1
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Chen W, Zhang K, Huang F, Zhao L, Waldren GC, Jiang Q, Chen SX, Wang B, Guo W, Zhang DY, Zhang JX. Advancing quantitative PCR with color cycle multiplex amplification. Nucleic Acids Res 2024:gkae683. [PMID: 39119904 DOI: 10.1093/nar/gkae683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024] Open
Abstract
Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.
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Affiliation(s)
- Wei Chen
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Kerou Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, Shanghai 200032, China
| | - Lan Zhao
- Department of Respiratory Diseases, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, Shanghai 200433, China
| | | | - Qi Jiang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Sherry X Chen
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Bonnie Wang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, Shanghai 200032, China
| | - David Y Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
| | - Jinny X Zhang
- Department of Innovation, NuProbe USA, Houston, TX 77054, USA
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2
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Cui X, Ngang S, Liu DD, Cheow LF. Rapid Single-Round Pool Testing of Infectious Disease Enabled by Multicolor Digital Melting PCR. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205636. [PMID: 37209020 DOI: 10.1002/smll.202205636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 04/27/2023] [Indexed: 05/21/2023]
Abstract
Pooled nucleic acid amplification test is a promising strategy to reduce cost and resources for screening large populations for infectious disease. However, the benefit of pooled testing is reversed when disease prevalence is high, because of the need to retest each sample to identify infected individual when a pool is positive. Split, Amplify, and Melt analysis of Pooled Assay (SAMPA) is presented, a multicolor digital melting PCR assay in nanoliter chambers that simultaneously identify infected individuals and quantify their viral loads in a single round of pooled testing. This is achieved by early sample tagging with unique barcodes and pooling, followed by single molecule barcode identification in a digital PCR platform using a highly multiplexed melt curve analysis strategy. The feasibility is demonstrated of SAMPA for quantitative unmixing and variant identification from pools of eight synthetic DNA and RNA samples corresponding to the N1 gene, as well as from heat-inactivated SARS-CoV-2 virus. Single round pooled testing of barcoded samples with SAMPA can be a valuable tool for rapid and scalable population testing of infectious disease.
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Affiliation(s)
- Xu Cui
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Dong Dong Liu
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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3
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Tokamani M, Figgou E, Papamichail L, Sakka E, Toros A, Bouchorikou A, Giannakakis A, Matthaiou EI, Sandaltzopoulos R. A Multiplex PCR Melting-Curve-Analysis-Based Detection Method for the Discrimination of Five Aspergillus Species. J Fungi (Basel) 2023; 9:842. [PMID: 37623613 PMCID: PMC10455196 DOI: 10.3390/jof9080842] [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: 06/17/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Aspergillus mold is a ubiquitously found, airborne pathogen that can cause a variety of diseases from mild to life-threatening in severity. Limitations in diagnostic methods combined with anti-fungal resistance render Aspergillus a global emerging pathogen. In industry, Aspergilli produce toxins, such as aflatoxins, which can cause food spoilage and pose public health risk issues. Here, we report a multiplex qPCR method for the detection and identification of the five most common pathogenic Aspergillus species, Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, and Aspergillus nidulans. Our approach exploits species-specific nucleotide polymorphisms within their ITS genomic regions. This novel assay combines multiplex single-color real time qPCR and melting curve analysis and provides a straight-forward, rapid, and cost-effective detection method that can identify five Aspergillus species simultaneously in a single reaction using only six unlabeled primers. Due to their unique fragment lengths, the resulting amplicons are directly linked to certain Aspergillus species like fingerprints, following either electrophoresis or melting curve analysis. Our method is characterized by high analytical sensitivity and specificity, so it may serve as a useful and inexpensive tool for Aspergillus diagnostic applications both in health care and the food industry.
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Affiliation(s)
- Maria Tokamani
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleftheria Figgou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Lito Papamichail
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Eleni Sakka
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Athanasios Toros
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Anastasia Bouchorikou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
| | - Efthymia Iliana Matthaiou
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA;
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (M.T.); (E.F.); (L.P.); (E.S.); (A.T.); (A.B.); (A.G.)
