1
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Nakamura Y, Hashimoto M. Droplet size affects the degree of separation between fluorescence-positive and fluorescence-negative droplet populations in droplet digital PCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:656-666. [PMID: 38113037 DOI: 10.1039/d3ay01689g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In droplet digital polymerase chain reaction (ddPCR) tests, a single sample solution is divided into many water-in-oil droplets. At the endpoint of PCR amplification, individual droplets are classified as either fluorescence-positive (FL(+)) or fluorescence-negative (FL(-)) droplets based upon their fluorescence amplitudes. Populations of FL(+) and FL(-) droplets can be seen in the histogram of fluorescence amplitude. The absolute copy number of a target molecule can be calculated from the fraction of FL(+) droplets relative to the total droplet number analyzed using Poisson statistics. It is crucial that the population of FL(+) droplets can be distinctly separated from that of the FL(-) droplets for accurately estimating the FL(+) droplet fraction and the absolute copy number. However, the distinct separation of the two populations is often impaired in actual ddPCR tests. Although many factors have been suggested to affect population separation, no study has addressed whether the droplet size influences the degree of separation. In this study, we compared the degrees of separation for ddPCR runs with three different droplet sizes. The experimental results showed an increasing degree of separation with decreasing droplet size. This discovery will potentially guide researchers to use smaller droplets in ddPCR to achieve higher accuracy and precision.
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Affiliation(s)
- Yusuke Nakamura
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
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2
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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3
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Bogožalec Košir A, Muller S, Žel J, Milavec M, Mallory AC, Dobnik D. Fast and Accurate Multiplex Identification and Quantification of Seven Genetically Modified Soybean Lines Using Six-Color Digital PCR. Foods 2023; 12:4156. [PMID: 38002213 PMCID: PMC10670894 DOI: 10.3390/foods12224156] [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: 10/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The proliferation of genetically modified organisms (GMOs) presents challenges to GMO testing laboratories and policymakers. Traditional methods, like quantitative real-time PCR (qPCR), face limitations in quantifying the increasing number of GMOs in a single sample. Digital PCR (dPCR), specifically multiplexing, offers a solution by enabling simultaneous quantification of multiple GMO targets. This study explores the use of the Naica six-color Crystal dPCR platform for quantifying five GM soybean lines within a single six-plex assay. Two four-color assays were also developed for added flexibility. These assays demonstrated high specificity, sensitivity (limit of detection or LOD < 25 copies per reaction) and precision (bias to an estimated copy number concentration <15%). Additionally, two approaches for the optimization of data analysis were implemented. By applying a limit-of-blank (LOB) correction, the limit of quantification (LOQ) and LOD could be more precisely determined. Pooling of reactions additionally lowered the LOD, with a two- to eight-fold increase in sensitivity. Real-life samples from routine testing were used to confirm the assays' applicability for quantifying GM soybean lines in complex samples. This study showcases the potential of the six-color Crystal dPCR platform to revolutionize GMO testing, facilitating comprehensive analysis of GMOs in complex samples.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Sabine Muller
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Allison C. Mallory
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
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4
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Heinrich T, Toepfer S, Steinmetzer K, Ruettger M, Walz I, Kanitz L, Lemuth O, Hubold S, Fritsch F, Loncarevic-Barcena I, Klingner S, Bocker HT, Ermantraut E. DNA-Binding Magnetic Nanoreactor Beads for Digital PCR Analysis. Anal Chem 2023; 95:14175-14183. [PMID: 37646599 PMCID: PMC10534990 DOI: 10.1021/acs.analchem.3c01418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Digital PCR (dPCR) is based on the separation of target amplification reactions into many compartments with randomly distributed template molecules. Here, we present a novel digital PCR format based on DNA binding magnetic nanoreactor beads (mNRBs). Our approach relies on the binding of all nucleic acids present in a sample to the mNRBs, which both provide a high-capacity binding matrix for capturing nucleic acids from a sample and define the space available for PCR amplification by the internal volume of their hydrogel core. Unlike conventional dPCR, this approach does not require a precise determination of the volume of the compartments used but only their number to calculate the number of amplified targets. We present a procedure in which genomic DNA is bound, the nanoreactors are loaded with PCR reagents in an aqueous medium, and amplification and detection are performed in the space provided by the nanoreactor suspended in fluorocarbon oil. mNRBs exhibit a high DNA binding capacity of 1.1 ng DNA/mNRB (95% CI 1.0-1.2) and fast binding kinetics with ka = 0.21 s-1 (95% CI 0.20-0.23). The dissociation constant KD was determined to be 0.0011 μg/μL (95% CI 0.0007-0.0015). A simple disposable chamber plate is used to accommodate the nanoreactor beads in a monolayer formation for rapid thermocycling and fluorescence detection. The performance of the new method was compared with conventional digital droplet PCR and found to be equivalent in terms of the precision and linearity of quantification. In addition, we demonstrated that mNRBs provide quantitative capture and loss-free analysis of nucleic acids contained in samples in different volumes.
