1
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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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2
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Optimization and performance evaluation of double-stranded probe in real-time PCR. Anal Biochem 2022; 650:114711. [PMID: 35561816 DOI: 10.1016/j.ab.2022.114711] [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: 01/11/2022] [Revised: 04/18/2022] [Accepted: 05/01/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND TaqMan probe-based real-time PCR (qPCR/RT-qPCR) has been widely used in various fields because of its high sensitivity and specificity. However, TaqMan probes are associated with a relatively higher background signal, and hence negatively affect the detection results. METHODS Double-stranded probes (DSPs) were designed for the high sensitive detection of hepatitis B virus (HBV) DNA and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using qPCR/RT-qPCR. DSPs consist of different lengths of positive and negative strands with complementary oligonucleotides. We systematically optimized DSP length, the free energy of hybridization (ΔG) between complementary oligonucleotides, and the length of sticky ends, and DSP performance was evaluated in comparison with other types of probes. RESULTS By using similar length positive and negative strands, controlling ΔG between complementary oligonucleotides to approximately -30 kcal/mol, and maintaining the sticky end length at 4-6 nt, the analytical performance of DSP was significantly improved. Compared with other types of probes, DSP is advantageous in fluorescence signal intensity and sensitivity. CONCLUSION DSPs can further improve the detection sensitivity and the detection rate of low-concentration samples in molecular diagnosis.
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3
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Kireev DE, Farzan VM, Shipulin GA, Korshun VA, Zatsepin TS. RT-qPCR Detection of Low-Copy HIV RNA with Yin-Yang Probes. Methods Mol Biol 2020; 2063:27-35. [PMID: 31667760 DOI: 10.1007/978-1-0716-0138-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Accurate monitoring of low levels of viral load (the number of viral particles per milliliter of plasma) in HIV-infected patients is important in terms of evaluation of the progress of antiretroviral therapy. The general approach for detection of low copy HIV RNA is reverse transcription combined with quantitative real-time PCR based on fluorescence detection. The selection of primers and the structure of fluorogenic oligonucleotide probes are crucial for sensitivity and accuracy of the assay. In this chapter, we report the RT-qPCR protocol for detection of low copy HIV RNA using double stranded Yin-Yang DNA probes containing identical fluorescent dyes on each strand of the probe. Dye residues attached to the 3'-end of an oligonucleotide and 5'-end of the complementary oligonucleotide form a self-quenched aggregate in a Yin-Yang duplex probe, and display fluorescence light up upon probe strand displacement with the target sequence amplified in the course of PCR. Among several fluorescent dyes tested (R6G, ROX, Cy5) the ROX labeled Yin-Yang probes showed better fluorescence increase and lower Ct values. All the homo Yin-Yang probes were superior to corresponding dye-quencher probes and allowed reliable detection of 10-10,000 copies of HIV RNA per mL.
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Affiliation(s)
| | | | - German A Shipulin
- Federal State Budgetary Institution "Center for Strategic Planning and Management of Biomedical Health Risks" of the Ministry of Health, Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Gause Institute of New Antibiotics, Moscow, Russia.,Department of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Moscow, Russia. .,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
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4
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Upadhyay A, Yang H, Zaman B, Zhang L, Wu Y, Wang J, Zhao J, Liao C, Han Q. ZnO Nanolower-Based NanoPCR as an Efficient Diagnostic Tool for Quick Diagnosis of Canine Vector-Borne Pathogens. Pathogens 2020; 9:pathogens9020122. [PMID: 32075178 PMCID: PMC7169380 DOI: 10.3390/pathogens9020122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/27/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Polymerase chain reaction (PCR) is a unique technique in molecular biology and biotechnology for amplifying target DNA strands, and is also considered as a gold standard for the diagnosis of many canine diseases as well as many other infectious diseases. However, PCR still faces many challenges and issues related to its sensitivity, specificity, efficiency, and turnaround time. To address these issues, we described the use of unique ZnO nanoflowers in PCR reaction and an efficient ZnO nanoflower-based PCR (nanoPCR) for the molecular diagnosis of canine vector-borne diseases (CVBDs). A total of 1 mM of an aqueous solution of ZnO nanoflowers incorporated in PCR showed a significant enhancement of the PCR assay with respect to its sensitivity and specificity for the diagnosis of two important CVBDs, Babesia canis vogeli and Hepatozoon canis. Interestingly, it drastically reduced the turnaround time of the PCR assay without compromising the yield of the amplified DNA, which can be of benefit for veterinary practitioners for the improved management of diseases. This can be attributed to the favorable adsorption of ZnO nanoflowers to the DNA and thermal conductivity of ZnO nanoflowers. The unique ZnO nanoflower-assisted nanoPCR greatly improved the yield, purity, and quality of the amplified products, but the mechanism behind these properties and the effects and changes due to the different concentrations of ZnO nanoflowers in the PCR system needs to be further studied.
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Affiliation(s)
- Archana Upadhyay
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Huan Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Material Science and Engineering, Haikou 570228, China;
| | - Bilal Zaman
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources, College of Material Science and Engineering, Hainan University, Haikou 570228, China
| | - Lei Zhang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Yundi Wu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China;
| | - Jinhua Wang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Jianguo Zhao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
| | - Chenghong Liao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
- Correspondence: (C.L.); (Q.H.)