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4
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Kim JJ, Park HM, Kyoung AY, Lim SK, Cha SH, Lee JE, Park BC. Com probe implemented STexS II greatly enhances specificity in SARS-CoV-2 variant detection. Sci Rep 2023; 13:1036. [PMID: 36658190 PMCID: PMC9850334 DOI: 10.1038/s41598-022-24530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 01/20/2023] Open
Abstract
The initial introduction of utilizing double helix structural oligonucleotides known as SNP typing with excellent specificity (STexS) in a standard PCR greatly improved the detection of single nucleotide polymorphisms (SNP) by enhancing amplification rates of primer-matching strands and interrupting mismatched strands by constant instability of kinetics regarding alignment attaching and detaching. The model was beneficial overall in detecting SNP variants consisting of large amounts of wildtype strands such as EGFR mutation genotyping for early detection of non-small cell lung cancer. While the STexS PCR is advantageous in detecting SNPs and biomarkers, limitations were yet observed. Despite the ability to detect variants 10 times more effective than a typical amplification-refractory mutation system PCR, it could only perform optimally in DNA concentrations around 101 ~ 105. To further enhance STexS specificity to perform detecting viral-RNA variants such as the infamous SARS-CoV-2, a novel improvement of the regular TaqMan Probe using Com-probes to inhibit high copy wild targets and amplify low copy mutant targets. By introducing the novel STexS II, omicron variants of SARS-CoV-2 were able to be successfully detected in high concentrations of normal genes.
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Affiliation(s)
- Jae Jong Kim
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Hyoung-Min Park
- Biometrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - A Young Kyoung
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Si-Kyu Lim
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Sun Ho Cha
- GenoTech Corporation, 26-69, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - J Eugene Lee
- Biometrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Byoung Chul Park
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34145, Republic of Korea.
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5
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Chen FE, Trick AY, Hasnain AC, Hsieh K, Chen L, Shin DJ, Wang TH. Ratiometric PCR in a Portable Sample-to-Result Device for Broad-Based Pathogen Identification. Anal Chem 2022; 94:9372-9379. [PMID: 35730588 DOI: 10.1021/acs.analchem.2c01357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Polymerase chain reaction (PCR)-based diagnostic testing is the gold standard method for pathogen identification (ID) with recent developments enabling automated PCR tests for point-of-care (POC) use. However, multiplexed identification of several pathogens in PCR assays typically requires optics for an equivalent number of fluorescence channels, increasing instrumentation's complexity and cost. In this study, we first developed ratiometric PCR that surpassed one target per color barrier to allow multiplexed identification while minimizing optical components for affordable POC use. We realized it by amplifying pathogenic targets with fluorescently labeled hydrolysis probes with a specific ratio of red-to-green fluorophores for each bacterial species. We then coupled ratiometric PCR and automated magnetic beads-based sample preparation within a thermoplastic cartridge and a portable droplet magnetofluidic platform. We named the integrated workflow POC-ratioPCR. We demonstrated that the POC-ratioPCR could detect one out of six bacterial targets related to urinary tract infections (UTIs) in a single reaction using only two-color channels. We further evaluated POC-ratioPCR using mock bacterial urine samples spiked with good agreement. The POC-ratioPCR presents a simple and effective method for enabling broad-based POC PCR identification of pathogens directly from crude biosamples with low optical instrumentation complexity.
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Affiliation(s)
- Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander C Hasnain
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dong Jin Shin
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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6
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PlexProbes enhance qPCR multiplexing by discriminating multiple targets in each fluorescent channel. PLoS One 2022; 17:e0263329. [PMID: 35263349 PMCID: PMC8906580 DOI: 10.1371/journal.pone.0263329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022] Open
Abstract
The probe technology described in this paper facilitates detection and discrimination of multiple targets in a single fluorescent channel during PCR. This provides a strategy for doubling the number of targets that can be analysed simultaneously on existing PCR instruments. These probes are referred to as PlexProbes and produce fluorescence that can be switched ‘on’ or ‘off’ in the presence of target by manipulating the temperature. During PCR, fluorescence can be measured at multiple temperatures allowing discrimination of specific targets at defined temperatures. In a single fluorescent channel, a model duplex assay allowed either real-time or endpoint detection of Chlamydia trachomatis (CT) at 52°C and end-point detection of Neisseria gonorrhoeae (GC) at 74°C. Using this model system, as few as 40 copies of each specific target could be detected as single infection or co-infection, regardless of the presence or absence of the other target. A PlexProbe prototype assay for sexually transmitted infections (PP-STI) which simultaneously enables detection and differentiation of six targets using only three fluorescent channels was then constructed and evaluated. The PP-STI assay detects GC (2 gene targets), CT, Mycoplasma genitalium (MG), Trichomonas vaginalis (TV) and an internal control (IC). To evaluate assay performance, a panel of archived clinical samples (n = 337) were analysed using PP-STI and results compared to those obtained with a commercially available diagnostic assay. The overall agreement between results obtained with the PP-STI assay and the reference test was greater than 99.5%. PlexProbes offer a method of detecting more targets from a single diagnostic test, empowering physicians to make evidence-based treatment decisions while conserving time, labour, sample volume and reagent costs.
