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Original Research

A Sensitive PCR-Based Method for Somatic Mutations Enrichment and Screening

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Pages 8099-8107 | Published online: 27 Oct 2021

References

  • Gerber DE, Gandhi L, Costa DB. Management and future directions in non-small cell lung cancer with known activating mutations. Am Soc Clin Oncol Educ Book. 2014;e353–e365. doi:10.14694/EdBook_AM.2014.34.e35324857124
  • Gonzalez DCD, Clarke PA, Al-Lazikani B, Workman P. Personalized cancer medicine: molecular diagnostics, predictive biomarkers, and drug resistance. Clin Pharmacol Ther. 2013;93(3):252–259. doi:10.1038/clpt.2012.23723361103
  • Kalia M. Personalized oncology: recent advances and future challenges. Metabolism. 2013;62(Suppl 1):S11–S14. doi:10.1016/j.metabol.2012.08.01622999010
  • Normanno N, Rachiglio AM, Roma C, et al. Molecular diagnostics and personalized medicine in oncology: challenges and opportunities. J Cell Biochem. 2013;114(3):514–524. doi:10.1002/jcb.2440122991232
  • Kim H, Ruby AE, Shandilya HG, et al. T-blocker: a simple and robust probe-free quantitative PCR assay to detect somatic mutations down to 0.1% frequency. Biotechniques. 2018;65(4):205–210. doi:10.2144/btn-2018-011130284934
  • 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/17.7.25032785681
  • Bolton L, Reiman A, Lucas K, Timms J, Cree IA. KRAS mutation analysis by PCR: a comparison of two methods. PLoS One. 2015;10(1):e115672. doi:10.1371/journal.pone.0115672
  • Morlan J, Baker J, Sinicropi D. Mutation detection by real-time PCR: a simple, robust and highly selective method. PLoS One. 2009;4(2):e4584. doi:10.1371/journal.pone.000458419240792
  • Wang H, Jiang J, Mostert B, et al. Allele-specific, non-extendable primer blocker PCR (AS-NEPB-PCR) for DNA mutation detection in cancer. J Mol Diagn. 2013;15(1):62–69. doi:10.1016/j.jmoldx.2012.08.00723159590
  • Pender A, Garcia-Murillas I, Rana S, et al. Efficient genotyping of KRAS mutant non-small cell lung cancer using a multiplexed droplet digital PCR approach. PLoS One. 2015;10(9):e139074. doi:10.1371/journal.pone.0139074
  • Wood-Bouwens C, Lau BT, Handy CM, Lee H, Ji HP. Single-color digital PCR provides high-performance detection of cancer mutations from circulating DNA. J Mol Diagn. 2017;19(5):697–710. doi:10.1016/j.jmoldx.2017.05.00328818432
  • Qiu P, Shandilya H, D’Alessio JM, O’Connor K, Durocher J, Gerard GF. Mutation detection using Surveyor nuclease. Biotechniques. 2004;36(4):702–707. doi:10.2144/04364PF0115088388
  • Huang MC, Cheong WC, Lim LS, Li MH. A simple, high sensitivity mutation screening using Ampligase mediated T7 endonuclease I and Surveyor nuclease with microfluidic capillary electrophoresis. Electrophoresis. 2012;33(5):788–796. doi:10.1002/elps.20110046022437793
  • Tsuji T, Niida Y. Development of a simple and highly sensitive mutation screening system by enzyme mismatch cleavage with optimized conditions for standard laboratories. Electrophoresis. 2008;29(7):1473–1483. doi:10.1002/elps.20070072918300207
  • Wada T, Fukushima Y, Saitoh S. A new detection method for ATRX gene mutations using a mismatch-specific endonuclease. Am J Med Genet a. 2006;140(14):1519–1523. doi:10.1002/ajmg.a.3131016763962
  • Pagniez-Mammeri H, Lombes A, Brivet M, et al. Rapid screening for nuclear genes mutations in isolated respiratory chain complex I defects. Mol Genet Metab. 2009;96(4):196–200. doi:10.1016/j.ymgme.2008.12.00319167255
  • Jackman DM, Holmes AJ, Lindeman N, et al. Response and resistance in a non-small-cell lung cancer patient with an epidermal growth factor receptor mutation and leptomeningeal metastases treated with high-dose gefitinib. J Clin Oncol. 2006;24(27):4517–4520. doi:10.1200/JCO.2006.06.612616983123
  • Qiu P, Shandilya H, Gerard GF. A method for clone sequence confirmation using a mismatch-specific DNA endonuclease. Mol Biotechnol. 2005;29(1):11–18. doi:10.1385/MB:29:1:1115668515
  • Oleykowski CA, Bronson MC, Godwin AK, Yeung AT. Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 1998;26(20):4597–4602. doi:10.1093/nar/26.20.45979753726
  • Aggeli D, Karas VO, Sinnott-Armstrong NA, et al. Diff-seq: a high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Res. 2018;46(7):e42. doi:10.1093/nar/gky02229361139
  • Wan JCM, Heider K, Gale D, et al. CtDNA monitoring using patient-specific sequencing and integration of variant reads. Sci Transl Med. 2020;12(548):z8084. doi:10.1126/scitranslmed.aaz8084
  • Luo H, Zhao Q, Wei W, et al. Circulating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer. Sci Transl Med. 2020;12(524):x7533. doi:10.1126/scitranslmed.aax7533
  • Kandoth C, Mclellan MD, Vandin F, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502(7471):333–339. doi:10.1038/nature1263424132290
  • Sequist LV, Bell DW, Lynch TJ, Haber DA. Molecular predictors of response to epidermal growth factor receptor antagonists in non-small-cell lung cancer. J Clin Oncol. 2007;25(5):587–595. doi:10.1200/JCO.2006.07.358517290067
  • Paez JG, Janne PA, Lee JC, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004;304(5676):1497–1500. doi:10.1126/science.109931415118125
  • Lynch TJ, Bell DW, Sordella R, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med. 2004;350(21):2129–2139. doi:10.1056/NEJMoa04093815118073
  • Pao W, Miller V, Zakowski M, et al. EGF receptor gene mutations are common in lung cancers from “never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci USA. 2004;101(36):13306–13311. doi:10.1073/pnas.040522010115329413
  • Shigematsu H, Lin L, Takahashi T, et al. Clinical and biological features associated with epidermal growth factor receptor gene mutations in lung cancers. J Natl Cancer Inst. 2005;97(5):339–346. doi:10.1093/jnci/dji05515741570
  • Keraite I, Alvarez-Garcia V, Garcia-Murillas I, et al. PIK3CA mutation enrichment and quantitation from blood and tissue. Sci Rep. 2020;10(1). doi:10.1038/s41598-020-74086-w
  • Jin S, Zhu D, Shao F, et al. Efficient detection and post-surgical monitoring of colon cancer with a multi-marker DNA methylation liquid biopsy. Proc Natl Acad Sci USA. 2021;118(5):e2017421118. doi:10.1073/pnas.201742111833495330
  • Alvarez-Garcia V, Bartos C, Keraite I, et al. A simple and robust real-time qPCR method for the detection of PIK3CA mutations. Sci Rep. 2018;8(1):4290. doi:10.1038/s41598-018-22473-929523855