 10.1016/j.bios.2019.111523 PMID: 31336224
  16. Lamberts V, Aldea M, Mezquita L, et al. P34.06 The Clinical utility of liquid biopsy by digital droplet PCR in patients with advanced NSCLC. J Thorac Oncol 2021; 16(3): S417. doi: 10.1016/j.jtho.2021.01.697
  17. Zhong X, Liu X, Lou B, Zhou C, Wang X. Development of a sensitive and reliable droplet digital PCR assay for the detection of ‘Candidatus Liberibacter asiaticus’. J Integr Agric 2018; 17(2): 483-7. doi: 10.1016/S2095-3119(17)61815-X
  18. Rougemont M, Van Saanen M, Sahli R, Hinrikson HP, Bille J, Jaton K. Detection of four Plasmodium species in blood from humans by 18S rRNA gene subunit-based and species-specific real- time PCR assays. J Clin Microbiol 2004; 42(12): 5636-43. doi: 10.1128/JCM.42.12.5636-5643.2004 PMID: 15583293
  19. Li H, Bai R, Zhao Z, et al. Application of droplet digital PCR to detect the pathogens of infectious diseases. Biosci Rep 2018; 38(6): BSR20181170. doi: 10.1042/BSR20181170 PMID: 30341241
  20. Hindson BJ, Ness KD, Masquelier DA, et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 2011; 83(22): 8604-10. doi: 10.1021/ac202028g PMID: 22035192
  21. Hall Sedlak R, Jerome KR. The potential advantages of digital PCR for clinical virology diagnostics. Expert Rev Mol Diagn 2014; 14(4): 501-7. doi: 10.1586/14737159.2014.910456 PMID: 24724628
  22. Bhat S, Emslie KR. Digital polymerase chain reaction for characterisation of DNA reference materials. Biomol Detect Quantif 2016; 10: 47-9. doi: 10.1016/j.bdq.2016.04.001 PMID: 27990349
  23. Raurich S, Weber B, Klose V, Mohnl M, Petri D, Fibi-Smetana S. Optimisation of a droplet digital PCR for strain specific quantification of a probiotic Bifidobacterium animalis strain in poultry feed. J Microbiol Methods 2019; 163: 105646. doi: 10.1016/j.mimet.2019.105646 PMID: 31152751
  24. Lindner L, Cayrou P, Jacquot S, Birling MC, Herault Y, Pavlovic G. Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies. Methods 2021; 191: 95-106. doi: 10.1016/j.ymeth.2020.07.004 PMID: 32721466
  25. Xu X, Ma X, Zhang X, et al. Detection of BRAF V600E mutation in fine-needle aspiration fluid of papillary thyroid carcinoma by droplet digital PCR. Clin Chim Acta 2019; 491: 91-6. doi: 10.1016/j.cca.2019.01.017 PMID: 30682328
  26. Maggi RG, Richardson T, Breitschwerdt EB, Miller JC. Development and validation of a droplet digital PCR assay for the detection and quantification of Bartonella species within human clinical samples. J Microbiol Methods 2020; 176: 106022. doi: 10.1016/j.mimet.2020.106022 PMID: 32795640
  27. Lou Y, Chen C, Long X, et al. Detection and quantification of chimeric antigen receptor transgene copy number by droplet digital PCR versus real-time PCR. J Mol Diagn 2020; 22(5): 699-707. doi: 10.1016/j.jmoldx.2020.02.007 PMID: 32409121
  28. Dong L, Wang X, Wang S, et al. Interlaboratory assessment of droplet digital PCR for quantification of BRAF V600E mutation using a novel DNA reference material. Talanta 2020; 207: 120293. doi: 10.1016/j.talanta.2019.120293 PMID: 31594564
  29. Gassa A, Fassunke J, Schueten S, et al. Detection of circulating tumor DNA by digital droplet PCR in resectable lung cancer as a predictive tool for recurrence. Lung Cancer 2021; 151: 91-6. doi: 10.1016/j.lungcan.2020.10.019 PMID: 33257044
  30. Jiang Y, Wang H, Hao S, et al. Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications. Clin Chim Acta 2020; 511: 346-51. doi: 10.1016/j.cca.2020.10.032 PMID: 33159953
  31. Sun Y, Ding C, Chen Q, et al. Digital PCR assay for the effective detection of COVID-19 patients with SARS-CoV-2 low viral load. J Virol Methods 2021; 295: 114185. doi: 10.1016/j.jviromet.2021.114185 PMID: 34051244
  32. Navarro Sanchez ME, Devard N, Houy C, et al. Multiplex reverse transcriptase droplet digital PCR for the simultaneous quantification of four dengue serotypes: Proof of concept study. Biologicals 2020; 67: 62-8. doi: 10.1016/j.biologicals.2020.06.001 PMID: 32843276
  33. Xiang Z, Zou B, Zhang L, et al. Ultra-sensitive and multiplex digital-PCR for quantifying the mutants in cell free DNA by employing invasive reaction as identifier. Sens Actuators B Chem 2020; 320: 128362. doi: 10.1016/j.snb.2020.128362
  34. Jikumaru A, Ishii S, Fukudome T, et al. Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration. J Biosci Bioeng 2020; 130(1): 76-81. doi: 10.1016/j.jbiosc.2020.02.004 PMID: 32147250