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7
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Zhang K, Rodriguez L, Cheng LY, Wang M, Zhang DY. Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction. Anal Chem 2021; 94:934-943. [PMID: 34932306 DOI: 10.1021/acs.analchem.1c03716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing common detection technologies are either complex and time-consuming in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous single nucleotide variant or small insertions and deletions (INDELs) profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR on peripheral blood mononuclear cell clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.
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Affiliation(s)
- Kerou Zhang
- Bioengineering, Rice University, Houston, Texas 77030, United States
| | | | | | - Michael Wang
- Bioengineering, Rice University, Houston, Texas 77030, United States
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8
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Hrdy J, Vasickova P, Nesvadbova M, Novotny J, Mati T, Kralik P. MOL-PCR and xMAP Technology: A Multiplex System for Fast Detection of Food- and Waterborne Viruses. J Mol Diagn 2021; 23:765-776. [PMID: 33864939 DOI: 10.1016/j.jmoldx.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses are common causes of food- and waterborne diseases worldwide. Conventional identification of these agents is based on cultivation, antigen detection, electron microscopy, or real-time PCR. Because recent technological advancements in detection methods are focused on fast and robust analysis, a rapid multiplexing technology, which can detect a broad spectrum of pathogenic viruses connected to food or water contamination, was utilized. A new semiquantitative magnetic bead-based multiplex system has been designed for simultaneous detection of several targets in one reaction. The system includes adenoviruses 40/41 (AdV), rotavirus A (RVA), norovirus (NoV), hepatitis E virus (HEV), hepatitis A virus (HAV), and a target for external control of the system. To evaluate the detection system, interlaboratory ring tests were performed in four independent laboratories. Analytical specificity of the tool was tested on a cohort of pathogenic agents and biological samples with quantitative PCR as a reference method. Limit of detection (analytical sensitivity) of 5 × 100 (AdV, HEV, and RVA) and 5 × 101 (HAV and NoV) genome equivalents per reaction was reached. This robust, senstivie, and rapid multiplexing technology may be used to routinely monitor and manage viruses in food and water to prevent food and waterborne diseases.
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Affiliation(s)
- Jakub Hrdy
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Petra Vasickova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic
| | - Michaela Nesvadbova
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jiri Novotny
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Tomas Mati
- Military Veterinary Institute, Hlucin, Czech Republic
| | - Petr Kralik
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
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9
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Li Y, Wan Z, Zuo L, Li S, Liu H, Ma Y, Zhou L, Jin X, Li Y, Zhang C. A Novel 2-dimensional Multiplex qPCR Assay for Single-Tube Detection of Nine Human Herpesviruses. Virol Sin 2021; 36:746-754. [PMID: 33635517 DOI: 10.1007/s12250-021-00354-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022] Open
Abstract
Human herpesviruses are double-stranded DNA viruses that are classified into nine species. More than 90% of adults are ever infected with one or more herpesviruses. The symptoms of infection with different herpesviruses are diverse ranging from mild or asymptomatic infections to deadly diseases such as aggressive lymphomas and sarcomas. Timely and accurate detection of herpesvirus infection is critical for clinical management and treatment. In this study, we established a single-tube nonuple qPCR assay for detection of all nine herpesviruses using a 2-D multiplex qPCR method with a house-keeping gene as the internal control. The novel assay can detect and distinguish different herpesviruses with 30 to 300 copies per 25 µL single-tube reaction, and does not cross-react with 20 other human viruses, including DNA and RNA viruses. The robustness of the novel assay was evaluated using 170 clinical samples. The novel assay showed a high consistency (100%) with the single qPCR assay for HHVs detection. The features of simple, rapid, high sensitivity, specificity, and low cost make this assay a high potential to be widely used in clinical diagnosis and patient treatment.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, China
| | - Lulu Zuo
- Viral Hemorrhagic Fevers Research Unit, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, China
| | - Honglian Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lianqun Zhou
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.,School of Biomedical Engineering, University of Science and Technology of China, Hefei, 260026, China
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yuye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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10
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Park JS, Pisanic T, Zhang Y, Wang TH. Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection. Anal Chem 2021; 93:2351-2358. [PMID: 33427441 DOI: 10.1021/acs.analchem.0c04221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymerase chain reaction (PCR) is by far the most commonly used method of nucleic acid amplification and has likewise been employed for a plethora of diagnostic purposes. Nonetheless, multiplexed PCR-based detection schemes have hitherto been largely limited by technical challenges associated with nonspecific interactions and other limitations inherent to traditional fluorescence-based assays. Here, we describe a novel strategy for multiplexed PCR-based analysis called Ligation-eNabled fluorescence-Coding PCR (LiNC PCR) that exponentially enhances the multiplexing capability of standard fluorescence-based PCR assays. The technique relies upon a simple, preliminary ligation reaction in which target DNA sequences are converted to PCR template molecules with distinct endpoint fluorescence signatures. Universal TaqMan probes are used to create target-specific multicolor fluorescence signals that can be readily decoded to identify amplified targets of interest. We demonstrate the LiNC PCR technique by implementing a two-color-based assay for detection of 10 ovarian cancer epigenetic biomarkers at analytical sensitivities as low as 60 template molecules with no detectable target cross-talk. Overall, LiNC PCR provides a simple and inexpensive method for achieving high-dimensional multiplexing that can be implemented in manifold molecular diagnostic applications.