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China; (A.U.); (L.Z.); (J.W.); (J.Z.)
- Correspondence: (C.L.); (Q.H.)
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5
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Farzan VM, Kvach MV, Aparin IO, Kireev DE, Prikazchikova TA, Ustinov AV, Shmanai VV, Shipulin GA, Korshun VA, Zatsepin TS. Novel homo Yin-Yang probes improve sensitivity in RT-qPCR detection of low copy HIV RNA. Talanta 2019; 194:226-232. [DOI: 10.1016/j.talanta.2018.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 12/31/2022]
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6
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Myint NNM, Verma AM, Fernandez-Garcia D, Sarmah P, Tarpey PS, Al-Aqbi SS, Cai H, Trigg R, West K, Howells LM, Thomas A, Brown K, Guttery DS, Singh B, Pringle HJ, McDermott U, Shaw JA, Rufini A. Circulating tumor DNA in patients with colorectal adenomas: assessment of detectability and genetic heterogeneity. Cell Death Dis 2018; 9:894. [PMID: 30166531 PMCID: PMC6117318 DOI: 10.1038/s41419-018-0934-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/04/2018] [Accepted: 07/27/2018] [Indexed: 12/14/2022]
Abstract
Improving early detection of colorectal cancer (CRC) is a key public health priority as adenomas and stage I cancer can be treated with minimally invasive procedures. Population screening strategies based on detection of occult blood in the feces have contributed to enhance detection rates of localized disease, but new approaches based on genetic analyses able to increase specificity and sensitivity could provide additional advantages compared to current screening methodologies. Recently, circulating cell-free DNA (cfDNA) has received much attention as a cancer biomarker for its ability to monitor the progression of advanced disease, predict tumor recurrence and reflect the complex genetic heterogeneity of cancers. Here, we tested whether analysis of cfDNA is a viable tool to enhance detection of colon adenomas. To address this, we assessed a cohort of patients with adenomas and healthy controls using droplet digital PCR (ddPCR) and mutation-specific assays targeted to trunk mutations. Additionally, we performed multiregional, targeted next-generation sequencing (NGS) of adenomas and unmasked extensive heterogeneity, affecting known drivers such as APC, KRAS and mismatch repair (MMR) genes. However, tumor-related mutations were undetectable in patients' plasma. Finally, we employed a preclinical mouse model of Apc-driven intestinal adenomas and confirmed the inability to identify tumor-related alterations via cfDNA, despite the enhanced disease burden displayed by this experimental cancer model. Therefore, we conclude that benign colon lesions display extensive genetic heterogeneity, that they are not prone to release DNA into the circulation and are unlikely to be reliably detected with liquid biopsies, at least with the current technologies.
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Affiliation(s)
- Ni Ni Moe Myint
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Ajay M Verma
- University of Leicester, University Hospital of Leicester, Leicester, LE2 7LX, UK
| | | | - Panchali Sarmah
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | | | - Saif Sattar Al-Aqbi
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
- Department of Pathology and Poultry Diseases, Faculty of Veterinary Medicine, University of Kufa, Kufa, Iraq
| | - Hong Cai
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Ricky Trigg
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Kevin West
- Kettering General Hospital NHS Foundation Trust, Kettering, NN16 8UZ, UK
| | - Lynne M Howells
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Anne Thomas
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Karen Brown
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - David S Guttery
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Baljit Singh
- University of Leicester, University Hospital of Leicester, Leicester, LE2 7LX, UK
| | - Howard J Pringle
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | | | - Jacqui A Shaw
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK
| | - Alessandro Rufini
- Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 7LX, UK.
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7
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Kim HY, Li T, Jung C, Fu R, Cho DY, Park KS, Park HG. Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs. RSC Adv 2018; 8:37391-37395. [PMID: 35557795 PMCID: PMC9089284 DOI: 10.1039/c8ra06675b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 11/21/2022] Open
Abstract
We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost. A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).![]()
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Taihua Li
- College of Biology and the Environment
- Co-Innovation Centre for Sustainable Forestry in Southern China
- Nanjing Forestry University
- Nanjing
- China
| | - Cheulhee Jung
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Rongzhan Fu
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Dae-Yeon Cho
- Labgenomics Clinical Research Institute
- Labgenomics Co. Ltd
- Yong-In
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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8
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Boonlua C, Charoenpakdee C, Vilaivan T, Praneenararat T. Preparation and Performance Evaluation of a Pyrrolidinyl Peptide Nucleic-Acid-Based Displacement Probe as a DNA Sensor. ChemistrySelect 2016. [DOI: 10.1002/slct.201601075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
| | - Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
| | - Thanit Praneenararat
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
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9
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Shi C, Shang F, Pan M, Liu S, Ma C. The isothermal amplification detection of double-stranded DNA based on a double-stranded fluorescence probe. Biosens Bioelectron 2016; 80:54-58. [DOI: 10.1016/j.bios.2016.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 12/14/2022]
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10
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Irshad M, Gupta P, Mankotia DS, Ansari MA. Multiplex qPCR for serodetection and serotyping of hepatitis viruses: A brief review. World J Gastroenterol 2016; 22:4824-4834. [PMID: 27239109 PMCID: PMC4873875 DOI: 10.3748/wjg.v22.i20.4824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/09/2016] [Accepted: 03/30/2016] [Indexed: 02/06/2023] Open
Abstract
The present review describes the current status of multiplex quantitative real time polymerase chain reaction (qPCR) assays developed and used globally for detection and subtyping of hepatitis viruses in body fluids. Several studies have reported the use of multiplex qPCR for the detection of hepatitis viruses, including hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). In addition, multiplex qPCR has also been developed for genotyping HBV, HCV, and HEV subtypes. Although a single step multiplex qPCR assay for all six hepatitis viruses, i.e., A to G viruses, is not yet reported, it may be available in the near future as the technologies continue to advance. All studies use a conserved region of the viral genome as the basis of amplification and hydrolysis probes as the preferred chemistries for improved detection. Based on a standard plot prepared using varying concentrations of template and the observed threshold cycle value, it is possible to determine the linear dynamic range and to calculate an exact copy number of virus in the specimen. Advantages of multiplex qPCR assay over singleplex or other molecular techniques in samples from patients with co-infection include fast results, low cost, and a single step investigation process.