  35. Bao CY, Hung HC, Chen YW, Fan CY, Huang CJ, Huang W. Requirement of cyclin-dependent kinase function for hepatitis B virus cccDNA synthesis as measured by digital PCR. Ann Hepatol 2020; 19(3): 280-6. doi: 10.1016/j.aohep.2019.12.005 PMID: 31964596
  36. Sperduti S, Lazzaretti C, Paradiso E, et al. Quantification of hormone membrane receptor FSHR, GPER and LHCGR transcripts in human primary granulosa lutein cells by real-time quantitative PCR and digital droplet PCR. Gene Rep 2021; 23: 101194. doi: 10.1016/j.genrep.2021.101194
  37. Assou S, Girault N, Plinet M, et al. Recurrent genetic abnormalities in human pluripotent stem cells: Definition and routine detection in culture supernatant by targeted droplet digital PCR. Stem Cell Reports 2020; 14(1): 1-8. doi: 10.1016/j.stemcr.2019.12.004 PMID: 31902703
  38. Park S, Lee H, Shin S, Lee ST, Lee KA, Choi JR. Analytical validation of the droplet digital PCR assay for diagnosis of spinal muscular atrophy. Clin Chim Acta 2020; 510: 787-9. doi: 10.1016/j.cca.2020.09.024 PMID: 32956702
  39. Lei S, Chen S, Zhong Q. Digital PCR for accurate quantification of pathogens: Principles, applications, challenges and future prospects. Int J Biol Macromol 2021; 184: 750-9. doi: 10.1016/j.ijbiomac.2021.06.132 PMID: 34171259
  40. Persson S, Eriksson R, Lowther J, Ellström P, Simonsson M. Comparison between RT droplet digital PCR and RT real-time PCR for quantification of noroviruses in oysters. Int J Food Microbiol 2018; 284: 73-83. doi: 10.1016/j.ijfoodmicro.2018.06.022 PMID: 30005929
  41. Romsos EL, Vallone PM. Estimation of extraction efficiency by droplet digital PCR. Forensic Sci Int Genet Suppl Ser 2019; 7(1): 515-7. doi: 10.1016/j.fsigss.2019.10.072
  42. Xu L, Qu H, Alonso DG, et al. Portable integrated digital PCR system for the point-of-care quantification of BK virus from urine samples. Biosens Bioelectron 2021; 175: 112908. doi: 10.1016/j.bios.2020.112908 PMID: 33360627
  43. Demeke T, Beecher B, Eng M. Assessment of genetically engineered events in heat-treated and non-treated samples using droplet digital PCR and real-time quantitative PCR. Food Control 2020; 115: 107291. doi: 10.1016/j.foodcont.2020.107291
  44. Morcia C, Ghizzoni R, Delogu C, Andreani L, Carnevali P, Terzi V. Digital PCR: What relevance to plant studies? Biology 2020; 9(12): 433. doi: 10.3390/biology9120433 PMID: 33266157
  45. Liu H, Lestari SD. Application of digital PCR (dPCR) in the detection of COVID-19 in food. E3S Web Conf 2021; 271: 02022. doi: 10.1051/e3sconf/202127102022
  46. Tsakogiannis D, Papacharalampous M, Toska E, et al. Duplex Real-time PCR assay and SYBR green I melting curve analysis for molecular identification of HPV genotypes 16, 18, 31, 35, 51 and 66. Mol Cell Probes 2015; 29(1): 13-8. doi: 10.1016/j.mcp.2014.09.003 PMID: 25281890
  47. Walters G, Alexander SI. T cell receptor BV repertoires using real time PCR: A comparison of SYBR green and a dual-labelled HuTrec™ fluorescent probe. J Immunol Methods 2004; 294(1-2): 43-52. doi: 10.1016/j.jim.2004.08.015 PMID: 15604015
  48. Sultani M, Mokhtari Azad T, Eshragian M, et al. Multiplex SYBR green real-time PCR assay for detection of respiratory viruses. Jundishapur J Microbiol 2015; 8(8): e19041. doi: 10.5812/jjm.19041v2 PMID: 26468358
  49. Rodríguez A, Rodríguez M, Luque MI, Justesen AF, Córdoba JJ. Quantification of ochratoxin A-producing molds in food products by SYBR green and TaqMan real-time PCR methods. Int J Food Microbiol 2011; 149(3): 226-35. doi: 10.1016/j.ijfoodmicro.2011.06.019 PMID: 21802757
  50. Quek MC, Chin NL, Tan SW, Yusof YA, Law CL. Molecular identification of species and production origins of edible bird’s nest using FINS and SYBR green I based real-time PCR. Food Control 2018; 84: 118-27. doi: 10.1016/j.foodcont.2017.07.027
  51. Tan LL, Ahmed SA, Ng SK, et al. Rapid detection of porcine DNA in processed food samples using a streamlined DNA extraction method combined with the SYBR green real-time PCR assay. Food Chem 2020; 309: 125654. doi: 10.1016/j.foodchem.2019.125654 PMID: 31678669
  52. Zheng HH, Zhang SJ, Cui JT, et al. Simultaneous detection of classical swine fever virus and porcine circovirus 3 by SYBR green I-based duplex real-time fluorescence quantitative PCR. Mol Cell Probes 2020; 50: 101524. doi: 10.1016/j.mcp.2020.101524 PMID: 31972226
  53. Yang K, Xu L, Liang Y, et al. Simultaneous differentiation and diagnosis of goose parvovirus and astrovirus in clinical samples with duplex SYBR green I real-time PCR. Mol Cell Probes 2020; 52: 101561. doi: 10.1016/j.mcp.2020.101561 PMID: 32173537
