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Article

Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay

  • Authors:
    • Sanpeng Xu
    • Yaqi Duan
    • Liping Lou
    • Fengjuan Tang
    • Juan Shou
    • Guoping Wang
  • View Affiliations / Copyright

    Affiliations: Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
  • Pages: 4238-4244
    |
    Published online on: September 26, 2016
       https://doi.org/10.3892/ol.2016.5184
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Abstract

The present study aimed to explore the influence of T790M neighboring single nucleotide polymorphism (SNP) on the sensitivity of amplification refractory mutation system (ARMS)‑based T790M mutation assay. Three ARMS‑quantitative polymerase chain reaction (qPCR) systems (system 1 had a forward ARMS primer without rs1050171, system 2 included a forward ARMS primer with rs1050171 and system 3 contained the above two forward ARMS primers) were used to detect the T790M mutation in two series plasmid samples and genomic DNA (gDNA) of the cell line H1975. A total of 670 formalin-fixed paraffin‑embedded (FFPE) tumor samples from non‑small cell lung cancer patients were used to detect the epidermal growth factor receptor (EGFR) gene T790M mutation by direct sequencing and ARMS‑qPCR. The ARMS‑qPCR system 1 effectively detected samples with as low as 1% T790M mutant plasmid 1 (without rs1050171) and with 50% T790M mutant plasmid 2 (with rs1050171), while the ARMS‑qPCR system 2 detected samples with 20 and 50% T790M mutant plasmid 1, in addition to samples with 1% T790M mutant plasmid 2. For the ARMS‑qPCR system 3, samples with as low as 1% T790M mutant plasmids 1 or 2 were effectively detected. For gDNA analysis of the cell line H1975, the T790M mutation was effectively detected by the ARMS‑qPCR systems 2 and 3 (~50% mutation rate), but was detected with a low mutation abundance by the ARMS‑qPCR system 1 (~1% mutation rate). Of the 670 FFPE samples, 5 cases were identified to have the T790M mutation by sequencing and by the ARMS‑qPCR system 1. One sample (named N067), which was considered as T790M‑negative by sequencing, was demonstrated to have the T790M mutation using the ARMS‑qPCR system 1. Sample N094, which was variant homozygous for rs1050171 and was indicated to be T790M‑negative by sequencing and by the ARMS‑qPCR system 1, was identified to have the T790M mutation with the ARMS‑qPCR system 3. The A‑variant allele frequency of rs1050171 was observed to be 28.2% in the 670 FFPE tumor samples, while the presence of rs148188503 (c. C2355T, p. T785T) was observed in sample N558, and a novel SNP with a base substitution (c. T2375C) at position 792 (p. L792P) in exon 20 of the EGFR gene was observed in sample N310. rs1050171 is a high‑frequency SNP located near T790M, and the mutation statuses of rs1050171 appear to influence the sensitivity of the ARMS‑based T790M detection system, thus generating a 14.3% false‑negative rate (1/7). The present study proposes the risk that target neighboring SNPs (as far as 8 bp away in the present study) may exert on the sensitivity of ARMS‑based detection methods.
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1 

Wang J, Ramakrishnan R, Tang Z, Fan W, Kluge A, Dowlati A, Jones RC and Ma PC: Quantifying EGFR alterations in the lung cancer genome with nanofluidic digital PCR arrays. Clini Chem. 56:623–632. 2010. View Article : Google Scholar

2 

Kim Y, Ko J, Cui Z, Abolhoda A, Ahn JS, Ou SH, Ahn MJ and Park K: The EGFR T790M mutation in acquired resistance to an irreversible second-generation EGFR inhibitor. Mol Cancer Ther. 11:784–791. 2012. View Article : Google Scholar : PubMed/NCBI

3 

Kobayashi S, Boggon TJ, Dayaram T, Jänne PA, Kocher O, Meyerson M, Johnson BE, Eck MJ, Tenen DG and Halmos B: EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med. 352:786–792. 2005. View Article : Google Scholar : PubMed/NCBI

4 

Kuang Y, Rogers A, Yeap BY, Wang L, Makrigiorgos M, Vetrand K, Thiede S, Distel RJ and Jänne PA: Noninvasive detection of EGFR T790M in gefitinib or erlotinib resistant non-small cell lung cancer. Clinical cancer research: An official journal of the American Association for Cancer Research. 15:2630–2636. 2009. View Article : Google Scholar : PubMed/NCBI