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Affiliation(s)
- Joon Soo Park
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Thomas Pisanic
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ye Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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11
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Li Y, Xu P, Wan Z, Du H, Jin X, Zhang C. Single-tube detection of nine bacterial antibiotic-resistance genes by a 2-dimensional multiplex qPCR assay based on fluorescence and melting temperature. Mol Biol Rep 2020; 47:7341-7348. [PMID: 32888129 DOI: 10.1007/s11033-020-05789-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/28/2020] [Indexed: 12/21/2022]
Abstract
Simple, multiplex qPCR methods are advantages for rapid molecular diagnosis of multiple antibiotics-resistant genes simultaneously. However, the number of genes can be detected in a single reaction tube is often limited by the fluorescence channels of a real-time PCR instrument. In this study, we developed a simple 2-D multiplex qPCR method by combining the probe colors and amplicon Tm values to overcome the mechanical limit of the machine. The principle of the novel assay was validated by detection of nine bacterial antibiotic-resistance genes (KPC, NDM, VIM, OXA-48, GES, CIT, EBC, ACC and DHA) in a single reaction tube. This assay is highly sensitive within a range of 30-3000 copies per reaction. The simplicity, rapidity, high sensitivity and specificity, and low cost of the novel method make it a promising tool for developing clinical diagnostic kits for monitoring resistance and other genetic determinants of infectious diseases.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Ping Xu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, Suzhou, 215000, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215000, China.
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
- Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China.
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12
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Marras SAE, Tyagi S, Antson DO, Kramer FR. Color-coded molecular beacons for multiplex PCR screening assays. PLoS One 2019; 14:e0213906. [PMID: 30883590 PMCID: PMC6422326 DOI: 10.1371/journal.pone.0213906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 03/04/2019] [Indexed: 11/19/2022] Open
Abstract
The number of different fluorescent colors that can be distinguished in a PCR screening assay restricts the number of different targets that can be detected. If only six colors can be distinguished, and the probe for each target is labeled with a unique color, then only six different targets can be identified. Yet, it is often desirable to identify more targets. For instance, the rapid identification of which bacterial species (if any) is present in a patient's normally sterile blood sample, out of a long list of species, would enable appropriate actions to be taken to prevent sepsis. We realized that the number of different targets that can be identified in a screening assay can be increased significantly by utilizing a unique combination of two colors for the identification of each target species. We prepared a demonstration assay in which 15 different molecular beacon probe pairs were present, each pair specific for the same identifying sequence in the 16S ribosomal RNA gene of a different bacterial species, and each pair labeled with a unique combination of two fluorophores out of the six differently colored fluorophores that our PCR instrument could distinguish. In a set of PCR assays, each containing all 30 color-coded molecular beacons, and each containing DNA from a different bacterial species, the only two colors that arose in each real-time assay identified the species-specific target sequence that was present. Due to the intrinsic low background of molecular beacon probes, these reactions were specific and extremely sensitive, and the threshold cycle reflected the abundance of the target sequence present in each sample.