  54. Li J, Wei Y, Li J, et al. A novel duplex SYBR green real-time PCR with melting curve analysis method for beef adulteration detection. Food Chem 2021; 338: 127932. doi: 10.1016/j.foodchem.2020.127932 PMID: 32932080
  55. KrishnanNair Geetha D, Sivaraman B, Rammohan R, Venkatapathy N, Solai Ramatchandirane P. A SYBR green based multiplex real-time PCR assay for rapid detection and differentiation of ocular bacterial pathogens. J Microbiol Methods 2020; 171: 105875. doi: 10.1016/j.mimet.2020.105875 PMID: 32087185
  56. Tian RB, Jin Y, Xu T, Zhao Y, Wang ZY, Chen HY. Development of a SYBR green I-based duplex real-time PCR assay for detection of pseudorabies virus and porcine circovirus 3. Mol Cell Probes 2020; 53: 101593. doi: 10.1016/j.mcp.2020.101593 PMID: 32387303
  57. Malkamäki S, Näreaho A, Lavikainen A, Oksanen A, Sukura A. A new SYBR green real-time PCR assay for semi-quantitative detection of Echinococcus multilocularis and Echinococcus canadensis DNA on bilberries (Vaccinium myrtillus). Food Waterborne Parasitol 2019; 17: e00068. doi: 10.1016/j.fawpar.2019.e00068 PMID: 32095636
  58. Yılmaz R, Bayraç C, Başman A, Köksel H. Development of SYBR green-based real time PCR assays for detection and quantification of adulteration in wheat-based composite breads and their in- house validation. J Cereal Sci 2019; 85: 91-7. doi: 10.1016/j.jcs.2018.11.020
  59. Sacristán C, Catão-Dias JL, Ewbank AC, et al. Novel and highly sensitive SYBR® green real-time pcr for poxvirus detection in odontocete cetaceans. J Virol Methods 2018; 259: 45-9. doi: 10.1016/j.jviromet.2018.06.002 PMID: 29890240
  60. Abera T, Thangavelu A. Development of a two-step SYBR green I based real time RT-PCR assay for detecting and quantifying peste des petits ruminants virus in clinical samples. J Virol Methods 2014; 209: 25-9. doi: 10.1016/j.jviromet.2014.08.017 PMID: 25194891
  61. Şakalar E, Abasıyanık MF. The devolopment of duplex real-time PCR based on SYBR green florescence for rapid ıdentification of ruminant and poultry origins in foodstuff. Food Chem 2012; 130(4): 1050-4. doi: 10.1016/j.foodchem.2011.07.130
  62. Hosmillo MDT, Jeong YJ, Kim HJ, et al. Development of universal SYBR green real-time RT-PCR for the rapid detection and quantitation of bovine and porcine toroviruses. J Virol Methods 2010; 168(1-2): 212-7. doi: 10.1016/j.jviromet.2010.06.001 PMID: 20558206
  63. Mohamed N, Nilsson E, Johansson P, et al. Development and evaluation of a broad reacting SYBR-green based quantitative real- time PCR for the detection of different hantaviruses. J Clin Virol 2013; 56(4): 280-5. doi: 10.1016/j.jcv.2012.12.001 PMID: 23290388
  64. Jiang W, Wang P, Yu H, et al. Development of a SYBR green I based one-step real-time PCR assay for the detection of Hantaan virus. J Virol Methods 2014; 196: 145-51. doi: 10.1016/j.jviromet.2013.11.004 PMID: 24269331
  65. Anthony Johnson AM, Dasgupta I, Sai Gopal DVR. Development of loop-mediated isothermal amplification and SYBR green real- time PCR methods for the detection of Citrus yellow mosaic badnavirus in citrus species. J Virol Methods 2014; 203: 9-14. doi: 10.1016/j.jviromet.2014.03.013 PMID: 24675064
  66. Gibellini D, Vitone F, Schiavone P, Ponti C, La Placa M, Re MC. Quantitative detection of human immunodeficiency virus type 1 (HIV-1) proviral DNA in peripheral blood mononuclear cells by SYBR green real-time PCR technique. J Clin Virol 2004; 29(4): 282-9. doi: 10.1016/S1386-6532(03)00169-0 PMID: 15018857
  67. Gibellini D, Vitone F, Gori E, Placa ML, Re MC. Quantitative detection of human immunodeficiency virus type 1 (HIV-1) viral load by SYBR green real-time RT-PCR technique in HIV-1 seropositive patients. J Virol Methods 2004; 115(2): 183-9. doi: 10.1016/j.jviromet.2003.09.030 PMID: 14667534
  68. Pafundo S, Gullì M, Marmiroli N. SYBR® green ER™ real-time PCR to detect almond in traces in processed food. Food Chem 2009; 116(3): 811-5. doi: 10.1016/j.foodchem.2009.03.040
  69. Sariya L, Chatsirivech J, Suksai P, et al. Development of a SYBR green I-based real-time PCR for detection of elephant endotheliotropic herpesvirus 1 infection in Asian elephants (Elephas maximus). J Virol Methods 2012; 185(1): 160-5. doi: 10.1016/j.jviromet.2012.06.005 PMID: 22728215
