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Liu Z, Li X, Zhang R, Ji L, Gong L, Ji Y, Zhou F, Yin Y, Li K, Sun P, Pu Z, Wang Q, Zou J. Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers. Anal Bioanal Chem 2023; 415:6537-6549. [PMID: 37702773 DOI: 10.1007/s00216-023-04931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Detecting mutations related to tumors holds immense clinical significance for cancer diagnosis and treatment. However, the presence of highly redundant wild DNA poses a challenge for the advancement of low-copy mutant ctDNA genotyping in cancer cases. To address this, a Taqman qPCR strategy to identify rare mutations at low variant allele fractions (VAFs) has been developed. This strategy combines mutant-specific primers with wild-specific blockers. Diverging from other blocker-mediated PCRs, which rely on primer-induced strand displacement or the use of modified oligos resistant to Taq polymerase, our innovation is built upon the cleavage of specific blockers by Taq polymerase. Given its unique design, which does not hinge on strand displacement or base modification, we refer to this novel method as unmodified-blocker cleavage PCR (UBC-PCR). Multiple experiments consistently confirmed that variant distinction was improved significantly by introduction of 5' unmatched blockers into the reaction. Moreover, UBC-PCR successfully detected mutant DNA at VAFs as low as 0.01% across six different variant contexts. Multiplex UBC-PCR was also performed to identify a reference target and three mutations with a sensitivity of 0.01% VAFs in one single tube. In profiling the gene status from 12 lung cancer ctDNA samples and 22 thyroid cancer FNA DNA samples, UBC-PCR exhibited a 100% concordance rate with ddPCR and a commercial ARMS kit, respectively. Our work demonstrates that UBC-PCR can identify low-abundance variants with high sensitivity in multiplex reactions, independent of strand displacement and base modification. This strategy holds the potential to significantly impact clinical practice and precision medicine.
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Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Xiushuai Li
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Lingli Gong
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ying Yin
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi, 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Qing Wang
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China.
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China.
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China.
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Liu Z, Zhang R, Jiang X, Ji L, Sun P, Ji Y, Zhang Y, Ding Y, Li K, Pu Z, Zhou F, Zou J. Highly Sensitive Enrichment of Low-Frequency Variants by Hairpin Competition Amplification. Anal Chem 2023; 95:12015-12023. [PMID: 37527514 DOI: 10.1021/acs.analchem.3c01803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Gene mutations are inevitably accumulated in cells of the human body. It is of great significance to detect mutations at the earliest possible time in physiological and pathological processes. However, genotyping low-copy tumor DNA (ctDNA) in patients is challenging due to abundant wild DNA backgrounds. One novel strategy to enrich rare mutations at low variant allele fractions (VAFs) with quantitative polymerase chain reaction (qPCR) and Sanger sequencing was contrived by introducing artificial hairpins into amplicons to compete with primers, coined as the hairpin competition amplification (HCA) system. The influence imposed by artificial hairpins on primer-binding in a high-temperature PCR system was investigated for the first time in this work, paving the way for the optimization of HCA. HCA differs from the previously reported work in which hairpins are formed to inhibit extension of wild-type DNA using 5-exonuclease-negative polymerase, where the readout is dependent on melting curve analysis after asymmetric PCR. Targeted at six different variants, HCA qPCR and HCA Sanger-enriched mutant DNA at VAFs as low as 0.1 or 0.01% were performed. HCA demonstrated advantages in multiplex reaction and temperature robustness. In profiling gene status from 12 lung cancer ctDNA samples and 16 thyroid cancer FNA DNA samples, HCA demonstrated a 100% concordance rate compared to ddPCR and commercial ARMS kit. HCA qPCR and Sanger sequencing can enrich low-abundance variants with high sensitivity and temperature robustness, presenting a novel and effective tool for precision diagnosis and treatment of rare variant diseases.
