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Hu L, Ji YY, Zhu P, Lu RQ. Mutation-Selected Amplification droplet digital PCR: A new single nucleotide variant detection assay for TP53 R249S mutant in tumor and plasma samples. Anal Chim Acta 2024; 1318:342929. [PMID: 39067934 DOI: 10.1016/j.aca.2024.342929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/21/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024]
Abstract
The early detection of gene mutations in physiological and pathological processes is a powerful approach to guide decisions in precision medicine. However, detecting low-copy mutant DNA from clinical samples poses a challenge due to the enrichment of wild-type DNA backgrounds. In this study, we devised a novel strategy, named Mutation-Selected Amplification droplet digital PCR (MSA-ddPCR), to quantitatively analyze single nucleotide variants (SNVs) at low variant allele frequencies (VAFs). Using TP53R249S (a hotspot mutation associated with hepatocellular carcinoma) as a model, we optimized the concentration ratio of primers, the annealing temperature and nucleic acid amplification modifiers. Subsequently, we evaluated the linear range and precision of MSA-ddPCR by detecting TP53R249S and TP53wild-type (TP53WT) plasmid DNA, respectively. MSA-ddPCR demonstrated superior ability to discriminate between mutant DNA and wild-type DNA compared to traditional TaqMan-MGB PCR. We further applied MSA-ddPCR to analyze the TP53R249S mutation in 20 plasma samples and 15 formalin-fixed paraffin-embedded (FFPE) tissue samples, and assessed the agreement rates between MSA-ddPCR and amplicon high-throughput sequencing. The results showed that the limit of blanks of MSA-ddPCR are 0.449 copies μL-1 in the FAM channel and 0.452 copies μL-1 in the VIC channel. MSA-ddPCR could accurately quantify VAFs as low as 0.01 %, surpassing existing PCR and next-generation sequencing (NGS) methods. In the detection of clinical samples, a high correlation was found between MSA-ddPCR and amplicon high-throughput sequencing. Additionally, MSA-ddPCR outperformed sequencing methods in terms of detection time and simplicity of data analysis. MSA-ddPCR can be easily implemented into clinical practice and serve as a robust tool for detecting mutant genes due to its high sensitivity and accuracy.
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Affiliation(s)
- Ling Hu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 20032, China
| | - Yuan-Ye Ji
- Department of Medical Laboratory, Ningbo No.2 Hospital, Ningbo, 315010, China
| | - Peng Zhu
- Department of Medical Laboratory, Ningbo No.2 Hospital, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Ren-Quan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 20032, China.
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Xu L, Qi J, Wen Y, Liang W, Wang L, Yang Z, Yang X, Qi Y, Duan M, Zhao K, Gu J, Shen Y, Rao P, Ding M, Ren S, Li L, Liu G. A polyA DNA probe-based ultra-sensitive and structure-distinguishable electrochemical biosensor for the analysis of RNAi transgenic maize. Analyst 2021; 146:3526-3533. [PMID: 33881427 DOI: 10.1039/d1an00313e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Since the application of RNA interference (RNAi) is rapidly developing in GMO technology, accurate and sensitive detection of functional RNA molecules was urgently needed, for the safety and functional assessment of RNAi crops. In this work, we developed an electrochemical biosensor for transgene-derived long RNA based on a poly-adenine (polyA) DNA capture probe. The polyA self-assembling monolayer (SAM) provided enhanced interface stability and optimized surface density for the subsequent hybridization of the long RNA molecule. A multiple reporter probe system (MRP) containing 12 reporter probes (RPs) and 2 spacers was applied to open the complex molecular secondary structure and hybridize with the long RNA, with the critical assistance of dimethyl sulfoxide (DMSO). By using 3 addressable RPs, structural recognition was performed among long stem-loop RNA, long dsRNA (no loop), and siRNA. Excellent selectivity was achieved when the extracted total RNA samples were directly analyzed. When reverse transcription recombinase polymerase amplification (RT-RPA) technology was combined, the sensitivity was improved to 10 aM. To the best of our knowledge, this is the first electrochemical biosensor with the excellent capability of quantification and structural analysis of the long RNA of the RNAi GMO. Our work shows great potential in a wide range of RNAi GMO samples.
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Affiliation(s)
- Li Xu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Jiawei Qi
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China. and College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, P.R. China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Wen Liang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Lele Wang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Zhenzhou Yang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Xue Yang
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Yu Qi
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Manlei Duan
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Keke Zhao
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Jie Gu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Yiji Shen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Pinhua Rao
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, P.R. China
| | - Min Ding
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Shuzhen Ren
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and testing technology, Shanghai, 201203, P.R. China.