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MESH Headings
- DNA, Viral/blood
- DNA, Viral/genetics
- Hepatitis Viruses/classification
- Hepatitis Viruses/genetics
- Hepatitis Viruses/immunology
- Hepatitis, Viral, Human/blood
- Hepatitis, Viral, Human/diagnosis
- Hepatitis, Viral, Human/genetics
- Hepatitis, Viral, Human/immunology
- Humans
- Multiplex Polymerase Chain Reaction
- Predictive Value of Tests
- Reproducibility of Results
- Serogroup
- Serologic Tests/methods
- Serotyping
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11
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Chemiluminescence-imaging detection of DNA on a solid-phase membrane by using a peroxidase-labeled macromolecular probe. Talanta 2015; 139:138-42. [DOI: 10.1016/j.talanta.2015.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 01/01/2023]
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12
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Lahdenperä S, Spangar A, Lempainen AM, Joki L, Soukka T. An integrated closed-tube 2-plex PCR amplification and hybridization assay with switchable lanthanide luminescence based spatial detection. Analyst 2015; 140:3960-8. [PMID: 25882638 DOI: 10.1039/c5an00253b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Switchable lanthanide luminescence is a binary probe technology that inherently enables a high signal modulation in separation-free detection of DNA targets. A luminescent lanthanide complex is formed only when the two probes hybridize adjacently to their target DNA. We have now further adapted this technology for the first time in the integration of a 2-plex polymerase chain reaction (PCR) amplification and hybridization-based solid-phase detection of the amplification products of the Staphylococcus aureus gyrB gene and an internal amplification control (IAC). The assay was performed in a sealed polypropylene PCR chip containing a flat-bottom reaction chamber with two immobilized capture probe spots. The surface of the reaction chamber was functionalized with NHS-PEG-azide and alkyne-modified capture probes for each amplicon, labeled with a light harvesting antenna ligand, and covalently attached as spots to the azide-modified reaction chamber using a copper(i)-catalyzed azide-alkyne cycloaddition. Asymmetric duplex-PCR was then performed with no template, one template or both templates present and with a europium ion carrier chelate labeled probe for each amplicon in the reaction. After amplification europium fluorescence was measured by scanning the reaction chamber as a 10 × 10 raster with 0.6 mm resolution in time-resolved mode. With this assay we were able to co-amplify and detect the amplification products of the gyrB target from 100, 1000 and 10,000 copies of isolated S. aureus DNA together with the amplification products from the initial 5000 copies of the synthetic IAC template in the same sealed reaction chamber. The addition of 10,000 copies of isolated non-target Escherichia coli DNA in the same reaction with 5000 copies of the synthetic IAC template did not interfere with the amplification or detection of the IAC. The dynamic range of the assay for the synthetic S. aureus gyrB target was three orders of magnitude and the limit of detection of 8 pM was obtained. This proof-of-concept study shows that the switchable lanthanide luminescent probes enable separation-free array-based multiplexed detection of the amplification products in a closed-tube PCR which can enable a higher degree of multiplexing than is currently feasible by using different spectrally separated fluorescent probes.
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Affiliation(s)
- Susanne Lahdenperä
- Department of Biotechnology, University of Turku, Tykistökatu 6 A 6th floor, FI-20520 Turku, Finland.
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13
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Murray JL, Hu P, Shafer DA. Seven novel probe systems for real-time PCR provide absolute single-base discrimination, higher signaling, and generic components. J Mol Diagn 2015; 16:627-38. [PMID: 25307756 DOI: 10.1016/j.jmoldx.2014.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/14/2014] [Accepted: 06/11/2014] [Indexed: 12/19/2022] Open
Abstract
We have developed novel probe systems for real-time PCR that provide higher specificity, greater sensitivity, and lower cost relative to dual-labeled probes. The seven DNA Detection Switch (DDS)-probe systems reported here employ two interacting polynucleotide components: a fluorescently labeled probe and a quencher antiprobe. High-fidelity detection is achieved with three DDS designs: two internal probes (internal DDS and Flip probes) and a primer probe (ZIPR probe), wherein each probe is combined with a carefully engineered, slightly mismatched, error-checking antiprobe. The antiprobe blocks off-target detection over a wide range of temperatures and facilitates multiplexing. Other designs (Universal probe, Half-Universal probe, and MacMan probe) use generic components that enable low-cost detection. Finally, single-molecule G-Force probes employ guanine-mediated fluorescent quenching by forming a hairpin between adjacent C-rich and G-rich sequences. Examples provided show how these probe technologies discriminate drug-resistant Mycobacterium tuberculosis mutants, Escherichia coli O157:H7, oncogenic EGFR deletion mutations, hepatitis B virus, influenza A/B strains, and single-nucleotide polymorphisms in the human VKORC1 gene.