  70. Balboni A, Dondi F, Prosperi S, Battilani M. Development of a SYBR green real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of canine adenovirus type 1 and type 2. J Virol Methods 2015; 222: 34-40. doi: 10.1016/j.jviromet.2015.05.009 PMID: 26028428
  71. Donà V, Bernasconi OJ, Kasraian S, Tinguely R, Endimiani A. A SYBR® green-based real-time PCR method for improved detection of mcr-1-mediated colistin resistance in human stool samples. J Glob Antimicrob Resist 2017; 9: 57-60. doi: 10.1016/j.jgar.2017.01.007 PMID: 28400211
  72. Cruz-Flores R, Mai HN, Dhar AK. Multiplex SYBR green and duplex TaqMan real-time PCR assays for the detection of Photorhabdus insect-related (Pir) toxin genes pirA and pirB. Mol Cell Probes 2019; 43: 20-8. doi: 10.1016/j.mcp.2018.12.004 PMID: 30576786
  73. Liu Q, Yang Z, Hao H, et al. Development of a SYBR green real- time RT-PCR assay for the detection of avian encephalomyelitis virus. J Virol Methods 2014; 206: 46-50. doi: 10.1016/j.jviromet.2014.05.015 PMID: 24880065
  74. Park SI, Park DH, Saif LJ, et al. Development of SYBR green real-time RT-PCR for rapid detection, quantitation and diagnosis of unclassified bovine enteric calicivirus. J Virol Methods 2009; 159(1): 64-8. doi: 10.1016/j.jviromet.2009.03.001 PMID: 19442847
  75. Pawar SS, Meshram CD, Singh NK, Saini M, Mishra BP, Gupta PK. Development of a SYBR green I based duplex real-time PCR for detection of bovine herpesvirus-1 in semen. J Virol Methods 2014; 208: 6-10. doi: 10.1016/j.jviromet.2014.07.027 PMID: 25078112
  76. Jor E, Myrmel M, Jonassen CM. SYBR green based real-time RT-PCR assay for detection and genotype prediction of bovine noroviruses and assessment of clinical significance in Norway. J Virol Methods 2010; 169(1): 1-7. doi: 10.1016/j.jviromet.2010.03.028 PMID: 20381534
  77. Wang Y, Li Y, Cui Y, et al. Duplex SYBR green I-based real- time PCR assay for the rapid detection of canine kobuvirus and canine astrovirus. J Virol Methods 2021; 290: 114066. doi: 10.1016/j.jviromet.2021.114066 PMID: 33453300
  78. Zhong Y, Wang Y, Zhao T, et al. Multiplex real-time SYBR green I PCR assays for simultaneous detection of 15 common enteric pathogens in stool samples. Mol Cell Probes 2020; 53: 101619. doi: 10.1016/j.mcp.2020.101619 PMID: 32562853
  79. Cheng W, He X, Jia H, et al. Development of a SYBR green I real-time PCR for detection and quantitation of orthopoxvirus by using Ectromelia virus. Mol Cell Probes 2018; 38: 45-50. doi: 10.1016/j.mcp.2017.12.001 PMID: 29224776
  80. Shi H, Li M, Huang X, et al. Development of SYBR green real- time PCR for diagnosis of fasciolosis in sheep. Vet Parasitol 2020; 283: 109193. doi: 10.1016/j.vetpar.2020.109193 PMID: 32731054
  81. Xia Y, Shi Z, Wang X, et al. Development and application of SYBR green I real-time quantitative reverse transcription PCR assay for detection of swine Getah virus. Mol Cell Probes 2021; 57: 101730. doi: 10.1016/j.mcp.2021.101730 PMID: 33848593
  82. Duzlu O, Yildirim A, Yetismis G, et al. Development and field evaluation of a species-specific mt-COI targeted SYBR-green Real Time PCR for detection and quantification of Haemonchus contortus in cattle in Turkey. Vet Parasitol 2020; 277: 109020. doi: 10.1016/j.vetpar.2019.109020 PMID: 31896019
  83. Elsayed Metawlly D, Noby Amer A, Mostafa Mostafa H, El Din Elsawaf G, Abd El Kader O. Low cost detection of hepatitis C virus RNA in HCV infected patients by SYBR green I real-time PCR. Alex J Med 2018; 54(4): 481-5. doi: 10.1016/j.ajme.2017.11.004
  84. Acevedo AM, Perera CL, Vega A, et al. A duplex SYBR green I-based real-time RT-PCR assay for the simultaneous detection and differentiation of Massachusetts and non-Massachusetts serotypes of infectious bronchitis virus. Mol Cell Probes 2013; 27(5-6): 184-92. doi: 10.1016/j.mcp.2013.06.001 PMID: 23810983
  85. Kokkattunivarthil S, Krishnan R, Kezhedath J, Prasad KP, Naik TV. New set of PCR primers for SYBR green-based qPCR detection of IMNV in India. Aquaculture 2018; 495: 726-30. doi: 10.1016/j.aquaculture.2018.06.061
  86. Liu S, Hou G, Zhuang Q, et al. A SYBR green I real-time RT-PCR assay for detection and differentiation of influenza A(H1N1) virus in swine populations. J Virol Methods 2009; 162(1-2): 184-7. doi: 10.1016/j.jviromet.2009.07.035 PMID: 19682498
  87. Santhosh SR, Parida MM, Dash PK, et al. Development and evaluation of SYBR green I-based one-step real-time RT-PCR assay for detection and quantitation of Japanese encephalitis virus. J Virol Methods 2007; 143(1): 73-80. doi: 10.1016/j.jviromet.2007.02.011 PMID: 17403544
