Taqman-MGB nanoPCR for Highly Specific Detection of Single-Base Mutations

References

• Hart JR, Zhang Y, Liao L, et al. The butterfly effect in cancer: a single base mutation can remodel the cell. Proc Natl Acad Sci U S A. 2015;112(4):1131. doi:10.1073/pnas.1424012112
   PubMedGoogle Scholar
• Riva L, Pandiri AR, Li YR, et al. The mutational signature profile of known and suspected human carcinogens in mice. Nat Genet. 2020;52(11):1189–1197. doi:10.1038/s41588-020-0692-4
   PubMed Web of Science ®Google Scholar
• Doudna JA. The promise and challenge of therapeutic genome editing. Nature. 2020;578(7794):229–236. doi:10.1038/s41586-020-1978-5
   PubMed Web of Science ®Google Scholar
• Chen P, Pan D, Fan C, et al. Gold nanoparticles for high-throughput genotyping of long-range haplotypes. Nat Nanotechnol. 2011;6(10):639–644. doi:10.1038/nnano.2011.141
   PubMedGoogle Scholar
• Oxnard GR, Hu Y, Mileham KF, et al. Assessment of resistance mechanisms and clinical implications in patients with EGFR T790M-positive lung cancer and acquired resistance to osimertinib. JAMA Oncol. 2018;4(11):1527–1534. doi:10.1001/jamaoncol.2018.2969
   PubMed Web of Science ®Google Scholar
• Planchard D, Popat S, Kerr K, et al. Correction to: “Metastatic non-small cell lung cancer: ESMO clinical practice guidelines for diagnosis, treatment and follow-up”. Ann Oncol. 2019;30(5):863–870. doi:10.1093/annonc/mdy474
   PubMed Web of Science ®Google Scholar
• Eide I, Å H, Ekman S, et al. Osimertinib in T790M-positive and -negative patients with EGFR-mutated advanced non-small cell lung cancer (the TREM-study). Lung Cancer. 2020;143:27–35. doi:10.1016/j.lungcan.2020.03.009
   PubMed Web of Science ®Google Scholar
• Vollbrecht C, Lehmann A, Lenze D, Hummel M. Validation and comparison of two NGS assays for the detection of EGFR T790M resistance mutation in liquid biopsies of NSCLC patients. Oncotarget. 2018;9(26):18529–18539. doi:10.18632/oncotarget.24908
   PubMedGoogle Scholar
• Aravanis AM, Lee M, Klausner RD. Next-generation sequencing of circulating tumor DNA for early cancer detection. Cell. 2017;168(4):571–574. doi:10.1016/j.cell.2017.01.030
   PubMed Web of Science ®Google Scholar
• Van Amerongen RA, Retèl VP, Coupé VM, Nederlof PM, Vogel MJ, Van Harten WH. Next-generation sequencing in NSCLC and melanoma patients: a cost and budget impact analysis. Ecancermedicalscience. 2016;10. doi:10.3332/ecancer.2016.684
   PubMedGoogle Scholar
• Brychta N, Krahn T, von Ahsen O. Detection of KRAS mutations in circulating tumor DNA by digital PCR in early stages of pancreatic cancer. Clin Chem. 2016;62(11):1482–1491. doi:10.1373/clinchem.2016.257469
   PubMed Web of Science ®Google Scholar
• Xiang Z, Wan R, Zou B, et al. Highly sensitive and specific real-time PCR by employing serial invasive reaction as a sequence identifier for quantifying EGFR mutation abundance in cfDNA. Anal Bioanal Chem. 2018;410(26):6751–6759. doi:10.1007/s00216-018-1316-z
   PubMedGoogle Scholar
• Salipante SJ, Jerome KR. Digital PCR-an emerging technology with broad applications in microbiology. Clin Chem. 2020;66(1):117–123. doi:10.1373/clinchem.2019.304048
   PubMed Web of Science ®Google Scholar
• Newton CR, Graham A, Heptinstall LE, et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989;17(7):2503–2516. doi:10.1093/nar/17.7.2503
   PubMed Web of Science ®Google Scholar
• Xue B, Li Y, Wang X, et al. TaqMan-MGB probe quantitative PCR assays to genotype and quantify three mtDNA mutations of Leber hereditary optic neuropathy. Sci Rep. 2020;10(1):12264. doi:10.1038/s41598-020-69220-7
   PubMed Web of Science ®Google Scholar
• Belousov YS, Welch RA, Sanders S, Mills A. Single nucleotide polymorphism genotyping by two colour melting curve analysis using the MGB eclipse probe system in challenging sequence environment. Hum Genomics. 2004;1(3):1–9. doi:10.1186/1479-7364-1-3-209
   Google Scholar
• Park JY, Back SH, Chang SJ, Lee SJ, Lee KG, Park TJ. Dopamine-assisted synthesis of carbon-coated silica for PCR enhancement. ACS Appl Mater Interfaces. 2015;7(28):15633–15640. doi:10.1021/acsami.5b04404
   PubMedGoogle Scholar
• Tong W, Cao X, Wen S, et al. Enhancing the specificity and efficiency of polymerase chain reaction using polyethyleneimine-based derivatives and hybrid nanocomposites. Int J Nanomedicine. 2012;7:1069–1078. doi:10.2147/IJN.S28947
   PubMed Web of Science ®Google Scholar
• Sun C, Cheng Y, Pan Y, Yang J, Wang X, Xia F. Efficient polymerase chain reaction assisted by metal–organic frameworks. Chem Sci. 2020;11(3):797–802. doi:10.1039/C9SC03202A
   Google Scholar
• Chen F, Zhao Y, Fan C, Zhao Y. Mismatch extension of DNA polymerases and high-accuracy single nucleotide polymorphism diagnostics by gold nanoparticle-improved isothermal amplification. Anal Chem. 2015;87(17):8718–8723. doi:10.1021/acs.analchem.5b01545
   PubMedGoogle Scholar
• Li H, Huang J, Lv J, et al. Nanoparticle PCR: nanogold-assisted PCR with enhanced specificity. Angew Chem Int Ed Engl. 2005;44(32):5100–5103. doi:10.1002/anie.200500403
   PubMedGoogle Scholar
• Li M, Lin YC, Wu CC, Liu HS. Enhancing the efficiency of a PCR using gold nanoparticles. Nucleic Acids Res. 2005;33(21):e184. doi:10.1093/nar/gni183
   PubMed Web of Science ®Google Scholar
• Ye X, Fang X, Li X, Kong J. Gold nanoparticle-mediated nucleic acid isothermal amplification with enhanced specificity. Anal Chim Acta. 2018;1043:150–157. doi:10.1016/j.aca.2018.09.016
   PubMedGoogle Scholar
• Sedighi A, Oberc C, Whitehall V, Li PCH. NanoHDA: a nanoparticle-assisted isothermal amplification technique for genotyping assays. Nano Res. 2016.