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Affiliation(s)
| | - Peixu Hu
- GeneTAG Technology, Inc., Atlanta, Georgia; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia
| | - David A Shafer
- GeneTAG Technology, Inc., Atlanta, Georgia; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia.
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14
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Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta 2014; 439:231-50. [PMID: 25451956 DOI: 10.1016/j.cca.2014.10.017] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/28/2022]
Abstract
Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.
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Affiliation(s)
- E Navarro
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - G Serrano-Heras
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - M J Castaño
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - J Solera
- Internal Medicine Department, General University Hospital, Hermanos Falcó 37, 02006 Albacete, Spain.
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15
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Affiliation(s)
| | - Tea Meulia
- Ohio Agricultural Research and Development Center Wooster Ohio
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16
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Yuce M, Kurt H, Mokkapati VRSS, Budak H. Employment of nanomaterials in polymerase chain reaction: insight into the impacts and putative operating mechanisms of nano-additives in PCR. RSC Adv 2014. [DOI: 10.1039/c4ra06144f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The latest developments in the field of nanomaterial-assisted PCR are evaluated with a focus on putative operating mechanisms.
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Affiliation(s)
- Meral Yuce
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul, Turkey
| | - Hasan Kurt
- Sabanci University
- Faculty of Engineering and Natural Sciences
- Istanbul, Turkey
| | | | - Hikmet Budak
- Sabanci University
- Nanotechnology Research and Application Centre
- Istanbul, Turkey
- Sabanci University
- Faculty of Engineering and Natural Sciences
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17
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Boonlua C, Ditmangklo B, Reenabthue N, Suparpprom C, Poomsuk N, Siriwong K, Vilaivan T. Pyrene-labeled pyrrolidinyl peptide nucleic acid as a hybridization-responsive DNA probe: comparison between internal and terminal labeling. RSC Adv 2014. [DOI: 10.1039/c3ra47997h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Internally pyrene-labeled pyrrolidinyl PNA yields much larger fluorescence increase than terminally labeled PNA upon hybridization with complementary DNA.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Nisanath Reenabthue
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Nattawee Poomsuk
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
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18
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19
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Zhou Z, Wei W, Zhang Y, Liu S. DNA-responsive disassembly of AuNP aggregates: influence of nonbase-paired regions and colorimetric DNA detection by exonuclease III aided amplification. J Mater Chem B 2013; 1:2851-2858. [DOI: 10.1039/c3tb20206b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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20
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Zhelev DV, Hunt M, Le A, Dupuis C, Ren S, Gibbons HS. Effect of the Bacillus atrophaeus subsp. globigii Spo0F H101R mutation on strain fitness. Appl Environ Microbiol 2012; 78:8601-10. [PMID: 23042165 PMCID: PMC3502920 DOI: 10.1128/aem.01922-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/24/2012] [Indexed: 11/20/2022] Open
Abstract
Sporulation is a critical developmental process in Bacillus spp. that, once initiated, removes the possibility of further growth until germination. Therefore, the threshold conditions triggering sporulation are likely to be subject to evolutionary constraint. Our previous studies revealed two spontaneous hypersporulating mutants of Bacillus atrophaeus subsp. globigii, both containing point mutations in the spo0F gene. One of these strains (Detrick-2; contains the spo0F101 allele with a C:T [His101Arg] substitution) had been deliberately selected in the early 1940s as an anthrax surrogate. To determine whether the experimental conditions used during the selection of the "military" strains could have supported the emergence of hypersporulating variants, the relative fitness of strain Detrick-2 was measured in several experimental settings modeled on experimental conditions employed during its development in the 1940s as a simulant. The congenic strain Detrick-1 contained a wild-type spo0F gene and sporulated like the wild-type strain. The relative fitness of Detrick-1 and Detrick-2 was evaluated in competition experiments using quantitative single nucleotide polymorphism (SNP)-specific real-time PCR assays directed at the C:T substitution. The ancestral strain Detrick-1 had a fitness advantage under all conditions tested except when competing cultures were subjected to frequent heat shocks. The hypersporulating strain gained the maximum fitness advantage when cultures were grown at low oxygen tension and when heat shock was applied soon after the formation of the first heat-resistant spores. This is interpreted as gain of fitness by the hypersporulating strain in fast-changing fluctuating environments as a result of the increased rate of switching to the sporulating phenotype.