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Affiliation(s)
- Salvatore A. E. Marras
- Public Health Research Institute, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Sanjay Tyagi
- Public Health Research Institute, Department of Medicine, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Dan-Oscar Antson
- Center for Technology Licensing, Weill Cornell Medical Center, Cornell University, New York, New York, United States of America
| | - Fred Russell Kramer
- Public Health Research Institute, Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
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13
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Significant Expansion of Real-Time PCR Multiplexing with Traditional Chemistries using Amplitude Modulation. Sci Rep 2019; 9:1053. [PMID: 30705333 PMCID: PMC6355831 DOI: 10.1038/s41598-018-37732-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Abstract
The real time polymerase chain reaction (rtPCR) is an essential method for detecting nucleic acids that has a wide range of clinical and research applications. Current multiplexed rtPCR is capable of detecting four to six nucleic acid targets in a single sample. However, advances in clinical medicine are driving the need to measure many more targets at once. We demonstrate a novel method which significantly increases the multiplexing capability of any existing rtPCR instrument without new hardware, software, or chemistry. The technique works by varying the relative TaqMan probe concentrations amongst targets that are measured in a single fluorometric channel. Our fluorescent amplitude modulation method generates a unique rtPCR signature for every combination of targets present in a reaction. We demonstrate this technique by measuring nine different targets across three color channels with TaqMan reporting probes, yielding a detection accuracy of 98.9% across all combinations of targets. In principle this method could be extended to measure 6 or more targets per color channel across any number of color channels without loss in specificity.
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14
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Zhang Y, Chen L, Hsieh K, Wang TH. Ratiometric Fluorescence Coding for Multiplex Nucleic Acid Amplification Testing. Anal Chem 2018; 90:12180-12186. [PMID: 30251853 DOI: 10.1021/acs.analchem.8b03266] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although nucleic acid amplification testing (NAAT) has become the cornerstone for molecular diagnosis of diseases, expanding the multiplexed detection capacity of NAAT remains an important objective. To this end, encoding each nucleic acid target with a specific fluorescently labeled probe has been the most mature approach for multiplexed detection. Unfortunately, the number of targets that can be differentiated via this one-target-one-fluorophore multiplexed detection approach is restricted by spectral overlaps between fluorophores. In response, we present herein a new multiplexed detection approach termed ratiometric fluorescence coding, in which we encode each nucleic acid target with a specific ratio between two standard fluorophores. In ratiometric fluorescence coding, we employ the padlock probe chemistry to encode each nucleic acid target with a specific number of binding sites for two probes labeled with different fluorophores. Coupling the padlock probes with either rolling circle amplification (RCA) or hyperbranched rolling circle amplification (HRCA), we transform each nucleic acid target into a specific template that allows hybridization with the fluorescently labeled probes at predesigned ratios, thereby achieving multiplexed detection. For demonstration, we detected DNA targets from six infectious diseases and demonstrated the potential for further expanding the multiplexing capability of our approach. With further development, ratiometric fluorescence coding has the potential to enable highly multiplexed detection of nucleic acid targets and facilitate molecular diagnosis of diseases.
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Affiliation(s)
- Ye Zhang
- Department of Biomedical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Liben Chen
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States.,Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States.,Institute for NanoBioTechnology , Johns Hopkins University , Baltimore , Maryland 21218 , United States
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15
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Prakadan SM, Shalek AK, Weitz DA. Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat Rev Genet 2017; 18:345-361. [PMID: 28392571 DOI: 10.1038/nrg.2017.15] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures - whether valve-, droplet- or nanowell-based - have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.
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Affiliation(s)
- Sanjay M Prakadan
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alex K Shalek
- Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
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16
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Heissl A, Arbeithuber B, Tiemann-Boege I. High-Throughput Genotyping with TaqMan Allelic Discrimination and Allele-Specific Genotyping Assays. Methods Mol Biol 2017; 1492:29-57. [PMID: 27822855 DOI: 10.1007/978-1-4939-6442-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.
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Affiliation(s)
- Angelika Heissl
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020, Linz, Austria
| | - Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020, Linz, Austria
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020, Linz, Austria.