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Affiliation(s)
| | | | | | | | - Ines Walz
- BLINK AG, Bruesseler Strasse 20, 07747 Jena, Germany
| | - Lea Kanitz
- BLINK AG, Bruesseler Strasse 20, 07747 Jena, Germany
| | - Oliver Lemuth
- BLINK AG, Bruesseler Strasse 20, 07747 Jena, Germany
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5
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Parvez S, Brandt ZJ, Peterson RT. Large-scale F0 CRISPR screens in vivo using MIC-Drop. Nat Protoc 2023; 18:1841-1865. [PMID: 37069311 PMCID: PMC10419324 DOI: 10.1038/s41596-023-00821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Zachary J Brandt
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
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6
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Marx A, Osváth M, Szikora B, Pipek O, Csabai I, Nagy Á, Bödör C, Matula Z, Nagy G, Bors A, Uher F, Mikala G, Vályi-Nagy I, Kacskovics I. Liquid biopsy-based monitoring of residual disease in multiple myeloma by analysis of the rearranged immunoglobulin genes-A feasibility study. PLoS One 2023; 18:e0285696. [PMID: 37235573 DOI: 10.1371/journal.pone.0285696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The need for sensitive monitoring of minimal/measurable residual disease (MRD) in multiple myeloma emerged as novel therapies led to deeper responses. Moreover, the potential benefits of blood-based analyses, the so-called liquid biopsy is prompting more and more studies to assess its feasibility. Considering these recent demands, we aimed to optimize a highly sensitive molecular system based on the rearranged immunoglobulin (Ig) genes to monitor MRD from peripheral blood. We analyzed a small group of myeloma patients with the high-risk t(4;14) translocation, using next-generation sequencing of Ig genes and droplet digital PCR of patient-specific Ig heavy chain (IgH) sequences. Moreover, well established monitoring methods such as multiparametric flow cytometry and RT-qPCR of the fusion transcript IgH::MMSET (IgH and multiple myeloma SET domain-containing protein) were utilized to evaluate the feasibility of these novel molecular tools. Serum measurements of M-protein and free light chains together with the clinical assessment by the treating physician served as routine clinical data. We found significant correlation between our molecular data and clinical parameters, using Spearman correlations. While the comparisons of the Ig-based methods and the other monitoring methods (flow cytometry, qPCR) were not statistically evaluable, we found common trends in their target detection. Regarding longitudinal disease monitoring, the applied methods yielded complementary information thus increasing the reliability of MRD evaluation. We also detected indications of early relapse before clinical signs, although this implication needs further verification in a larger patient cohort.