  88. Meemetta W, Domingos JA, Dong HT, Senapin S. Development of a SYBR green quantitative PCR assay for detection of Lates calcarifer herpesvirus (LCHV) in farmed barramundi. J Virol Methods 2020; 285: 113920. doi: 10.1016/j.jviromet.2020.113920 PMID: 32579895
  89. Kumar JS, Saxena D, Parida M. Development and comparative evaluation of SYBR green I-based one-step real-time RT-PCR assay for detection and quantification of West Nile virus in human patients. Mol Cell Probes 2014; 28(5-6): 221-7. doi: 10.1016/j.mcp.2014.03.005 PMID: 24732288
  90. del Rio-Lavín A, Jiménez E, Pardo MÁ. SYBR-green real-time PCR assay with melting curve analysis for the rapid identification of Mytilus species in food samples. Food Control 2021; 130: 108257. doi: 10.1016/j.foodcont.2021.108257
  91. 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(1-2): 149-56. doi: 10.1016/j.jviromet.2009.05.006 PMID: 19447142
  92. Chen G, Tang X, Sun Y, et al. Development of a SYBR green-based real-time quantitative PCR assay to detect PCV3 in pigs. J Virol Methods 2018; 251: 129-32. doi: 10.1016/j.jviromet.2017.10.012 PMID: 29031627
  93. Zhang D, Bai C, Ge K, et al. Establishment of an SYBR green-based real-time PCR assay for porcine circovirus type 4 detection. J Virol Methods 2020; 285: 113963. doi: 10.1016/j.jviromet.2020.113963 PMID: 32882322
  94. Zheng LL, Cui JT, Han HY, et al. Development of a duplex SYBR green I based real-time PCR assay for detection of porcine epidemic diarrhea virus and porcine bocavirus3/4/5. Mol Cell Probes 2020; 51: 101544. doi: 10.1016/j.mcp.2020.101544 PMID: 32109535
  95. Hou CY, Xu T, Zhang LH, et al. Simultaneous detection and differentiation of porcine circovirus 3 and 4 using a SYBR green І-based duplex quantitative PCR assay. J Virol Methods 2021; 293: 114152. doi: 10.1016/j.jviromet.2021.114152 PMID: 33845107
  96. Martínez E, Riera P, Sitjà M, Fang Y, Oliveira S, Maldonado J. Simultaneous detection and genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) by real-time RT-PCR and amplicon melting curve analysis using SYBR green. Res Vet Sci 2008; 85(1): 184-93. doi: 10.1016/j.rvsc.2007.10.003 PMID: 18054369
  97. Zhou X, Zhang T, Song D, et al. Comparison and evaluation of conventional RT-PCR, SYBR green I and TaqMan real-time RT-PCR assays for the detection of porcine epidemic diarrhea virus. Mol Cell Probes 2017; 33: 36-41. doi: 10.1016/j.mcp.2017.02.002 PMID: 28188840
  98. Zhou H, Lei Y, Wang P, Liu M, Hu X. Development of SYBR green real-time PCR and nested RT-PCR for the detection of Potato Mop-top Virus (PMTV) and viral surveys in Progeny tubers derived from PMTV infected Potato tubers. Mol Cell Probes 2019; 47: 101438. doi: 10.1016/j.mcp.2019.101438 PMID: 31422073
  99. Pereira-Gómez M, Fajardo Á, Echeverría N, et al. Evaluation of SYBR green real time PCR for detecting SARS-CoV-2 from clinical samples. J Virol Methods 2021; 289: 114035. doi: 10.1016/j.jviromet.2020.114035 PMID: 33285190
  100. Mu S, Abdullah SW, Zhang Y, et al. Development of a novel SYBR green I-based quantitative RT-PCR assay for Senecavirus A detection in clinical samples of pigs. Mol Cell Probes 2020; 53: 101643. doi: 10.1016/j.mcp.2020.101643 PMID: 32768439
  101. Ma L, Zeng F, Cong F, et al. Development of a SYBR green-based real-time RT-PCR assay for rapid detection of the emerging swine acute diarrhea syndrome coronavirus. J Virol Methods 2019; 265: 66-70. doi: 10.1016/j.jviromet.2018.12.010 PMID: 30593837
  102. Ramesh kumar D, Sanjuktha M, Rajan JJS, et al. Development of SYBR green based real time PCR assay for detection of monodon baculovirus in Penaeus monodon. J Virol Methods 2014; 205: 81-6. doi: 10.1016/j.jviromet.2014.05.006 PMID: 24841550
  103. Xu MY, Liu SQ, Deng CL, Zhang QY, Zhang B. Detection of Zika virus by SYBR green one-step real-time RT-PCR. J Virol Methods 2016; 236: 93-7. doi: 10.1016/j.jviromet.2016.07.014 PMID: 27444120
  104. Snyder RP, Guerin MT, Hargis BM, et al. Exploiting digital droplet PCR and next generation sequencing technologies to determine the relative abundance of individual Eimeria species in a DNA sample. Vet Parasitol 2021; 296: 109443. doi: 10.1016/j.vetpar.2021.109443 PMID: 34147767
  105. Dingle TC, Sedlak RH, Cook L, Jerome KR. Tolerance of droplet-digital PCR vs. real-time quantitative PCR to inhibitory substances. Clin Chem 2013; 59(11): 1670-2. doi: 10.1373/clinchem.2013.211045 PMID: 24003063