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Wang C, Liu Y, Cai F, Zhang X, Xu X, Li Y, Zou Q, Zheng J, Zhang Y, Guo W, Cai C, Shu J. Rapid screening of MMACHC gene mutations by high-resolution melting curve analysis. Mol Genet Genomic Med 2020; 8:e1221. [PMID: 32198913 PMCID: PMC7284048 DOI: 10.1002/mgg3.1221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
Background Cobalamin (cbl) C is a treatable rare hereditary disorder of cbl metabolism with autosomal recessive inheritance. It is the most common organic acidemia, manifested as methylmalonic academia combined with homocysteinemia. Early screening and diagnosis are important. The mutation spectrum of the MMACHC gene causing cblC varies among populations. The mutation spectrum in Chinese population is notably different from that in other populations. Methods A PCR followed by high‐resolution melting curve analysis (PCR‐HRM) method covering all coding exons of MMACHC gene was designed to verify 14 pathogenic MMACHC gene variants found in patients with cblC, including all common mutations in Chinese patients with cblC. Result By PCR‐HRM analysis, 14 pathogenic variants of MMACHC showed distinctly different melting curves, which were consistent with Sanger sequencing. The homozygous type of the most common mutation c.609G > A (p.Trp203Ter) can also be analyzed by specially designed PCR‐HRM. Conclusion The established PCR‐HRM method for screening common pathogenic MMACHC variants in Chinese patients with cblC has the advantages of high accuracy, high throughput, low cost, and high speed. It is suitable for the large‐sample screening of suspected children with methylmalonic acidemia and carriers in population.
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Affiliation(s)
- Chao Wang
- Tianjin Pediatric Research InstituteTianjin Children’s HospitalTianjinChina
- Tianjin Key Laboratory of Prevention and Treatment of Birth DefectsTianjinChina
| | - Yang Liu
- Department of NeonatalogyTianjin Children’s HospitalThe Pediatric Clinical College in Tianjin Medical UniversityTianjinChina
| | - Fengying Cai
- Department of PhysiologyTianjin Medical CollegeTianjinChina
| | - Xinjie Zhang
- Tianjin Pediatric Research InstituteTianjin Children’s HospitalTianjinChina
- Tianjin Key Laboratory of Prevention and Treatment of Birth DefectsTianjinChina
| | - Xiaowei Xu
- Tianjin Pediatric Research InstituteTianjin Children’s HospitalTianjinChina
- Tianjin Key Laboratory of Prevention and Treatment of Birth DefectsTianjinChina
| | - Yani Li
- Department of Internal MedicineQuyang County People's HospitalBaodingChina
| | - Qianqian Zou
- Department of NeurosurgeryTianjin Children’s HospitalTianjinChina
| | - Jie Zheng
- Department of NeurosurgeryTianjin Children’s HospitalTianjinChina
| | - Yuqin Zhang
- Department of NeurologyTianjin Children’s HospitalTianjinChina
| | - Wei Guo
- Department of RespirationTianjin Children’s HospitalTianjinChina
| | - Chunquan Cai
- Department of NeurosurgeryTianjin Children’s HospitalTianjinChina
| | - Jianbo Shu
- Tianjin Pediatric Research InstituteTianjin Children’s HospitalTianjinChina
- Tianjin Key Laboratory of Prevention and Treatment of Birth DefectsTianjinChina
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Lu Y, Chen S, Wei L, Sun L, Liu H, Xu Y. A Microfluidic-Based SNP Genotyping Method for Hereditary Hearing-Loss Detection. Anal Chem 2019; 91:6111-6117. [PMID: 30917650 DOI: 10.1021/acs.analchem.9b00652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shan Chen
- Laboratory of ShenZhen Third People’s Hospital, ShenZhen, GuangDong 518112, China
| | - Li Wei
- CapitalBio Technology, Beijing 101111, China
| | - Lanhua Sun
- CapitalBio Technology, Beijing 101111, China
| | - Houming Liu
- Laboratory of ShenZhen Third People’s Hospital, ShenZhen, GuangDong 518112, China
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Development and Validation of a High-Resolution Melting Assay To Detect Azole Resistance in Aspergillus fumigatus. Antimicrob Agents Chemother 2017; 61:AAC.01083-17. [PMID: 28893791 DOI: 10.1128/aac.01083-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/03/2017] [Indexed: 01/04/2023] Open
Abstract
The global emergence of azole-resistant Aspergillus fumigatus strains is a growing public health concern. Different patterns of azole resistance are linked to mutations in cyp51A Therefore, accurate characterization of the mechanisms underlying azole resistance is critical to guide selection of the most appropriate antifungal agent for patients with aspergillosis. This study describes a new sequencing-free molecular screening tool for early detection of the most frequent mutations known to be associated with azole resistance in A. fumigatus PCRs targeting cyp51A mutations at positions G54, Y121, G448, and M220 and targeting different tandem repeats (TRs) in the promoter region were designed. All PCRs were performed simultaneously, using the same cycling conditions. Amplicons were then distinguished using a high-resolution melting assay. For standardization, 30 well-characterized azole-resistant A. fumigatus strains were used, yielding melting curve clusters for different resistance mechanisms for each target and allowing detection of the most frequent azole resistance mutations, i.e., G54E, G54V, G54R, G54W, Y121F, M220V, M220I, M220T, M220K, and G448S, and the tandem repeats TR34, TR46, and TR53 Validation of the method was performed using a blind panel of 80 A. fumigatus azole-susceptible or azole-resistant strains. All strains included in the blind panel were properly classified as susceptible or resistant with the developed method. The implementation of this screening method can reduce the time needed for the detection of azole-resistant A. fumigatus isolates and therefore facilitate selection of the best antifungal therapy in patients with aspergillosis.