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Affiliation(s)
- Anita Marx
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Magdolna Osváth
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bence Szikora
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Orsolya Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ákos Nagy
- Department of Pathology and Experimental Cancer Research, HCEMM-SE Molecular Oncohematology Research Group, Semmelweis University, Budapest, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, HCEMM-SE Molecular Oncohematology Research Group, Semmelweis University, Budapest, Hungary
| | - Zsolt Matula
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Ginette Nagy
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - András Bors
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Ferenc Uher
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Gábor Mikala
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - István Vályi-Nagy
- National Institute of Hematology and Infectious Diseases, Central Hospital of Southern Pest, Budapest, Hungary
| | - Imre Kacskovics
- Department of Immunology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
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7
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Mukherjee S, Perveen S, Negi A, Sharma R. Evolution of tuberculosis diagnostics: From molecular strategies to nanodiagnostics. Tuberculosis (Edinb) 2023; 140:102340. [PMID: 37031646 PMCID: PMC10072981 DOI: 10.1016/j.tube.2023.102340] [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: 01/19/2023] [Revised: 03/12/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Tuberculosis has remained a global concern for public health affecting the lives of people for ages. Approximately 10 million people are affected by the disease and 1.5 million succumb to the disease worldwide annually. The COVID-19 pandemic has highlighted the role of early diagnosis to win the battle against such infectious diseases. Thus, advancement in the diagnostic approaches to provide early detection forms the foundation to eradicate and manage contagious diseases like tuberculosis. The conventional diagnostic strategies include microscopic examination, chest X-ray and tuberculin skin test. The limitations associated with sensitivity and specificity of these tests demands for exploring new techniques like probe-based assays, CRISPR-Cas and microRNA detection. The aim of the current review is to envisage the correlation between both the conventional and the newer approaches to enhance the specificity and sensitivity. A significant emphasis has been placed upon nanodiagnostic approaches manipulating quantum dots, magnetic nanoparticles, and biosensors for accurate diagnosis of latent, active and drug-resistant TB. Additionally, we would like to ponder upon a reliable method that is cost-effective, reproducible, require minimal infrastructure and provide point-of-care to the patients.
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Affiliation(s)
| | - Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anjali Negi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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8
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Choi JW, Seo WH, Kang T, Kang T, Chung BG. Droplet digital recombinase polymerase amplification for multiplexed detection of human coronavirus. LAB ON A CHIP 2023; 23:2389-2398. [PMID: 37083004 DOI: 10.1039/d3lc00025g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Since the outbreak of coronavirus 2019 (COVID-19), detection technologies have been attracting a great deal of attention in molecular diagnosis applications. In particular, the droplet digital PCR (ddPCR) has become a promising tool as it offers absolute quantification of target nucleic acids with high specificity and sensitivity. In recent years, the combination of the isothermal amplification strategies has made ddPCR a popular method for on-site testing by enabling amplification at a constant temperature. However, the current isothermal ddPCR assays are still challenging due to inherent non-specific amplification. In this paper, we present a multiplexed droplet digital recombinase polymerase amplification (MddRPA) with precise initiation of the reaction. First, the reaction temperature and dynamic range of reverse transcription (RT) and RPA were characterized by real-time monitoring of fluorescence intensities. Using a droplet-based microfluidic chip, the master mix and the initiator were fractionated and rapidly mixed within well-confined droplets. Due to the high heat transfer and mass transfer of the droplets, the precise initiation of the amplification was enabled and the entire assay could be conducted within 30 min. The concentrations of target RNA in the range from 5 copies per μL to 2500 copies per μL could be detected with high linearity (R2 > 0.999). Furthermore, the multiplexed detection of three types of human coronaviruses was successfully demonstrated with high specificity (>96%). Finally, we compared the performance of the assay with a commercial RT-qPCR system using COVID-19 clinical samples. The MddRPA assay showed a 100% concordance with the RT-qPCR results, indicating its reliability and accuracy in detecting SARS-CoV-2 nucleic acids in clinical samples. Therefore, our MddRPA assay with rapid detection, precise quantification, and multiplexing capability would be an interesting method for molecular diagnosis of viral infections.