  106. Cao Z, Wu W, Wei H, et al. Using droplet digital PCR in the detection of Mycobacterium tuberculosis DNA in FFPE samples. Int J Infect Dis 2020; 99: 77-83. doi: 10.1016/j.ijid.2020.07.045 PMID: 32738487
  107. Smitalova D, Dvorakova D, Racil Z, Romzova M. Digital PCR can provide improved BCR-ABL1 detection in chronic myeloid leukemia patients in deep molecular response and sensitivity of standard quantitative methods using EAC assays. Pract Lab Med 2021; 25: e00210. doi: 10.1016/j.plabm.2021.e00210 PMID: 33778144
  108. Nyaruaba R, Mwaliko C, Kering KK, Wei H. Droplet digital PCR applications in the tuberculosis world. Tuberculosis 2019; 117: 85-92. doi: 10.1016/j.tube.2019.07.001 PMID: 31378274
  109. Pinheiro LB, Coleman VA, Hindson CM, et al. Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal Chem 2012; 84(2): 1003-11. doi: 10.1021/ac202578x PMID: 22122760
  110. Demeke T, Eng M. Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events. Biomol Detect Quantif 2018; 15: 24-9. doi: 10.1016/j.bdq.2018.03.002 PMID: 29922591
  111. Wang X, Tang T, Miao Q, et al. Detection of transgenic rice line TT51-1 in processed foods using conventional PCR, real-time PCR, and droplet digital PCR. Food Control 2019; 98: 380-8. doi: 10.1016/j.foodcont.2018.11.032
  112. Gou T, Hu J, Wu W, et al. Smartphone-based mobile digital PCR device for DNA quantitative analysis with high accuracy. Biosens Bioelectron 2018; 120: 144-52. doi: 10.1016/j.bios.2018.08.030 PMID: 30173010
  113. Manoj P. Droplet digital PCR technology promises new applications and research areas. Mitochondrial DNA 2016; 27(1): 742-6. doi: 10.3109/19401736.2014.913168 PMID: 24779593
  114. Lin J, Su G, Su W, Zhou C. Progress in digital PCR technology and application. Sheng Wu Gong Cheng Xue Bao 2017; 33(2): 170-7. PMID: 28956373
  115. Netzer R, Ribičić D, Aas M, Cavé L, Dhawan T. Absolute quantification of priority bacteria in aquaculture using digital PCR. J Microbiol Methods 2021; 183: 106171. doi: 10.1016/j.mimet.2021.106171 PMID: 33610596
  116. Nishimura N, Takeuchi K, Asaka R, et al. MYD88 L265P mutation detected by digital PCR as a prognostic factor in patients with diffuse large B-cell lymphoma in rituximab era. Leuk Res 2020; 97: 106426. doi: 10.1016/j.leukres.2020.106426 PMID: 32781214
  117. Chen B, Jiang Y, Cao X, Liu C, Zhang N, Shi D. Droplet digital PCR as an emerging tool in detecting pathogens nucleic acids in infectious diseases. Clin Chim Acta 2021; 517: 156-61. doi: 10.1016/j.cca.2021.02.008 PMID: 33662358
  118. Yu N, Ren J, Huang W, Xing R, Deng T, Chen Y. An effective analytical droplet digital PCR approach for identification and quantification of fur-bearing animal meat in raw and processed food. Food Chem 2021; 355: 129525. doi: 10.1016/j.foodchem.2021.129525 PMID: 33799266
  119. Fan HC, Blumenfeld YJ, El-Sayed YY, Chueh J, Quake SR. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy. Am J Obstet Gynecol 2009; 200(5): 543.e1-7. doi: 10.1016/j.ajog.2009.03.002 PMID: 19375573
  120. Morella NM, Yang SC, Hernandez CA, Koskella B. Rapid quantification of bacteriophages and their bacterial hosts in vitro and in vivo using droplet digital PCR. J Virol Methods 2018; 259: 18-24. doi: 10.1016/j.jviromet.2018.05.007 PMID: 29859196
  121. Schwartz SL, Lowen AC. Droplet digital PCR: A novel method for detection of influenza virus defective interfering particles. J Virol Methods 2016; 237: 159-65. doi: 10.1016/j.jviromet.2016.08.023 PMID: 27590979
  122. Pritchard JJG, Hamilton G, Hurst CD, et al. Monitoring of urothelial cancer disease status after treatment by digital droplet PCR liquid biopsy assays. Urol Oncol 2020; 38(9): 737.e1-737.e10. doi: 10.1016/j.urolonc.2020.05.012 PMID: 32532529
  123. Varela MF, Monteiro S, Rivadulla E, Santos R, Romalde JL. Development of a novel digital RT-PCR method for detection of human sapovirus in different matrices. J Virol Methods 2018; 254: 21-4. doi: 10.1016/j.jviromet.2018.01.005 PMID: 29407209
  124. Dasgupta K, Lessard S, Hann S, Fowler ME, Robling AG, Warman ML. Sensitive detection of Cre-mediated recombination using droplet digital PCR reveals Tg(BGLAP-Cre) and Tg(DMP1-Cre) are active in multiple non-skeletal tissues. Bone 2021; 142: 115674. doi: 10.1016/j.bone.2020.115674 PMID: 33031974
  125. Tan SYH, Kwek SYM, Low H, Pang YLJ. Absolute quantification of SARS-CoV-2 with clarity PlusTM digital PCR. Methods 2021; 2021: 26-33. doi: 10.1016/j.ymeth.2021.07.005 PMID: 34273478