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Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Xixi Jiang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Yu Zhang
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Yan Ding
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi 214023, Jiangsu, China
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Liu C, Lin J, Xun Z, Huang J, Huang E, Chen T, He Y, Lin N, Yang B, Ou Q. Establishment of Coamplification at Lower Denaturation Temperature PCR/Fluorescence Melting Curve Analysis for Quantitative Detection of Hepatitis B Virus DNA, Genotype, and Reverse Transcriptase Mutation and Its Application in Diagnosis of Chronic Hepatitis B. J Mol Diagn 2019; 21:1106-1116. [PMID: 31607557 DOI: 10.1016/j.jmoldx.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022] Open
Abstract
Dynamic and real-time hepatitis B virus (HBV) DNA, genotype, and reverse transcriptase mutation analysis plays an important role in diagnosing and monitoring chronic hepatitis B (CHB) and in assessing the therapeutic response. We established a highly sensitive coamplification at lower denaturation temperature PCR (COLD-PCR) coupled with probe-based fluorescence melting curve analysis (FMCA) for precision diagnosis of CHB patients. The imprecision with %CV and detection limit of HBV DNA detected by COLD-PCR/FMCA were 2.58% to 4.42% and 500 IU/mL, respectively. For mutation, the imprecision and detection limit were 3.35% to 6.49% and 1%, respectively. Compared with Sanger sequencing, the coincidence rates of genotype and mutation were 96.0% and 82.5%, respectively, whereas the inconsistent data resulted from a low proportion (<20%) of mixed genotypes or mixed mutations. The mutation ratio in HBV infection patients was as follows: hepatitis B e antigen (HBeAg)-positive infection (0/0.0%) < HBeAg-negative infection (16/4.5%) < HBeAg-positive hepatitis (30/5.5%) < HBeAg-negative hepatitis (36/6.5%). In patients with entecavir therapy, the proportion of mutation at baseline or week 4 in virologic response (VR) group was <4%, whereas in the partial VR group, it was mostly ≥4%. COLD-PCR/FMCA provides a novel tool with high sensitivity, convenience, and practicability for the simultaneous quantification of HBV DNA, genotype, and mutation. It might be used for distinguishing the different phases of HBV infection and predicting VR of CHB patients.
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Affiliation(s)
- Can Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinpiao Lin
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Zhen Xun
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Jinlan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Er Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Tianbin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Yujue He
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Ni Lin
- School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China
| | - Qishui Ou
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Gene Diagnostic Laboratory, Fujian Medical University, Fuzhou, People's Republic of China; Fujian Key Laboratory of Laboratory Medicine, Fuzhou, People's Republic of China.
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Na W, Rui-Rui Y, Ming-Kai C, Bin Z, Qing-Li B, Feng-Yun D, Feng-Rong L, Hai-Xin D, Hai-Hua W, Guang-Tao L, Cheng-Qiang J, Yan-Xia J. Establishment of a fluorescent PCR melting curve method for detecting asthma susceptibility using gene SNP typing. J Asthma 2019; 57:850-857. [PMID: 31082286 DOI: 10.1080/02770903.2019.1619084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: To develop a detection method for single nucleotide polymorphisms (SNPs) of bronchial asthma (BA) susceptibility genes (IL-13, IL-33, and GSDMA) based on fluorescence PCR melting curves.Methods: Peripheral blood samples from 33 patients with BA were collected. DNA was extracted, and positive plasmids were constructed. Probes and primers for fluorescence polymerase chain reaction (PCR) were designed according to IL-13, IL-33, and GSDMA sequences, and the SNPs were separately detected by gene sequencing and fluorescence PCR melting curve.Results: The system was successfully divided into 3 SNPs, including IL-13, IL-33, and GSDMA, and a comparison of sequencing methods showed that the results were completely consistent. The lowest detection limit was 1 ng/reaction, the sensitivity and specificity were 100%, and this method had high repeatability (CV = 2.8%).Conclusion: The fluorescence PCR melting curve method is suitable for the rapid and accurate classification of SNPs. The method is economical, simple, and efficient, and is suitable for the screening of the susceptible gene SNPs in a large-scale population of patients with BA.
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Affiliation(s)
- Wang Na
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Yang Rui-Rui
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan City, Shandong Province, PR China
| | - Chen Ming-Kai
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Zhang Bin
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Bie Qing-Li
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Dong Feng-Yun
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Liang Feng-Rong
- Department of Physical Examination, Medical Examination Center, Jining First People's Hospital, Jining City, Shandong Province, PR China
| | - Dong Hai-Xin
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Wang Hai-Hua
- Department of Central Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Li Guang-Tao
- Department of Respiratory Medicine, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China
| | - Jin Cheng-Qiang
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining City, Shandong Province, PR China.,Department of Clinical Laboratory Teaching and Research, College of Forensic Medicine and Medical Laboratory, Jining Medical University, Jining, Shandong Province, PR China
| | - Jia Yan-Xia
- Radiology Department, Jining First People's Hospital, Jining City, Shandong Province, PR China.,Department of Medical Imaging Teaching and Research, Basic Medical College, Jining Medical University, Jining City, Shandong Province, PR China
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Chen Y, Wang X, Zhang K, Bao Y. Intercalation of cytosine into Eu3+-doped hydrocalumite and their fluorescent responses. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2017. [DOI: 10.1007/s13738-017-1176-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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