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Affiliation(s)
- Ji Wook Choi
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
| | - Won Ho Seo
- Department of Biomedical Engineering, Sogang University, Seoul, Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon, Korea
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
- Institute of Integrated Biotechnology, Sogang University, Seoul, Korea
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Bogožalec Košir A, Lužnik D, Tomič V, Milavec M. Evaluation of DNA Extraction Methods for Reliable Quantification of Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. BIOSENSORS 2023; 13:bios13040463. [PMID: 37185538 PMCID: PMC10136035 DOI: 10.3390/bios13040463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
Detection and quantification of DNA biomarkers relies heavily on the yield and quality of DNA obtained by extraction from different matrices. Although a large number of studies have compared the yields of different extraction methods, the repeatability and intermediate precision of these methods have been largely overlooked. In the present study, five extraction methods were evaluated, using digital PCR, to determine their efficiency in extracting DNA from three different Gram-negative bacteria in sputum samples. The performance of two automated methods (GXT NA and QuickPick genomic DNA extraction kit, using Arrow and KingFisher Duo automated systems, respectively), two manual kit-based methods (QIAamp DNA mini kit; DNeasy UltraClean microbial kit), and one manual non-kit method (CTAB), was assessed. While GXT NA extraction kit and the CTAB method have the highest DNA yield, they did not meet the strict criteria for repeatability, intermediate precision, and measurement uncertainty for all three studied bacteria. However, due to limited clinical samples, a compromise is necessary, and the GXT NA extraction kit was found to be the method of choice. The study also showed that dPCR allowed for accurate determination of extraction method repeatability, which can help standardize molecular diagnostic approaches. Additionally, the determination of absolute copy numbers facilitated the calculation of measurement uncertainty, which was found to be influenced by the DNA extraction method used.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Dane Lužnik
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Viktorija Tomič
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, 4204 Golnik, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
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10
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Du L, Li Y, Wang J, Zhou Z, Lan T, Jing D, Wu W, Zhou J. Cost-Effective Droplet Generator for Portable Bio-Applications. MICROMACHINES 2023; 14:466. [PMID: 36838166 PMCID: PMC9966110 DOI: 10.3390/mi14020466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/03/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
The convenient division of aqueous samples into droplets is necessary for many biochemical and medical analysis applications. In this article, we propose the design of a cost-effective droplet generator for potential bio-chemical application, featuring two symmetric tubes. The new droplet generator revisits the relationship between capillary components and liquid flow rates. The size of generated droplets by prototype depends only on generator dimensions, without precisely needing to control external flow conditions or driving pressure, even when the relative extreme difference in flow rate for generating nL level droplets is over 57.79%, and the relative standard deviation (RSD) of the volume of droplets is barely about 9.80%. A dropper working as a pressure resource is used to verify the rapidity and robustness of this principle of droplet generation, which shows great potential for a wide range of droplet-based applications.
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Affiliation(s)
- Lin Du
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200433, China
| | - Yuxin Li
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200433, China
| | - Jie Wang
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200433, China
| | - Zijian Zhou
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200433, China
| | - Tian Lan
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200433, China
| | - Dalei Jing
- School of Mechanical Engineering, University of Shanghai for Science and Technology, Shanghai 200433, China
| | - Wenming Wu
- Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510075, China
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China
| | - Jia Zhou
- State Key Laboratory of ASIC and System, School of Microelectronics, Fudan University, Shanghai 200433, China
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11
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Loskyll M, Podbiel D, Guber A, Hoffmann J. Partitioning and subsampling statistics in compartment-based quantification methods. PLoS One 2023; 18:e0285784. [PMID: 37186607 PMCID: PMC10184943 DOI: 10.1371/journal.pone.0285784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/01/2023] [Indexed: 05/17/2023] Open
Abstract
The precision of compartment-based quantification methods is subject to multiple effects, of which partitioning and subsampling play a major role. Partitioning is the process of aliquoting the sample liquid and consequently the contained target molecules, whereas subsampling denotes the fact that usually only a portion of a sample is analyzed. In this work, we present a detailed statistical description comprising the effects of partitioning and subsampling on the relative uncertainty of the test result. We show that the state-of-the-art binomial model does not provide accurate results for the level of subsampling present when analyzing the nucleic acid content of single specific cells. Hence, in this work we address partitioning and subsampling effects separately and subsequently combine them to derive the relative uncertainty of a test system and compare it for single cell content analysis and body fluid analysis. In point-of-care test systems the area for partitioning and detection is usually limited, which means that a trade-off between the number of partitions (related to a partitioning uncertainty) and the amount of analyzed volume (related to a subsampling uncertainty) might be inevitable. In case of low target concentration, the subsampling uncertainty is dominant whereas for high target concentration, the partitioning uncertainty increases, and a larger number of partitions is beneficial to minimize the combined uncertainty. We show, that by minimizing the subsampling uncertainty in the test system, the quantification uncertainty of low target concentrations in single cell content analysis is much smaller than in body fluid analysis. In summary, the work provides the methodological basis for a profound statistical evaluation of partitioning and subsampling effects in compartment-based quantification methods and paves the way towards an improved design of future digital quantification devices for highly accurate molecular diagnostic analysis at the point-of-care.