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Affiliation(s)
- Doncho V. Zhelev
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Mia Hunt
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Anna Le
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Christopher Dupuis
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Suelynn Ren
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Henry S. Gibbons
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
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Xia QF, Wen YA, Liu P, Li P, Liu JB, Qin X, Qian SY, Tu ZG. Use of duplex mutation primers for real-time PCR quantification of hepatitis C virus RNA in serum. HEPATITIS MONTHLY 2011; 11:519-24. [PMID: 22087189 PMCID: PMC3212762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 03/24/2011] [Accepted: 04/01/2011] [Indexed: 12/11/2022]
Abstract
BACKGROUND The duplex mutation primers offer many advantages over other multi-labeled probes for real-time detection of amplification products. OBJECTIVES To develop and validate a novel real-time PCR for quantification of HCV RNA based on the duplex mutation primers technology. MATERIALS AND METHODS The duplex mutation primers were selected in the highly conservative 5' non-coding region (5'NCR) of the HCV RNA. The assay was validated with the Viral Quality Control panel, which also includes Chinese HCV RNA standards. RESULTS The detection limit was 57 IU/mL, and a good linear correlation in the range of 102-108 IU/mL was revealed (r(2) = 0.999) with the novel method. This assay has a dynamic range of at least 8 log10 without the need for specimen dilution, good clinical intra- and inter-run precision, and excellent correlation with a commercially available assay(r(2) = 0.95). CONCLUSIONS The high sensitivity, wide linear range, and good reproducibility, combined with low cost, make this novel quantitative HCV real-time PCR assay particularly well suited for application to clinical and epidemiological studies.
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Affiliation(s)
- Qian-Feng Xia
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, Chongqing, China,The Faculty of Laboratory Medicine and Tropical Medicine, Hainan Medical College, Haikou, China
| | - Yang-An Wen
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Ping Liu
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Pu Li
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Jin-Bo Liu
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xi Qin
- The Faculty of Laboratory Medicine and Tropical Medicine, Hainan Medical College, Haikou, China
| | - Shi-Yun Qian
- The Faculty of Laboratory Medicine and Tropical Medicine, Hainan Medical College, Haikou, China
| | - Zhi-Guang Tu
- The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, Chongqing, China,Corresponding author at: Zhi-Guang Tu, The Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, the Faculty of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China. Tel.: +86- 2368485759, Fax: +86-2368485005, E-mail:
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22
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Yang CJ, Cui L, Huang J, Yan L, Lin X, Wang C, Zhang WY, Kang H. Linear molecular beacons for highly sensitive bioanalysis based on cyclic Exo III enzymatic amplification. Biosens Bioelectron 2011; 27:119-24. [PMID: 21764287 DOI: 10.1016/j.bios.2011.06.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 06/11/2011] [Accepted: 06/21/2011] [Indexed: 12/21/2022]
Abstract
Sensitive analysis or monitoring of biomolecules and small molecules is very important for many biological researches, clinical diagnosis and forensic investigations. As a sequence-independent exonuclease, Exonuclease III (Exo III) has been widely used for amplified detection of proteins and nucleic acids where displacing probes or molecular beacons are used as the signaling probes. However, displacing probes suffer slow hybridization rate and high background signal and molecular beacons are difficult to design and prone to undesired nonspecific interactions. Herein, we report a new type of probes called linear molecular beacons (LMBs) for use in Exo III amplification assays to improve hybridization kinetics and reduce background noises. LMBs are linear oligonucleotide probes with a fluorophore and quencher attached to 3' terminal and penultimate nucleotides, respectively. Compared to conventional molecular beacons and displacing probes, LMBs are easy to design and synthesize. More importantly, LMBs have a much lower background noise and allow faster reaction rates. Using LMBs in cyclic Exo III amplification assay, ultrasensitive nucleic acid detection methods were developed with a detection limit of less than 120fM, which is 2 orders of magnitude lower than that of conventional molecular beacons or displacing probes-based Exo III amplification assays. Furthermore, LMBs can be extended as universal probes for detection of non-nucleic acid molecules such as cocaine with high sensitivity. These results demonstrate that the combination of Exo III amplification and LMB signaling provides a general method for ultrasensitive and selective detection of a wide range of targets.
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Affiliation(s)
- Chaoyong James Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, PR China.
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LATE-PCR and allied technologies: real-time detection strategies for rapid, reliable diagnosis from single cells. Methods Mol Biol 2011; 688:47-66. [PMID: 20938832 DOI: 10.1007/978-1-60761-947-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Accurate detection of gene sequences in single cells is the ultimate challenge of PCR sensitivity. Unfortunately, commonly used conventional and real-time PCR techniques are often too unreliable at that level to provide the accuracy needed for clinical diagnosis. Here we provide details of Linear-After-The-Exponential-PCR (LATE-PCR), a method similar to asymmetric PCR in the use of primers at -different concentrations, but with novel design criteria to insure high efficiency and specificity. LATE-PCR increases the signal strength and allele discrimination capability of oligonucleotide probes such as molecular beacons and reduces variability among replicate samples. The analysis of real-time kinetics of LATE-PCR signals provides a means for improving the accuracy of single-cell genetic diagnosis.
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24
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Abstract
Iron overload in humans is associated with a variety of genetic and acquired conditions. Of these, HFE hemochromatosis (HFE-HC) is by far the most frequent and most well-defined inherited cause when considering epidemiological aspects and risks for iron-related morbidity and mortality. The majority of patients with HFE-HC are homozygotes for the C282Y polymorphism [1]. Without therapeutic intervention, there is a risk that iron overload will occur, with the potential for tissue damage and disease. While a specific genetic test now allows for the diagnosis of HFE-HC, the uncertainty in defining cases and disease burden, as well as the low phenotypic penetrance of C282Y homozygosity poses a number of clinical problems in the management of patients with HC. This Clinical Practice Guideline will therefore, focus on HFE-HC, while rarer forms of genetic iron overload recently attributed to pathogenic mutations of transferrin receptor 2, (TFR2), hepcidin (HAMP), hemojuvelin (HJV), or to a sub-type of ferroportin (FPN) mutations, on which limited and sparse clinical and epidemiologic data are available, will not be discussed. We have developed recommendations for the screening, diagnosis, and management of HFE-HC.