5 

Sun JM, Ahn MJ, Choi YL, Ahn JS and Park K: Clinical implications of T790M mutation in patients with acquired resistance to EGFR tyrosine kinase inhibitors. Lung Cancer. 82:294–298. 2013. View Article : Google Scholar : PubMed/NCBI

6 

Yamada T, Azuma K, Muta E, Kim J, Sugawara S, Zhang GL, Matsueda S, Kasama-Kawaguchi Y, Yamashita Y, Yamashita T, et al: EGFR T790M mutation as a possible target for immunotherapy; identification of HLA-A*0201-restricted T cell epitopes derived from the EGFR T790M mutation. PloS One. 8:e783892013. View Article : Google Scholar : PubMed/NCBI

7 

Denis MG, Vallée A and Théoleyre S: EGFR T790M resistance mutation in non small-cell lung carcinoma. Clin Chim Acta. 444:81–85. 2015. View Article : Google Scholar : PubMed/NCBI

8 

Lin L and Bivona TG: Mechanisms of resistance to epidermal growth factor receptor inhibitors and novel therapeutic strategies to overcome resistance in NSCLC patients. Chemother Res Pract. 2012:8172972012.PubMed/NCBI

9 

Zhou W, Ercan D, Chen L, Yun CH, Li D, Capelletti M, Cortot AB, Chirieac L, Iacob RE, Padera R, et al: Novel mutant-selective EGFR kinase inhibitors against EGFR T790M. Nature. 462:1070–1074. 2009. View Article : Google Scholar : PubMed/NCBI

10 

Yung TK, Chan KC, Mok TS, Tong J, To KF and Lo YM: Single-molecule detection of epidermal growth factor receptor mutations in plasma by microfluidics digital PCR in non-small cell lung cancer patients. Clin Cancer Res. 15:2076–2084. 2009. View Article : Google Scholar : PubMed/NCBI

11 

Thomas RK, Nickerson E, Simons JF, Jänne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, et al: Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med. 12:852–855. 2006. View Article : Google Scholar : PubMed/NCBI

12 

Guha M, Castellanos-Rizaldos E and Makrigiorgos GM: DISSECT method using PNA-LNA clamp improves detection of T790M mutation. PloS One. 8:e677822013. View Article : Google Scholar : PubMed/NCBI

13 

Bai H, Wang Z, Wang Y, Zhuo M, Zhou Q, Duan J, Yang L, Wu M, An T, Zhao J and Wang J: Detection and clinical significance of intratumoral EGFR mutational heterogeneity in Chinese patients with advanced non-small cell lung cancer. PloS One. 8:e541702013. View Article : Google Scholar : PubMed/NCBI

14 

Board RE, Ellison G, Orr MC, Kemsley KR, McWalter G, Blockley LY, Dearden SP, Morris C, Ranson M, Cantarini MV, et al: Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study. Br J Cancer. 101:1724–1730. 2009. View Article : Google Scholar : PubMed/NCBI

15 

Chu H, Zhong C, Xue G, Liang X, Wang J, Liu Y, Zhao S, Zhou Q and Bi J: Direct sequencing and amplification refractory mutation system for epidermal growth factor receptor mutations in patients with non-small cell lung cancer. Oncol Rep. 30:2311–2315. 2013.PubMed/NCBI

16 

Ellison G, Donald E, McWalter G, Knight L, Fletcher L, Sherwood J, Cantarini M, Orr M and Speake G: A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples. J Exp Clin Cancer Res. 29:1322010. View Article : Google Scholar : PubMed/NCBI

17 

Franklin WA, Haney J, Sugita M, Bemis L, Jimeno A and Messersmith WA: KRAS mutation: Comparison of testing methods and tissue sampling techniques in colon cancer. J Mol Diagn. 12:43–50. 2010. View Article : Google Scholar : PubMed/NCBI

18 

Fukuoka M, Wu YL, Thongprasert S, Sunpaweravong P, Leong SS, Sriuranpong V, Chao TY, Nakagawa K, Chu DT, Saijo N, et al: Biomarker analyses and final overall survival results from a phase III, randomized, open-label, first-line study of gefitinib versus carboplatin/paclitaxel in clinically selected patients with advanced non-small-cell lung cancer in Asia (IPASS). J Clin Oncol. 29:2866–2874. 2011. View Article : Google Scholar : PubMed/NCBI

19 

Hamfjord J, Stangeland AM, Skrede ML, Tveit KM, Ikdahl T and Kure EH: Wobble-enhanced ARMS method for detection of KRAS and BRAF mutations. Diagn Mol Pathol. 20:158–165. 2011. View Article : Google Scholar : PubMed/NCBI