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Affiliation(s)
- Manuel Loskyll
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Daniel Podbiel
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Andreas Guber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Baden-Württemberg, Germany
- BioMEMS Consulting, Karlsruhe, Baden-Württemberg, Germany
| | - Jochen Hoffmann
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
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12
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Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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13
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Yalçınkaya B, Tastekin D, Güzelbulut F, Akgoz M, Pençe S. Quantification of cell-free circulating mitochondrial DNA copy number variation in hepatocellular carcinoma. Rev Assoc Med Bras (1992) 2022; 68:1161-1165. [PMID: 36228247 PMCID: PMC9575012 DOI: 10.1590/1806-9282.20210368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/16/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVE Hepatocellular carcinoma is the most common primary malignant liver tumor. Mitochondrial DNA copy number has been shown to be associated with various malignancies. However, there has not been any study on the absolute quantification of mtDNA copy number in hepatocellular carcinoma. The aim of this study was to develop a new method for absolute quantification of mtDNA copy number and to relatively quantify the variations in the mtDNA copy number in hepatocellular carcinoma patients in comparison with healthy individuals. METHODS Venous blood samples were collected from both hepatocellular carcinoma patients (34) and healthy individuals (34). Circulating cell-free DNAs were isolated and the relative quantification of mtDNA copy number variation was determined using quantitative polymerase chain reaction and digital polymerase chain reaction. RESULTS It was found that the relative mtDNA copy number was significantly decreased in hepatocellular carcinoma patients in comparison with the control group (p<0.05). The median (range) and average of relative mtDNA/β-actin gene of the patients were determined as 42.8 cp/μL (11.1-88.5) and 45.1 cp/μL, respectively, while the median (range) and average relative mtDNA/β-actin gene of the control group were determined as 102.8 cp/μL (55.1-291.8) and 138.7 cp/μL, respectively (p<0.05). When quantitative polymerase chain reaction and digital polymerase chain reaction were compared, mtDNA/β-actin gene copy number ratio of digital polymerase chain reaction results was found to be 1.76-fold more than that of quantitative polymerase chain reaction results. CONCLUSION Circulating mtDNA copy number was decreased in hepatocellular carcinoma patients in comparison with healthy individuals, and we suggest that it can be used as a noninvasive biomarker for hepatocellular carcinoma diagnosis in the future.
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Affiliation(s)
| | - Didem Tastekin
- Istanbul University, Institute of Oncology – Istanbul, Turkey
| | - Fatih Güzelbulut
- University of Health Sciences, Haydarpaşa Numune Training and Research Hospital – Istanbul, Turkey
| | - Muslum Akgoz
- TUBITAK National Metrology Institute – Kocaeli, Turkey
| | - Sadrettin Pençe
- Istanbul Medeniyet University, Faculty of Medicine – Istanbul, Turkey
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14
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Hsieh SA, Shamsaei D, Eitzmann DR, Anderson JL. Digital Droplet Loop-Mediated Isothermal Amplification Featuring a Molecular Beacon Assay, 3D Printed Droplet Generation, and Smartphone Imaging for Sequence-Specific DNA Detection. Anal Chem 2022; 94:11949-11956. [PMID: 35973866 DOI: 10.1021/acs.analchem.2c02979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleic acid detection is widely used in the amplification and quantitation of nucleic acids from biological samples. While polymerase chain reaction (PCR) enjoys great popularity, expensive thermal cyclers are required for precise temperature control. Loop-mediated isothermal amplification (LAMP) enables highly sensitive, rapid, and low-cost amplification of nucleic acids at constant temperatures. LAMP detection often relies on double-stranded DNA-binding dyes or metal indicators that lack sequence selectivity. Molecular beacons (MBs) are hairpin-shaped oligonucleotide probes whose sequence specificity in LAMP provides the capability of differentiating between single-nucleotide polymorphisms (SNPs). Digital droplet LAMP (ddLAMP) enables a large number of independent LAMP reactions to be performed and provides quantification of target DNA sequences. However, a major challenge with ddLAMP is the requirement of expensive droplet generators to form homogeneous microdroplets. In this study, we demonstrate for the first time that a three-dimensional (3D) printed droplet generation platform can be coupled to a LAMP assay featuring MBs as sequence-specific probes. The low-cost 3D printed droplet generator system was designed, and its customizability was demonstrated in the formation of monodisperse ddLAMP assay-in-oil microdroplets. Additionally, a smartphone-based imaging system is demonstrated to increase accessibility for point-of-care applications. The MB-ddLAMP assay is shown to discriminate between two SNPs at various amplification temperatures to afford a useful platform for sequence-specific, sensitive, and accurate DNA quantification. This work expands the utility of MBs to ddLAMP for quantitative studies in the detection of SNPs and exploits the customizability of 3D printing technologies to optimize the homogeneity, size, and volume of oil-in-water microdroplets.