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25
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Cui L, Ke G, Wang C, Yang CJ. A cyclic enzymatic amplification method for sensitive and selective detection of nucleic acids. Analyst 2010; 135:2069-73. [DOI: 10.1039/c0an00215a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Ruan L, Zhao H, Li Q. Multicolor real-time PCR genotyping of ABO system using displacing probes. J Forensic Sci 2009; 55:19-24. [PMID: 20002276 DOI: 10.1111/j.1556-4029.2009.01228.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Rapid and informative ABO genotyping has become increasingly popular in forensic use. We developed a multiplex real-time polymerase chain reaction (PCR) approach to genotype ABO major groups and subgroups. Seven differently fluorophor-labeled displacing probes for O(1)(261delG), A(261G), A(796C/803C), B(796A/803C), O(2) (802G>A), A(2) (1059delC), and A(2) (1009A>G) were combined in one or two PCRs to determine either ABO major groups or subgroups. The method correctly detected 13 reference DNA samples. A blind test of 237 samples resulted in complete agreement with their phenotypes, and 110 of these 237 samples as well as with PCR-SSP method. The whole analysis could be finished in less than 100 min at substantially low material cost and the template DNA ranging from 0.16 to 500 ng per reaction could be quantitatively detected. Despite the limited informativeness of ABO genotyping, the developed methods could find application in rapid and inexpensive screening of forensic settings.
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Affiliation(s)
- Li Ruan
- Molecular Diagnostics Laboratory, The Key Laboratory of The Ministry of Education for Cell Biology and Tumor Cell Engineering, Department of Biomedicine, School of Life Sciences, Xiamen University, Xiamen, Fujian 361005, China
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Huang Q, Li Q. Characterization of the 5′ to 3′ nuclease activity of Thermus aquaticus DNA polymerase on fluorogenic double-stranded probes. Mol Cell Probes 2009; 23:188-94. [DOI: 10.1016/j.mcp.2009.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/25/2009] [Accepted: 04/09/2009] [Indexed: 11/27/2022]
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Affiliation(s)
| | - Tea Meulia
- Ohio Agricultural Research and Development Center Wooster Ohio
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29
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Gill P, Forouzandeh M, Eshraghi N, Ghalami M, Safa M, Noori-Daloii MR. Detection of four β-thalassemia point mutations in Iranians using a PCR-ELISA genotyping system. Mol Cell Probes 2008; 22:103-9. [DOI: 10.1016/j.mcp.2007.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 08/30/2007] [Accepted: 10/08/2007] [Indexed: 12/25/2022]
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30
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Gu Y, Li Q. Real-time PCR genotyping of aldehyde dehydrogenase-2 using displacing probes. Clin Biochem 2007; 40:1325-7. [PMID: 17854793 DOI: 10.1016/j.clinbiochem.2007.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 07/02/2007] [Accepted: 07/09/2007] [Indexed: 11/21/2022]
Abstract
OBJECTIVES This study aimed to develop and validate a rapid, accurate method for aldehyde dehydrogenase-2 gene (ALDH2) genotyping. DESIGN AND METHODS We reported a single-tube, real-time PCR method for ALDH2 allele detection using two displacing probes. RESULTS The genotyping results of 136 human genomic DNA samples indicated 100% concordance between real-time PCR method and the PCR-RFLP analysis. CONCLUSIONS The developed method could be used for routine clinical testing and high throughput genetic screening of ALDH2.
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Affiliation(s)
- Yingying Gu
- Molecular Diagnostics Laboratory, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiamen 361005, Fujian, China
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31
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Ruan L, Pei B, Li Q. Multicolor real-time polymerase chain reaction genotyping of six human platelet antigens using displacing probes. Transfusion 2007; 47:1637-42. [PMID: 17725728 DOI: 10.1111/j.1537-2995.2007.01335.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Several genotyping methods for six clinically relevant human platelet antigens (HPAs) have been reported. A four-color real-time polymerase chain reaction (PCR) method using displacing probes for genotyping of the six HPAs is described. STUDY DESIGN AND METHODS Primers and four differently fluorophor-labeled displacing probes were designed and synthesized to detect single-nucleotide polymorphisms responsible for each of the HPA-1, -2, -3, -4, -5, and -15 genotypes. Two HPA systems were analyzed in a single PCR procedure. After validation with samples of known genotypes, a total of 150 blood samples from healthy donors were genotyped. The results were compared with PCR with sequence-specific primers (SSP), PCR-restriction fragment length polymorphism (RFLP), and/or direct DNA sequencing. The frequencies of each HPA allele were calculated. RESULTS Unequivocal real-time PCR genotyping results were obtained with minimal manual manipulation and carryover contamination. All 150 blood samples were correctly genotyped as confirmed by PCR-SSP, PCR-RFLP, and/or direct DNA sequencing. The allelic frequencies of HPA-1 through -5 and -15 among the Chinese population in Xiamen were comparable with those previously reported with Chinese living in other territories. For each specimen, genotyping of all six HPA biallelic systems was achieved in three tubes of PCR within 90 minutes and with material cost of no more than $1. CONCLUSION Genotyping of HPA with real-time PCR using displacing probes is more rapid and reliable compared with PCR-SSP and PCR-RFLP methods and is more affordable than existing real-time PCR-based HPA genotyping assays. Thus, our approach is more suitable for routine HPA analysis and ideal for both urgent clinical testing and high-throughput screening.