   Google Scholar
• Kim HR, Baek A, Lee IJ, Kim D. Facilitation of polymerase chain reaction with poly(ethylene glycol)-engrafted graphene oxide analogous to a single-stranded-DNA binding protein. Acs Appl Mater Inter. 2016;8(49):33521–33528. doi:10.1021/acsami.6b13223
   PubMedGoogle Scholar
• Lou X, Zhang Y. Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis. Appl Mater Interfaces. 2013;5(13):6276–6284. doi:10.1021/am4013209
   PubMedGoogle Scholar
• Cui D, Tian F, Kong Y, Titushikin I, Gao H. Effects of single-walled carbon nanotubes on the polymerase chain reaction. Nanotechnology. 2004;15(1):154–157. doi:10.1088/0957-4484/15/1/030
   Google Scholar
• Li A, Zhou B, Alves C, et al. Mechanistic studies of enhanced PCR using PEGylated PEI-entrapped gold nanoparticles. Acs Appl Mater Interfaces. 2016;8(39):25808–25817. doi:10.1021/acsami.6b09310
   PubMedGoogle Scholar
• Pan D, Mi L, Huang Q, Hu J, Fan C. Genetic analysis with nanoPCR. Integr Biol-Uk. 2012;4(10):1155–1163. doi:10.1039/c2ib20076g
   Google Scholar
• Pan D, Wen Y, Mi L, Fan C, Hu J. Nanomaterials-based polymerase chain reactions for DNA detection. Curr Org Chem. 2011;15(4):486–497. doi:10.2174/138527211794474447
   Google Scholar
• Bai Y, Cui Y, Paoli GC, Shi C, Shi X. Nanoparticles affect PCR primarily via surface interactions with PCR components: using amino-modified silica-coated magnetic nanoparticles as a main model. Acs Appl Mater Inter. 2015;7(24):13142–13153. doi:10.1021/am508842v
   PubMedGoogle Scholar
• Cao X, Shi X, Yang W, Zhang X, Fan C, Hu J. Enhanced specificity and efficiency of polymerase chain reactions using poly(amidoamine) dendrimers and derivatives. Analyst. 2008;134:87–92. doi:10.1039/B812176A
   PubMedGoogle Scholar
• Li X, Cai W, Yang G, et al. Comprehensive analysis of EGFR-mutant abundance and its effect on efficacy of EGFR TKIs in advanced NSCLC with EGFR mutations. J Thorac Oncol. 2017;12(9):1388–1397. doi:10.1016/j.jtho.2017.06.006
   PubMedGoogle Scholar
• Malapelle U, Sirera R, Jantus-Lewintre E, et al. Profile of the Roche cobas® EGFR mutation test v2 for non-small cell lung cancer. Expert Rev Mol Diagn. 2017;17(3):209–215. doi:10.1080/14737159.2017.1288568
   PubMed Web of Science ®Google Scholar
• Wu S, Chiang C, Liu C, et al. An observational study of acquired EGFR T790M-dependent resistance to EGFR-TKI treatment in lung adenocarcinoma patients in Taiwan. Front Oncol. 2020;10.
   Google Scholar
• Vallée A, Le Loupp A, Denis MG. Efficiency of the Therascreen® RGQ PCR kit for the detection of EGFR mutations in non-small cell lung carcinomas. Clin Chim Acta. 2014;429:8–11. doi:10.1016/j.cca.2013.11.014
   PubMedGoogle Scholar
• Feng Q, Gai F, Sang Y, et al. A comparison of QuantStudio™ 3D Digital PCR and ARMS-PCR for measuring plasma EGFR T790M mutations of NSCLC patients. Cancer Manag Res. 2018;10:115–121. doi:10.2147/CMAR.S148134
   PubMed Web of Science ®Google Scholar
• Yang Y, Meng Y, Zhang H, et al. Detection of EGFR and BRAF mutations by competitive allele-specific TaqMan polymerase chain reaction in lung adenocarcinoma. Oncol Lett. 2018;15(3):3295–3304. doi:10.3892/ol.2017.7652
   PubMed Web of Science ®Google Scholar
• Wang M, Yan Y, Wang R, et al. Simultaneous detection of bovine rotavirus, bovine parvovirus, and bovine viral diarrhea virus using a gold nanoparticle-assisted PCR assay with a dual-priming oligonucleotide system. Front Microbiol. 2019;10:2884. doi:10.3389/fmicb.2019.02884
   PubMedGoogle Scholar