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Affiliation(s)
- Shu-An Hsieh
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Danial Shamsaei
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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15
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Le Duff Y, Gärtner K, Busby EJ, Dalzini A, Danaviah S, Fuentes JLJ, Giaquinto C, Huggett JF, Hurley M, Marcellin AG, Muñoz-Fernández MÁ, O’Sullivan DM, Persaud D, Powell L, Rigsby P, Rossi P, de Rossi A, Siems L, Smit T, Watters SA, Almond N, Nastouli E. Assessing the Variability of Cell-Associated HIV DNA Quantification through a Multicenter Collaborative Study. Microbiol Spectr 2022; 10:e0024322. [PMID: 35658711 PMCID: PMC9241949 DOI: 10.1128/spectrum.00243-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Reliable and accurate quantification of cell-associated HIV DNA (CA HIV DNA) is critical for early infant diagnosis, clinical management of patients under therapy, and to inform new therapeutics efficacy. The present study assessed the variability of CA HIV DNA quantification obtained from various assays and the value of using reference materials to help harmonize the measurements. Using a common set of reagents, our multicenter collaborative study highlights significant variability of CA HIV DNA quantification and lower limit of quantification across assays. The quantification of CA HIV DNA from a panel of infected PBMCs can be harmonized through cross-subtype normalization but assay calibration with the commonly used 8E5 cell line failed to reduce quantification variability between assays, demonstrating the requirement to thoroughly evaluate reference material candidates to help improve the comparability of CA HIV DNA diagnostic assay performance. IMPORTANCE Despite a global effort, HIV remains a major public health burden with an estimated 1.5 million new infections occurring in 2020. HIV DNA is an important viral marker, and its monitoring plays a critical role in the fight against HIV: supporting diagnosis in infants and underpinning clinical management of patients under therapy. Our study demonstrates that HIV DNA measurement of the same samples can vary significantly from one laboratory to another, due to heterogeneity in the assay, protocol, and reagents used. We show that when carefully selected, reference materials can reduce measurement variability and harmonize HIV DNA quantification across laboratories, which will help contribute to improved diagnosis and clinical management of patients living with HIV.