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17
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Nishimura T, Ogura Y, Tanida J. Multiplexed fluorescence readout using time responses of color coded signals for biomolecular detection. BIOMEDICAL OPTICS EXPRESS 2016; 7:5284-5293. [PMID: 28018742 PMCID: PMC5175569 DOI: 10.1364/boe.7.005284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 11/02/2016] [Accepted: 11/18/2016] [Indexed: 05/05/2023]
Abstract
Fluorescence readout is an important technique for detecting biomolecules. In this paper, we present a multiplexed fluorescence readout method using time varied fluorescence signals. To generate the fluorescence signals, coded strands and a set of universal molecular beacons are introduced. Each coded strand represents the existence of an assigned target molecule. The coded strands have coded sequences to generate temporary fluorescence signals through binding to the molecular beacons. The signal generating processes are modeled based on the reaction kinetics between the coded strands and molecular beacons. The model is used to decode the detected fluorescence signals using maximum likelihood estimation. Multiplexed fluorescence readout was experimentally demonstrated with three molecular beacons. Numerical analysis showed that the readout accuracy was enhanced by the use of time-varied fluorescence signals.
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18
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A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides. PLoS One 2016; 11:e0166911. [PMID: 27861573 PMCID: PMC5115841 DOI: 10.1371/journal.pone.0166911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently separated from the major product by HPLC or electrophoretic methods, which hampers precise physicochemical experiments with the labeled oligonucleotides. Studies of the transformation mechanism allowed us to select optimal conditions for avoiding the side reaction. The novel method for the post-synthetic deblocking of hexachlorofluorescein-labeled oligodeoxyribonucleotides described in this paper prevents the formation of the arylacridine derivative, enhances the yield of target oligomers, and allows them to be proper real-time PCR probes.
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19
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Zhang D, Feng Z, Zhao M, Wang H, Wang L, Yang S, Li G, Lu L, Ma X. Clinical Evaluation of a Single-Tube Multiple RT-PCR Assay for the Detection of 13 Common Virus Types/Subtypes Associated with Acute Respiratory Infection. PLoS One 2016; 11:e0152702. [PMID: 27043208 PMCID: PMC4820107 DOI: 10.1371/journal.pone.0152702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/17/2016] [Indexed: 12/12/2022] Open
Abstract
Respiratory viruses are among the most important causes of human morbidity and mortality worldwide, especially for infants and young children. In the past years, a few commercial multiplex RT-PCR assays have been used to detect respiratory viruses in spite of the high cost. In the present study, an improved single-tube multiplex reverse transcription PCR assay for simultaneous detection of 13 respiratory viruses was evaluated and compared with a previously reported two-tube assay as the reference method using clinical nasopharyngeal aspirates samples. Of 310 prospectively tested respiratory specimens selected from children hospitalized with acute respiratory illness, 226 (72.90%, 226/310) and 214 (69.03%, 214/310) positive for one or more viruses were identified by the single-tube and the two-tube assays, respectively, with combined test results showing good concordance (Kappa value = 0.874). Individually, the single-tube assay for adenovirus (Adv), human metapneumovirus (HMPV), human rhinovirus (HRV), parainfluenza virus type 1 (PIV1), parainfluenza virus type 3 (PIV3) and parainfluenza virus type 4 (PIV4) showed the significantly superior sensitivities to those of the two-tube assay. No false positives were found. In conclusion, our results demonstrates the one-tube assay revealed significant improvements over the two-tube assay in terms of the better sensitivity, more accurate quality control, less nonspecific amplification, more cost-effective and shorter turn-around time and will be a valuable tool for routine surveillance of respiratory virus infection in China.
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Affiliation(s)
- Dan Zhang
- Department of Pathophysiology, Guangzhou Medical University, Guangzhou city, Guangdong, China
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping district, Beijing, China
| | - Zhishan Feng
- Pediatric Research Institute, Children’s Hospital of Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Mengchuan Zhao
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping district, Beijing, China
- Pediatric Research Institute, Children’s Hospital of Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Hao Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping district, Beijing, China
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Le Wang
- Pediatric Research Institute, Children’s Hospital of Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Shuo Yang
- Pediatric Research Institute, Children’s Hospital of Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Guixia Li
- Pediatric Research Institute, Children’s Hospital of Hebei Province, Hebei Medical University, Shijiazhuang, China
| | - Li Lu
- Department of Pathophysiology, Guangzhou Medical University, Guangzhou city, Guangdong, China
- * E-mail: (XM); (LL)
| | - Xuejun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping district, Beijing, China
- * E-mail: (XM); (LL)
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20
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Schuler F, Trotter M, Zengerle R, von Stetten F. Monochrome Multiplexing in Polymerase Chain Reaction by Photobleaching of Fluorogenic Hydrolysis Probes. Anal Chem 2016; 88:2590-5. [DOI: 10.1021/acs.analchem.5b02960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Friedrich Schuler
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Martin Trotter
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- BIOSS-Centre
for Biological Signalling Studies, University of Freiburg, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory
for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
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21
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Abstract
The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCR-based mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial real-time PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.