  126. Wang Y, Cooper R, Bergelson S, Feschenko M. Quantification of residual BHK DNA by a novel droplet digital PCR technology. J Pharm Biomed Anal 2018; 159: 477-82. doi: 10.1016/j.jpba.2018.07.022 PMID: 30048895
  127. Borsu L, Intrieri J, Thampi L, et al. Clinical application of picodroplet digital PCR technology for rapid detection of EGFR T790M in next-generation sequencing libraries and DNA from limited tumor samples. J Mol Diagn 2016; 18(6): 903-11. doi: 10.1016/j.jmoldx.2016.07.004 PMID: 27631691
  128. Caviglia GP, Abate ML, Olivero A, et al. Absolute quantification of intrahepatic hepatitis B virus covalently-closed-circular DNA by droplet digital PCR technology. J Hepatol 2017; 66(1): S262-3. doi: 10.1016/S0168-8278(17)30836-X
  129. Pan Y, Ma T, Meng Q, et al. Droplet digital PCR enabled by microfluidic impact printing for absolute gene quantification. Talanta 2020; 211: 120680. doi: 10.1016/j.talanta.2019.120680 PMID: 32070562
  130. Powell L, Dhummakupt A, Siems L, et al. Clinical validation of a quantitative HIV-1 DNA droplet digital PCR assay: Applications for detecting occult HIV-1 infection and monitoring cell-associated HIV-1 dynamics across different subtypes in HIV-1 prevention and cure trials. J Clin Virol 2021; 139: 104822. doi: 10.1016/j.jcv.2021.104822 PMID: 33930698
  131. Yin H, Wu Z, Shi N, et al. Ultrafast multiplexed detection of SARS-CoV-2 RNA using a rapid droplet digital PCR system. Biosens Bioelectron 2021; 188: 113282. doi: 10.1016/j.bios.2021.113282 PMID: 34020234
  132. Martin A, Storto A, Le Hingrat Q, et al. High-sensitivity SARS- CoV-2 group testing by digital PCR among symptomatic patients in hospital settings. J Clin Virol 2021; 141: 104895. doi: 10.1016/j.jcv.2021.104895 PMID: 34246075
  133. Lee SS, Park JH, Bae YK. Comparison of two digital PCR methods for EGFR DNA and SARS-CoV-2 RNA quantification. Clin Chim Acta 2021; 521: 9-18. doi: 10.1016/j.cca.2021.06.016 PMID: 34144041
  134. Colafigli G, Scalzulli E, Di Prima A, et al. Digital droplet PCR as a predictive tool for successful discontinuation outcome in chronic myeloid leukemia: Is it time to introduce it in the clinical practice? Crit Rev Oncol Hematol 2021; 157: 103163. doi: 10.1016/j.critrevonc.2020.103163 PMID: 33246263
  135. Pierboni E, Rondini C, Torricelli M, et al. Digital PCR for analysis of peanut and soybean allergens in foods. Food Control 2018; 92: 128-36. doi: 10.1016/j.foodcont.2018.04.039
  136. Han J, Lee JY, Bae YK. Application of digital PCR for assessing DNA fragmentation in cytotoxicity response. Biochim Biophys Acta, Gen Subj 2019; 1863(8): 1235-42. doi: 10.1016/j.bbagen.2019.05.001 PMID: 31071410
  137. Maremonti E, Brede DA, Olsen AK, Eide DM, Berg ES. Ionizing radiation, genotoxic stress, and mitochondrial DNA copy-number variation in Caenorhabditis elegans: Droplet digital PCR analysis. Mutat Res Genet Toxicol Environ Mutagen 2020; 858-860: 503277. doi: 10.1016/j.mrgentox.2020.503277 PMID: 33198926
  138. Jiang X, Chen S, Zhu X, Xu X, Liu Y. Development and validation of a droplet digital PCR assay for the evaluation of PML-RARα fusion transcripts in acute promyelocytic leukemia. Mol Cell Probes 2020; 53: 101617. doi: 10.1016/j.mcp.2020.101617 PMID: 32585184
  139. He L, Simpson DJ, Gänzle MG. Detection of enterohaemorrhagic Escherichia coli in food by droplet digital PCR to detect simultaneous virulence factors in a single genome. Food Microbiol 2020; 90: 103466. doi: 10.1016/j.fm.2020.103466 PMID: 32336350
  140. Bogožalec Košir A, Cvelbar T, Kammel M, Grunert HP, Zeichhardt H, Milavec M. Digital PCR method for detection and quantification of specific antimicrobial drug-resistance mutations in human cytomegalovirus. J Virol Methods 2020; 281: 113864. doi: 10.1016/j.jviromet.2020.113864 PMID: 32380093
  141. Sun W, Shahrajabian MH. The golden spice for life: Turmeric with the pharmacological benefits of curcuminoids components, including curcumin, bisdemethoxycurcumin, and demethoxycurcumin. Curr Org Synth 2023; 20. doi: 10.2174/1570179420666230607124949 PMID: 37287298
  142. Cui H, Shahrajabian MH, Kuang Y, Zhang HY, Sun W. Heterologous expression and function of cholesterol oxidase: A review. Protein Pept Lett 2023; 30(7): 531-40. doi: 10.2174/0929866530666230525162545 PMID: 37231716