20 

Harlé A, Lion M, Lozano N, Husson M, Harter V, Genin P and Merlin JL: Analysis of PIK3CA exon 9 and 20 mutations in breast cancers using PCR-HRM and PCR-ARMS: Correlation with clinicopathological criteria. Oncol Rep. 29:1043–1052. 2013.PubMed/NCBI

21 

Huang T, Zhuge J and Zhang WW: Sensitive detection of BRAF V600E mutation by amplification refractory mutation system (ARMS)-PCR. Biomark Res. 1:32013. View Article : Google Scholar : PubMed/NCBI

22 

Liu Y, Liu B, Li XY, Li JJ, Qin HF, Tang CH, Guo WF, Hu HX, Li S, Chen CJ, et al: A comparison of ARMS and direct sequencing for EGFR mutation analysis and tyrosine kinase inhibitors treatment prediction in body fluid samples of non-small-cell lung cancer patients. J Exp Clin Cancer Res. 30:1112011. View Article : Google Scholar : PubMed/NCBI

23 

Machnicki MM, Glodkowska-Mrowka E, Lewandowski T, Ploski R, Wlodarski P and Stoklosa T: ARMS-PCR for detection of BRAF V600E hotspot mutation in comparison with real-time PCR-based techniques. Acta Biochim Pol. 60:57–64. 2013.PubMed/NCBI

24 

Ogasawara N, Bando H, Kawamoto Y, Yoshino T, Tsuchihara K, Ohtsu A and Esumi H: Feasibility and robustness of amplification refractory mutation system (ARMS)-based KRAS testing using clinically available formalin-fixed, paraffin-embedded samples of colorectal cancers. Jpn J Clin Oncol. 41:52–56. 2011. View Article : Google Scholar : PubMed/NCBI

25 

Zhang B, Xu CW, Shao Y, Wang HT, Wu YF, Song YY, Li XB, Zhang Z, Wang WJ, Li LQ and Cai CL: Comparison of droplet digital PCR and conventional quantitative PCR for measuring gene mutation. Exp Ther Med. 9:1383–1388. 2015.PubMed/NCBI

26 

Pettersson M, Bylund M and Alderborn A: Molecular haplotype determination using allele-specific PCR and pyrosequencing technology. Genomics. 82:390–396. 2003. View Article : Google Scholar : PubMed/NCBI

27 

Vlassov VV, Laktionov PP and Rykova EY: Circulating nucleic acids as a potential source for cancer biomarkers. Curr Mol Med. 10:142–165. 2010. View Article : Google Scholar : PubMed/NCBI

28 

Ye S, Dhillon S, Ke X, Collins AR and Day IN: An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res. 29:E88. 2001. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Xu S, Duan Y, Lou L, Tang F, Shou J and Wang G: Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncol Lett 12: 4238-4244, 2016.
APA
Xu, S., Duan, Y., Lou, L., Tang, F., Shou, J., & Wang, G. (2016). Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncology Letters, 12, 4238-4244. https://doi.org/10.3892/ol.2016.5184
MLA
Xu, S., Duan, Y., Lou, L., Tang, F., Shou, J., Wang, G."Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay". Oncology Letters 12.5 (2016): 4238-4244.
Chicago
Xu, S., Duan, Y., Lou, L., Tang, F., Shou, J., Wang, G."Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay". Oncology Letters 12, no. 5 (2016): 4238-4244. https://doi.org/10.3892/ol.2016.5184
Copy and paste a formatted citation
x
Spandidos Publications style
Xu S, Duan Y, Lou L, Tang F, Shou J and Wang G: Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncol Lett 12: 4238-4244, 2016.
APA
Xu, S., Duan, Y., Lou, L., Tang, F., Shou, J., & Wang, G. (2016). Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay. Oncology Letters, 12, 4238-4244. https://doi.org/10.3892/ol.2016.5184
MLA
Xu, S., Duan, Y., Lou, L., Tang, F., Shou, J., Wang, G."Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay". Oncology Letters 12.5 (2016): 4238-4244.
Chicago
Xu, S., Duan, Y., Lou, L., Tang, F., Shou, J., Wang, G."Exploring the impact of EGFR T790M neighboring SNPs on ARMS-based T790M mutation assay". Oncology Letters 12, no. 5 (2016): 4238-4244. https://doi.org/10.3892/ol.2016.5184
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