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Ren XD, Liu DY, Guo HQ, Wang L, Zhao N, Su N, Wei K, Ren S, Qu XM, Dai XT, Huang Q. Sensitive detection of low-abundance in-frame deletions in EGFR exon 19 using novel wild-type blockers in real-time PCR. Sci Rep 2019; 9:8276. [PMID: 31164704 PMCID: PMC6547704 DOI: 10.1038/s41598-019-44792-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/24/2019] [Indexed: 01/29/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) mutations are associated with response of tyrosine kinase inhibitors (TKIs) for patients with advanced non-small cell lung cancer (NSCLC). However, the existing methods for detection of samples having rare mutations(i.e. ~0.01%) have limits in terms of specificity, time consumption or cost. In the current study, novel wild-type blocking (WTB) oligonucleotides modified with phosphorothioate or inverted dT at the 5'-termini were designed to precisely detect 11 common deletion mutations in exon 19 of EGFR gene (E19del) using a WTB-PCR assay. And internal competitive leptin amplifications were further applied to enhance the specificity of the WTB-PCR system. Our results showed that WTB-PCR could completely block amplification of wild-type EGFR when 200 ng of DNA was used as template. Furthermore, the current WTB-PCR assay facilitated the detection of E19del mutations with a selectivity of 0.01% and sensitivity as low as a single copy. And, the results showed that the current WTB-PCR system exceeded detection limits afforded by the ARMS-PCR assay. In conclusion, the current WTB-PCR strategy represents a simple and cost-effective method to precisely detect various low-abundance deletion mutations.
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Affiliation(s)
- Xiao-Dong Ren
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Ding-Yuan Liu
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Hai-Qin Guo
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Liu Wang
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Na Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Kun Wei
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Sai Ren
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Xue-Mei Qu
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Xiao-Tian Dai
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China.
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China.
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China.
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Hao W, Fan L, Chen Q, Chen X, Zhang S, Lan K, Lu J, Zhang C. Modified Proofreading PCR for Detection of Point Mutations, Insertions and Deletions Using a ddNTP-Blocked Primer. PLoS One 2015; 10:e0123468. [PMID: 25915410 PMCID: PMC4411138 DOI: 10.1371/journal.pone.0123468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 03/03/2015] [Indexed: 11/18/2022] Open
Abstract
The development of simple, accurate, rapid and cost-effective technologies for mutation detection is crucial to the early diagnosis and prevention of numerous genetic diseases, pharmacogenetics, and drug resistance. Proofreading PCR (PR-PCR) was developed for mutation detection in 1998 but is rarely applied due to its low efficiency in allele discrimination. Here we developed a modified PR-PCR method using a ddNTP-blocked primer and a mixture of DNA polymerases with and without the 3'-5' proofreading function. The ddNTP-blocked primer exhibited the best blocking efficiency to avoid nonspecific primer extension while the mixture of a tiny amount of high-fidelity DNA polymerase with a routine amount of Taq DNA polymerase provided the best discrimination and amplification effects. The modified PR-PCR method is quite capable of detecting various mutation types, including point mutations and insertions/deletions (indels), and allows discrimination amplification when the mismatch is located within the last eight nucleotides from the 3'-end of the ddNTP-blocked primer. The modified PR-PCR has a sensitivity of 1-5 × 102 copies and a selectivity of 5 × 10-5 mutant among 107 copies of wild-type DNA. It showed a 100% accuracy rate in the detection of P72R germ-line mutation in the TP53 gene among 60 clinical blood samples, and a high potential to detect rifampin-resistant mutations at low frequency in Mycobacterium tuberculosis using an adaptor and a fusion-blocked primer. These results suggest that the modified PR-PCR technique is effective in detection of various mutations or polymorphisms as a simple, sensitive and promising approach.
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Affiliation(s)
- Weiming Hao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Lujuan Fan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Qianqian Chen
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxiang Chen
- Department of Gynecologic Oncology, Jiangsu Cancer Hospital, Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sichao Zhang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Ke Lan
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jian Lu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- * E-mail: (CZ); (JL)
| | - Chiyu Zhang
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (CZ); (JL)
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Xiao L, Zhang J, Yin Y, Chen C, Li K, Chang A, Sirois P. Molecular diagnosis of HIV and relevant novel technologies in mutation analysis. Biotechnol Adv 2008; 26:389-97. [DOI: 10.1016/j.biotechadv.2008.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 04/01/2008] [Accepted: 04/27/2008] [Indexed: 12/12/2022]
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Zhang J, Li K, Pardinas JR, Sommer SS, Yao KT. Proofreading genotyping assays mediated by high fidelity exo+ DNA polymerases. Trends Biotechnol 2005; 23:92-6. [PMID: 15661346 DOI: 10.1016/j.tibtech.2004.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerases with 3'-5' proofreading function mediate high fidelity DNA replication but their application for mutation detection was almost completely neglected before 1998. The obstacle facing the use of exo(+) polymerases for mutation detection could be overcome by primer-3'-termini modification, which has been tested using allele-specific primers with 3' labeling, 3' exonuclease-resistance and 3' dehydroxylation modifications. Accordingly, three new types of single nucleotide polymorphism (SNP) assays have been developed to carry out genome-wide genotyping making use of the fidelity advantage of exo(+) polymerases. Such SNP assays might also provide a novel approach for re-sequencing and de novo sequencing. These new mutation detection assays are widely adaptable to a variety of platforms, including real-time PCR, multi-well plate and microarray technologies. Application of exo(+) polymerases to genetic analysis could accelerate the pace of personalized medicine.
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Affiliation(s)
- Jia Zhang
- SNP Institute, North District of the School, Nanhua University, Hengyang, Hunan, 421001, China
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Li K, Zhang J, Chen L, Sommer SS. Superb nucleotide discrimination by a novel on/off switch for DNA polymerization and its applications. Mol Biotechnol 2005; 29:93-100. [PMID: 15699566 DOI: 10.1385/mb:29:2:093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
With the use of polymerases having 3' to 5' exonuclease activity and 3' phosphorothioate-modified allele-specific primers, we recently devised a SNP-operated on/off switch controlling DNA polymerization. One advantage of this novel on/off switch is its adaptability to arrayed primer extension. To further expand its application in genetic analysis, this new on/off switch was evaluated in discrimination of the match/mismatch status of single nucleotides upstream from the primer 3' terminal. A set of seven amplicons was developed with the templates differing from each other by a single nucleotide. Using this set of amplicons, the new on/off switch was shown to be able to efficiently discriminate single nucleotide polymorphisms from the primer 3' terminus to the -6 position from the primer 3' terminus. These data, illustrating the broad single nucleotide discrimination ability of this novel on/off switch, explain why the SNP-operated on/off switch is powerful in SNP analysis, and also indicate useful applications to genetic analysis additional to SNP assay. First, these data broaden the application of the novel on/off switch in the analysis of mutations other than SNPs. Second, it raises a nucleotide-walking algorithm suitable for de novo array-based sequencing analysis.
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Affiliation(s)
- Kai Li
- SNP Institute, Hengyang, Hunan, China.
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