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Affiliation(s)
- Li Ruan
- Molecular Diagnostics Laboratory, Department of Biomedicine, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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32
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Tison CK, Milam VT. Reversing DNA-mediated adhesion at a fixed temperature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:9728-36. [PMID: 17696456 DOI: 10.1021/la700601j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recognition-based assembly of micron- to nano-sized colloidal particles functionalized with DNA has generated great interest in the past decade; however, reversing the assembly process is typically achieved by thermal denaturation of the oligonucleotide duplexes. Here, we report an alternative disassembly approach at a fixed temperature using competitive hybridization events between immobilized and soluble oligonucleotide strands. Microspheres are first aggregated via primary hybridization events between immobilized DNA strands with a weak, but sufficient, affinity for partner strands to link complementary surfaces together. To reverse the aggregation process, soluble oligonucleotides are then added to competitively displace the original hybridization partners through secondary hybridization events. Using flow cytometry to quantify hybridization events and microscopy to examine DNA-mediated aggregation and redispersion, we found that the efficiency of competitive displacement is based upon (1) the difference in base pair matches between the primary and secondary target for the same probe sequence and (2) the concentration of hybridizing oligonucleotides participating in microsphere aggregation. To the best of our knowledge, this study is the first to employ DNA hybridization events to mediate reversible adhesion between colloidal particles at a fixed temperature.
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Affiliation(s)
- Christopher K Tison
- School of Materials Science & Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, Georgia 30332-0245, USA
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33
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Huang S, Salituro J, Tang N, Luk KC, Hackett J, Swanson P, Cloherty G, Mak WB, Robinson J, Abravaya K. Thermodynamically modulated partially double-stranded linear DNA probe design for homogeneous real-time PCR. Nucleic Acids Res 2007; 35:e101. [PMID: 17693434 PMCID: PMC2018630 DOI: 10.1093/nar/gkm551] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Real-time PCR assays have recently been developed for diagnostic and research purposes. Signal generation in real-time PCR is achieved with probe designs that usually depend on exonuclease activity of DNA polymerase (e.g. TaqMan probe) or oligonucleotide hybridization (e.g. molecular beacon). Probe design often needs to be specifically tailored either to tolerate or to differentiate between sequence variations. The conventional probe technologies offer limited flexibility to meet these diverse requirements. Here, we introduce a novel partially double-stranded linear DNA probe design. It consists of a hybridization probe 5′-labeled with a fluorophore and a shorter quencher oligo of complementary sequence 3′-labeled with a quencher. Fluorescent signal is generated when the hybridization probe preferentially binds to amplified targets during PCR. This novel class of probe can be thermodynamically modulated by adjusting (i) the length of hybridization probe, (ii) the length of quencher oligo, (iii) the molar ratio between the two strands and (iv) signal detection temperature. As a result, pre-amplification signal, signal gain and the extent of mismatch discrimination can be reliably controlled and optimized. The applicability of this design strategy was demonstrated in the Abbott RealTime HIV-1 assay.
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Affiliation(s)
- Shihai Huang
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - John Salituro
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - Ning Tang
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - Ka-Cheung Luk
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - John Hackett
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - Priscilla Swanson
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - Gavin Cloherty
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - Wai-Bing Mak
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - John Robinson
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
| | - Klara Abravaya
- Abbott Molecular Inc., Des Plaines, IL, USA and Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL, USA
- *To whom correspondence should be addressed. +1 224 361 7310+1 224 361 7507
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Mo ZH, Yang XC, Guo KP, Wen ZY. A nanogold-quenched fluorescence duplex probe for homogeneous DNA detection based on strand displacement. Anal Bioanal Chem 2007; 389:493-7. [PMID: 17641878 DOI: 10.1007/s00216-007-1477-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 06/24/2007] [Accepted: 06/26/2007] [Indexed: 01/12/2023]
Abstract
A nanogold-quenched fluorescence duplex probe has been developed for lighting up homogenous hybridization assays. This novel probe is constructed from two strands of different lengths, and labeled by nanogold and a fluorophore at the long-strand 5'-end and the short-strand 3'-end, respectively. The two tags are in close contact, resulting in complete quenching of the probe fluorescence. If perfectly complemented to the nanogold-labeled strand, a long target oligonucleotide would displace the short fluorophore-labeled strand, and as a result, restore the fluorescence. By using nanogold in the probe, an extremely high quenching efficiency (99.1%) and removal of free fluorophore-labeled strand is achieved. The signal-to-noise ratio and the detection limit (50 pmol L(-1)) of homogenous assays are therefore improved significantly, in comparison with similar probes using organic acceptors. Moreover, the probe has a great inhibition effect on hybridization to a mismatched oligonucleotide. This effect provides the assay with a high specificity, and particularly the assay has great potential in applications for discriminating variations in sequences. The assay sensitivity could be markedly enhanced by using fluorescent materials in the signal strand that are brighter and not quenched by nucleobases.