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Affiliation(s)
| | - Pavel Neužil
- 1] Kist-Europe, Saarbrücken, Saarland, 66123, Germany [2] Central European Institute of Technology, Brno University of Technology, Technická 3058/10, CZ-616 00 Brno, Czech Republic [3] Northwestern Polytechnical University, School of Mechanical Engineering, 127 West Youyi Road, Xi'an, Shaanxi, 710072, P.R.China
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22
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Single Fluorescence Channel-based Multiplex Detection of Avian Influenza Virus by Quantitative PCR with Intercalating Dye. Sci Rep 2015; 5:11479. [PMID: 26088868 PMCID: PMC5155576 DOI: 10.1038/srep11479] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2015] [Indexed: 12/03/2022] Open
Abstract
Since its invention in 1985 the polymerase chain reaction (PCR) has become a well-established method for amplification and detection of segments of double-stranded DNA. Incorporation of fluorogenic probe or DNA intercalating dyes (such as SYBR Green) into the PCR mixture allowed real-time reaction monitoring and extraction of quantitative information (qPCR). Probes with different excitation spectra enable multiplex qPCR of several DNA segments using multi-channel optical detection systems. Here we show multiplex qPCR using an economical EvaGreen-based system with single optical channel detection. Previously reported non quantitative multiplex real-time PCR techniques based on intercalating dyes were conducted once the PCR is completed by performing melting curve analysis (MCA). The technique presented in this paper is both qualitative and quantitative as it provides information about the presence of multiple DNA strands as well as the number of starting copies in the tested sample. Besides important internal control, multiplex qPCR also allows detecting concentrations of more than one DNA strand within the same sample. Detection of the avian influenza virus H7N9 by PCR is a well established method. Multiplex qPCR greatly enhances its specificity as it is capable of distinguishing both haemagglutinin (HA) and neuraminidase (NA) genes as well as their ratio.
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23
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Hamza IA, Jurzik L, Wilhelm M. Development of a Luminex assay for the simultaneous detection of human enteric viruses in sewage and river water. J Virol Methods 2014; 204:65-72. [DOI: 10.1016/j.jviromet.2014.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/06/2014] [Accepted: 04/04/2014] [Indexed: 12/28/2022]
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24
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Simultaneous detection of five enteric viruses associated with gastroenteritis by use of a PCR assay: a single real-time multiplex reaction and its clinical application. J Clin Microbiol 2014; 52:1266-8. [PMID: 24478418 DOI: 10.1128/jcm.00245-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We developed a highly sensitive reverse transcription and multiplex real-time PCR (rtPCR) assay that can identify five viruses, including six genogroups, in a single reaction: norovirus genogroups I and II; sapovirus genogroups I, II, IV, and V; human rotavirus A; adenovirus serotypes 40 and 41; and human astrovirus. In comparison to monoplex rtPCR assays, the sensitivities and specificities of the multiplex rtPCR ranged from 75% to 100% and from 99% to 100%, respectively, evaluated on 812 clinical stool specimens.
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25
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Rajagopal A, Scherer A, Homyk A, Kartalov E. Supercolor coding methods for large-scale multiplexing of biochemical assays. Anal Chem 2013; 85:7629-36. [PMID: 23763357 DOI: 10.1021/ac401304t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a novel method for the encoding and decoding of multiplexed biochemical assays. The method enables a theoretically unlimited number of independent targets to be detected and uniquely identified in any combination in the same sample. For example, the method offers easy access to 12-plex and larger PCR assays, as contrasted to the current 4-plex assays. This advancement would allow for large panels of tests to be run simultaneously in the same sample, saving reagents, time, consumables, and manual labor, while also avoiding the traditional loss of sensitivity due to sample aliquoting. Thus, the presented method is a major technological breakthrough with far-reaching impact on biotechnology, biomedical science, and clinical diagnostics. Herein, we present the mathematical theory behind the method as well as its experimental proof of principle using Taqman PCR on sequences specific to infectious diseases.
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Affiliation(s)
- Aditya Rajagopal
- California Institute of Technology, Department of Electrical Engineering, Pasadena, California 91125, United States.