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Feng Y, Cai S, Xiong G, Zhang G, Wang S, Su X, Yu C. Sensitive Detection of DNA Lesions by Bulge-Enhanced Highly Specific Coamplification at Lower Denaturation Temperature Polymerase Chain Reaction. Anal Chem 2017; 89:8084-8091. [PMID: 28675037 DOI: 10.1021/acs.analchem.7b01599] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mutagenic modifications of nucleotides or DNA lesions that result from environmental stress have proven to be associated with a variety of diseases, particularly cancer. The method for accurately detecting the lesions is therefore of great importance for biomedical research and toxicity study. We develop a sensitive and low-cost bulge-enhanced coamplification at lower denaturation temperature polymerase chain reaction (COLD-PCR) method for detecting DNA lesions (uracil and 8-oxoguanine) by combining an in vitro base excision repair (BER) pathway and COLD-PCR. The modified bases are converted to bulge via the BER pathway involving converting modified bases to an apurinic/apyrimidinic (AP) site, cleavage at the AP site, and break ligation. The presence of the bulge induces a large change of the hybridization thermodynamics of double-stranded DNA, eventually enhancing the specificity of COLD-PCR. Besides, we used the free energy of hybridization as a reference to optimize the critical denaturation temperature (Tc) of COLD-PCR obtaining more specific amplification than empirical Tc. Taking advantage of the proposed bulge-enhanced COLD-PCR, we are able to identify the presence of DNA lesion-containing strands at low abundance down to 0.01%. This method also exhibits high sensitivity for glycosylase with a detection limit of 10-4 U/mL [3 S/N (signal-to-noise ratio)] that is superior than some recently reported methods. With the design of the repair guide probe, the level of oxidative damage in genomic DNA caused by chemicals and photodynamic therapy (PDT) can be evaluated, heralding more applications in clinical diagnosis and epigenetic study.
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Affiliation(s)
- Yu Feng
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Shuang Cai
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Guoliang Xiong
- Department of Nephrology, Shenzhen Affiliated Hospital, Guangzhou University of Chinese Medicine , Shenzhen 518033, Guangdong, China
| | - Guanfei Zhang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Shihui Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Xin Su
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
| | - Changyuan Yu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology , Beijing 100029, China
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Chambliss AB, Resnick M, Petrides AK, Clarke WA, Marzinke MA. Rapid screening for targeted genetic variants via high-resolution melting curve analysis. Clin Chem Lab Med 2017; 55:507-516. [PMID: 27732553 DOI: 10.1515/cclm-2016-0603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/02/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Current methods for the detection of single nucleotide polymorphisms (SNPs) associated with aberrant drug-metabolizing enzyme function are hindered by long turnaround times and specialized techniques and instrumentation. In this study, we describe the development and validation of a high-resolution melting (HRM) curve assay for the rapid screening of variant genotypes for targeted genetic polymorphisms in the cytochrome P450 enzymes CYP2C9, CYP2C19, and CYP3A5. METHODS Sequence-specific primers were custom-designed to flank nine SNPs within the genetic regions of aforementioned drug metabolizing enzymes. PCR amplification was performed followed by amplicon denaturation by precise temperature ramping in order to distinguish genotypes by melting temperature (Tm). A standardized software algorithm was used to assign amplicons as 'reference' or 'variant' as compared to duplicate reference sequence DNA controls for each SNP. RESULTS Intra-assay (n=5) precision of Tms for all SNPs was ≤0.19%, while inter-assay (n=20) precision ranged from 0.04% to 0.21%. When compared to a reference method of Sanger sequencing, the HRM assay produced no false negative results, and overcall frequency ranged from 0% to 26%, depending on the SNP. Furthermore, HRM genotyping displayed accuracy over input DNA concentrations ranging from 10 to 200 ng/μL. CONCLUSIONS The presented assay provides a rapid method for the screening for genetic variants in targeted CYP450 regions with a result of 'reference' or 'variant' available within 2 h from receipt of extracted DNA. The method can serve as a screening approach to rapidly identify individuals with variant sequences who should be further investigated by reflexed confirmatory testing for aberrant cytochrome P450 enzymatic activity. Rapid knowledge of variant status may aid in the avoidance of adverse clinical events by allowing for dosing of normal metabolizer patients immediately while identifying the need to wait for confirmatory testing in those patients who are likely to possess pharmacogenetically-relevant variants.
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