  143. Shahrajabian MH, Sun W. Various techniques for molecular and rapid detection infectious and epidemic diseases. Lett Org Chem 2023; 20(9): 779-801. doi: 10.2174/1570178620666230331095720
  144. Shahrajabian MH, Sun W. Sun, The importance of salicylic acid, humic acid and fulvic acid on crop production. Lett Drug Des Discov 2023; 20: 1-16. doi: 10.2174/1570180820666230411102209
  145. Shahrajabian MH, Sun W. Survey on multi-omics and multi- omics data analysis, integration and application. Curr Pharm Anal 2023; 19(4): 267-81. doi: 10.2174/1573412919666230406100948
  146. Minato T, Ito S, Li B, et al. Liquid biopsy with droplet digital PCR targeted to specific mutations in plasma cell-free tumor DNA can detect ovarian cancer recurrence earlier than CA125. Gynecol Oncol Rep 2021; 38: 100847. doi: 10.1016/j.gore.2021.100847 PMID: 34557579
  147. Sefrioui D, Mauger F, Leclere L, et al. Comparison of the quantification of KRAS mutations by digital PCR and E-ice-COLD-PCR in circulating-cell-free DNA from metastatic colorectal cancer patients. Clin Chim Acta 2017; 465: 1-4. doi: 10.1016/j.cca.2016.12.004 PMID: 27940131
  148. Shahrajabian MH, Sun W. Assessment of wine quality, traceability and detection of grapes wine, detection of harmful substances in alcohol and liquor composition analysis. Lett Drug Des Discov 2023; 20: 1570180820666230228115450. doi: 10.2174/1570180820666230228115450
  149. Sun W, Shahrajabian MH. Therapeutic potential of phenolic compounds in medicinal plants-natural health products for human health. Molecules 2023; 28(4): 1845. doi: 10.3390/molecules28041845 PMID: 36838831
  150. Jahne MA, Brinkman NE, Keely SP, Zimmerman BD, Wheaton EA, Garland JL. Droplet digital PCR quantification of norovirus and adenovirus in decentralized wastewater and graywater collections: Implications for onsite reuse. Water Res 2020; 169: 115213. doi: 10.1016/j.watres.2019.115213 PMID: 31671297
  151. Liao Y, Chen Y, Kou X, Xiao Y, Ye J, Wu A. Diagnostic test accuracy of droplet digital PCR for the detection of EGFR mutation (T790M) in plasma: Systematic review and meta-analysis. Clin Chim Acta 2020; 503: 190-6. doi: 10.1016/j.cca.2019.11.023 PMID: 31805270
  152. Shahrajabian MH, Petropoulos SA, Sun W. Survey of the influences of microbial biostimulants on horticultural crops: Case studies and successful paradigms. Horticulturae 2023; 9(2): 193. doi: 10.3390/horticulturae9020193
  153. Shahrajabian MH, Sun W. Survey on medicinal plants and herbs in traditional Iranian medicine with anti-oxidant, anti-viral, anti-microbial, and anti-inflammatory properties. Lett Drug Des Discov 2023; 20(11): 1707-43. doi: 10.2174/1570180819666220816115506
  154. Shahrajabian MH, Sun W. Importance thymoquinone, sulforaphane, phloretin, and epigallocatechin and their health benefits. Lett Drug Des Discov 2024; 21(2): 209-25. doi: 10.2174/1570180819666220902115521
  155. Sun W, Shahrajabian MH, Lin M. Research progress of fermented functional foods and protein factory-microbial fermentation technology. Fermentation 2022; 8(12): 688. doi: 10.3390/fermentation8120688
  156. Sun W, Shahrajabian MH, Petropoulos SA, Shahrajabian N. Developing sustainable agriculture systems in medicinal and aromatic plant production by using chitosan and chitin-based biostimulants. Plants 2023; 12(13): 2469. doi: 10.3390/plants12132469 PMID: 37447031
  157. Shahrajabian MH, Sun W. Five important seeds in traditional medicine, and pharmacological benefits. Seeds 2023; 2(3): 290-308. doi: 10.3390/seeds2030022
  158. Shahrajabian MH, Sun W. Study of different types of fermentation in wine-making process and considering aromatic substances and organic acid. Curr Org Synth 2023; 20. doi: 10.2174/1570179420666230803102253 PMID: 37534487
  159. Sun W, Shahrajabian MH. The application of arbuscular mycorrhizal fungi as microbial biostimulant, sustainable approaches in modern agriculture. Plants 2023; 12(17): 3101. doi: 10.3390/plants12173101 PMID: 37687348
  160. Shahrajabian MH, Sun W. Mechanism of action of collagen and epidermal growth factor: A review on theory and research methods. Mini Rev Med Chem 2023; 23. doi: 10.2174/1389557523666230816090054 PMID: 37587815
  161. Shahrajabian MH, Kuang Y, Cui H, Fu L, Sun W. Metabolic changes of active components of important medicinal plants on the basis of traditional Chinese medicine under different environmental stresses. Curr Org Chem 2023; 27(9): 782-806. doi: 10.2174/1385272827666230807150910

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