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26
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Oblath EA, Henley WH, Alarie JP, Ramsey JM. A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva. LAB ON A CHIP 2013; 13:1325-32. [PMID: 23370016 PMCID: PMC3617581 DOI: 10.1039/c3lc40961a] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A microfluidic chip integrating DNA extraction, amplification, and detection for the identification of bacteria in saliva is described. The chip design integrated a monolithic aluminum oxide membrane (AOM) for DNA extraction with seven parallel reaction wells for real-time polymerase chain reaction (rtPCR) amplification of the extracted DNA. Samples were first heated to lyse target organisms and then added to the chip and filtered through the nanoporous AOM to extract the DNA. PCR reagents were added to each of the wells and the chip was thermocycled. Identification of Streptococcus mutans in a saliva sample is demonstrated along with the detection of 300 fg (100-125 copies) of both methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) genomic DNA (gDNA) spiked into a saliva sample. Multiple target species and strains of bacteria can be simultaneously identified in the same sample by varying the primers and probes used in each of the seven reaction wells. In initial tests, as little as 30 fg (8-12 copies) of MSSA gDNA in buffer has been successfully amplified and detected with this device.
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Affiliation(s)
- Emily A Oblath
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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27
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Liao Y, Wang X, Sha C, Xia Z, Huang Q, Li Q. Combination of fluorescence color and melting temperature as a two-dimensional label for homogeneous multiplex PCR detection. Nucleic Acids Res 2013; 41:e76. [PMID: 23335787 PMCID: PMC3627564 DOI: 10.1093/nar/gkt004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Multiplex analytical systems that allow detection of multiple nucleic acid targets in one assay can provide rapid characterization of a sample while still saving cost and resources. However, few systems have proven to offer a solution for mid-plex (e.g. 10- to 50-plex) analysis that is high throughput and cost effective. Here we describe the combined use of fluorescence color and melting temperature (Tm) as a virtual 2D label that enables homogenous detection of one order of magnitude more targets than current strategies on real-time polymerase chain reaction platform. The target was first hybridized with a pair of ligation oligonucleotides, one of which harbored an artificial sequence that had a unique Tm when hybridized with a reporter fluorogenic probe. The ligated products were then amplified by a universal primer pair and denatured by a melting curve analysis procedure. The targets were identified by their respective Tm values in the corresponding fluorescence detection channels. The proof-of-principle of this approach was validated by genotyping 15 high-risk human papillomaviruses and 48 human single-nucleotide polymorphisms. The robustness of this method was demonstrated by analyzing a large number of clinical samples in both cases. The combined merits of multiplexity, flexibility and simplicity should make this approach suitable for a variety of applications.
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Affiliation(s)
- Yiqun Liao
- Department of Translational Medicine, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China
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28
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Kolpashchikov DM. An elegant biosensor molecular beacon probe: challenges and recent solutions. SCIENTIFICA 2012; 2012:928783. [PMID: 24278758 PMCID: PMC3820487 DOI: 10.6064/2012/928783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/10/2012] [Indexed: 05/02/2023]
Abstract
Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
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29
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Fu G, Miles A, Alphey L. Multiplex detection and SNP genotyping in a single fluorescence channel. PLoS One 2012; 7:e30340. [PMID: 22272339 PMCID: PMC3260291 DOI: 10.1371/journal.pone.0030340] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 12/14/2011] [Indexed: 12/30/2022] Open
Abstract
Probe-based PCR is widely used for SNP (single nucleotide polymorphism) genotyping and pathogen nucleic acid detection due to its simplicity, sensitivity and cost-effectiveness. However, the multiplex capability of hydrolysis probe-based PCR is normally limited to one target (pathogen or allele) per fluorescence channel. Current fluorescence PCR machines typically have 4–6 channels. We present a strategy permitting the multiplex detection of multiple targets in a single detection channel. The technique is named Multiplex Probe Amplification (MPA). Polymorphisms of the CYP2C9 gene (cytochrome P450, family 2, subfamily C, polypeptide 9, CYP2C9*2) and human papillomavirus sequences HPV16, 18, 31, 52 and 59 were chosen as model targets for testing MPA. The allele status of the CYP2C9*2 determined by MPA was entirely concordant with the reference TaqMan® SNP Genotyping Assays. The four HPV strain sequences could be independently detected in a single fluorescence detection channel. The results validate the multiplex capacity, the simplicity and accuracy of MPA for SNP genotyping and multiplex detection using different probes labeled with the same fluorophore. The technique offers a new way to multiplex in a single detection channel of a closed-tube PCR.
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Affiliation(s)
- Guoliang Fu
- Oxitec Limited, Oxford, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GF); (LA)
| | | | - Luke Alphey
- Oxitec Limited, Oxford, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GF); (LA)
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