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Affiliation(s)
- Z-H Mo
- Micro-System Research Center, College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
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35
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Liu GM, Cai HN, Cao MJ, Su WJ. Fluorophore double stranded probe-multiplex quantitative PCR method for detecting transgenic component of promoter derived from Cauliflower Mosaic Virus and nos terminator derived from Agrobacterium tumefaciens simultaneously. Food Control 2007. [DOI: 10.1016/j.foodcont.2005.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Luk KC, Devare SG, Hackett JR. Partially double-stranded linear DNA probes: novel design for sensitive detection of genetically polymorphic targets. J Virol Methods 2007; 144:1-11. [PMID: 17434605 DOI: 10.1016/j.jviromet.2007.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2006] [Revised: 03/09/2007] [Accepted: 03/12/2007] [Indexed: 02/05/2023]
Abstract
Genetically polymorphic targets present a significant challenge to the reliability of detection and quantification by nucleic acid-based assays. A probe system with enhanced mismatch tolerance would be advantageous for such applications. The present study introduces a novel class of DNA probes, designated as partially double-stranded linear probes, composed of a long target-specific strand 5' labeled with a fluorophore and a markedly shorter quencher strand, complementary to the 5' end of the target-specific strand, that is 3' end-labeled with a quencher moiety. The utility of this probe system for sensitive detection of amplification products was demonstrated in a real-time PCR format. Comparison of multiple partially double-stranded linear probe combinations revealed that increased asymmetry in strand length was associated with improved mismatch tolerance. Notably, for a 45-mer/11-mer combination, the difference in threshold cycle values obtained for a perfectly matched target and one containing six mismatches was <1.5 cycles. The capacity for superior mismatch tolerance, ease of design, simplicity and flexibility of application are characteristics that make this new class of probes a desirable alternative for homogeneous detection of targets with a high level of genetic heterogeneity.
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Affiliation(s)
- Ka-Cheung Luk
- Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, IL 60064, USA
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Wen H, Li Q. Real-time PCR detection of multiple lamivudine-resistant mutations with displacing probes in a single tube. J Clin Virol 2007; 38:334-40. [PMID: 17329165 DOI: 10.1016/j.jcv.2007.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 01/10/2007] [Accepted: 01/24/2007] [Indexed: 12/15/2022]
Abstract
BACKGROUND Detection of lamivudine-resistant hepatitis B virus (HBV) is essential to clinical diagnosis and treatment. OBJECTIVES To establish a single tube, real-time PCR assay for simultaneous detection of multiple lamivudine-resistant mutations in serum samples. STUDY DESIGN By using four sequence-specific displacing probes labeled with different fluorophores, a single real-time PCR reaction can tell whether a sample contains any of the following HBV variants: wild-type, rtM204 mutant; mixtures of wild-type and rtM204 mutant; mixtures of rtM204 and rtL180 mutant; mixtures of wild-type, rtM204 mutant and rtL180 mutant. The assay was evaluated with 50 HBV mutation(s)-containing samples and 36 HBeAg-positive samples. RESULTS The results of the real-time PCR assay were consistent with the DNA sequencing, but with much higher sensitivity for detecting a mixture of quasispecies. As few as 10(2)-10(3)copies/ml HBV of all four sequences in pure population and as little as 5% mutant DNA in the presence of wild-type DNA can be detected. CONCLUSIONS Application of this high throughput assay into clinical use should enable earlier diagnosis and better treatment of lamivudine-resistant HBV.
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Affiliation(s)
- Huixin Wen
- The Key Laboratory of Cell Biology and Tumor Cell Engineering of the Ministration of Education, and the Molecular Diagnostics Laboratory, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Fujian, China
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Linear-After-The-Exponential Polymerase Chain Reaction and Allied Technologies. METHODS IN MOLECULAR MEDICINE™ 2007. [DOI: 10.1007/978-1-59745-298-4_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Callegaro A, Spinelli R, Beltrame L, Bicciato S, Caristina L, Censuales S, De Bellis G, Battaglia C. Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data. Nucleic Acids Res 2006; 34:e56. [PMID: 16617143 PMCID: PMC1440877 DOI: 10.1093/nar/gkl185] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) are often determined using TaqMan real-time PCR assays (Applied Biosystems) and commercial software that assigns genotypes based on reporter probe signals at the end of amplification. Limitations to the large-scale application of this approach include the need for positive controls or operator intervention to set signal thresholds when one allele is rare. In the interest of optimizing real-time PCR genotyping, we developed an algorithm for automatic genotype calling based on the full course of real-time PCR data. Best cycle genotyping algorithm (BCGA), written in the open source language R, is based on the assumptions that classification depends on the time (cycle) of amplification and that it is possible to identify a best discriminating cycle for each SNP assay. The algorithm is unique in that it classifies samples according to the behavior of blanks (no DNA samples), which cluster with heterozygous samples. This method of classification eliminates the need for positive controls and permits accurate genotyping even in the absence of a genotype class, for example when one allele is rare. Here, we describe the algorithm and test its validity, compared to the standard end-point method and to DNA sequencing.
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Affiliation(s)
- A Callegaro
- Department of Chemical Process Engineering, University of Padua, Padua, Italy
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Kofiadi IA, Rebrikov DV. Methods for detecting single nucleotide polymorphisms: Allele-specific PCR and hybridization with oligonucleotide probe. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406010029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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