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Affiliation(s)
- Yann Le Duff
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Kathleen Gärtner
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Eloise J. Busby
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Annalisa Dalzini
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | - José Luis Jiménez Fuentes
- Instituto Investigación Sanitaria Gregorio Marañón, Laboratorio InmunoBiología Molecular and Spanish HIV HGM BioBank, Madrid, Spain
| | - Carlo Giaquinto
- Department for Woman’s and Child’s Health, University of Padova, Padua, Italy
| | - Jim F. Huggett
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Matthew Hurley
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Anne-Geneviève Marcellin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - María Ángeles Muñoz-Fernández
- Instituto Investigación Sanitaria Gregorio Marañón, Laboratorio InmunoBiología Molecular and Spanish HIV HGM BioBank, Madrid, Spain
| | - Denise M. O’Sullivan
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Deborah Persaud
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Laura Powell
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter Rigsby
- Division of Analytical Biological Sciences, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Paolo Rossi
- Department of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Anita de Rossi
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Lilly Siems
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Theresa Smit
- Africa Health Research Institute, Durban, South Africa
| | - Sarah A. Watters
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Neil Almond
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Eleni Nastouli
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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16
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Beshir KB, Parr JB, Cunningham J, Cheng Q, Rogier E. Screening strategies and laboratory assays to support Plasmodium falciparum histidine-rich protein deletion surveillance: where we are and what is needed. Malar J 2022; 21:201. [PMID: 35751070 PMCID: PMC9233320 DOI: 10.1186/s12936-022-04226-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/17/2022] [Indexed: 11/10/2022] Open
Abstract
Rapid diagnostic tests (RDTs) detecting Plasmodium falciparum histidine-rich protein 2 (HRP2) have been an important tool for malaria diagnosis, especially in resource-limited settings lacking quality microscopy. Plasmodium falciparum parasites with deletion of the pfhrp2 gene encoding this antigen have now been identified in dozens of countries across Asia, Africa, and South America, with new reports revealing a high prevalence of deletions in some selected regions. To determine whether HRP2-based RDTs are appropriate for continued use in a locality, focused surveys and/or surveillance activities of the endemic P. falciparum population are needed. Various survey and laboratory methods have been used to determine parasite HRP2 phenotype and pfhrp2 genotype, and the data collected by these different methods need to be interpreted in the appropriate context of survey and assay utilized. Expression of the HRP2 antigen can be evaluated using point-of-care RDTs or laboratory-based immunoassays, but confirmation of a deletion (or mutation) of pfhrp2 requires more intensive laboratory molecular assays, and new tools and strategies for rigorous but practical data collection are particularly needed for large surveys. Because malaria diagnostic strategies are typically developed at the national level, nationally representative surveys and/or surveillance that encompass broad geographical areas and large populations may be required. Here is discussed contemporary assays for the phenotypic and genotypic evaluation of P. falciparum HRP2 status, consider their strengths and weaknesses, and highlight key concepts relevant to timely and resource-conscious workflows required for efficient diagnostic policy decision making.
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Affiliation(s)
- Khalid B Beshir
- Faculty of Infectious Diseases, London School of Hygiene and Tropical Diseases, Keppel Street, London, WC1E 7HT, UK
| | - Jonathan B Parr
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Eric Rogier
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30029, USA.
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17
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Park J, Su MY, Kang KN, Kim AS, Ahn JH, Cho E, Lee JH, Kim YU. Body Map of Droplet Distributions During Oropharyngeal Suction to Protect Health Care Workers From Airborne Diseases. J Perianesth Nurs 2022; 38:180-185. [PMID: 36229328 PMCID: PMC9186442 DOI: 10.1016/j.jopan.2022.05.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/01/2022]
Abstract
PURPOSE Health care workers (HCWs), and in particular anesthesia providers, often must perform aerosol-generating medical procedures (AGMPs). However, no studies have analyzed droplet distributions on the bodies of HCWs during AGMPs. Therefore, the purpose of this study was to assess and analyze droplet distributions on the bodies of HCWs during suction of oral cavities with and without oral airways and during extubations. DESIGN Using a quasi-experiemental design, we assumed the HCWs perform suction and extubation on intubated patients, and we prepared an intubated mannequin mimicking a patient. This study performed the oral suction and extubation on the intubated mannequin (with or without oral airways in place) and analyzed the droplet distributions. METHODS We prepared a mannequin intubated with an 8.0 mm endotracheal tube, assuming the situation of general anesthesia. We designed the body mapping gown, and divided it into 10 areas including the head, neck, chest, abdomen, upper arms, forearms, and hands. We classified experiments into group O when suctions were performed on the mannequin with an oral airway, and into group X when the suctions were performed on the mannequin without an oral airway. An experienced board-certified anesthesiologist performed 10 oral suctions on each mannequin, and 10 extubations. We counted the droplets on the anesthesiologist's gown according to the divided areas after each procedure. FINDINGS The mean droplet count after suction was 6.20 ± 2.201 in group O and 13.6 ± 4.300 in group X, with a significant difference between the two groups (P < .001). The right and left hands were the most contaminated areas in group O (2.8 ± 1.033 droplets and 2.0 ± 0.943 droplets, respectively). The abdomen, right hand, left forearm, and left hand showed many droplets in group X. (1.3 ± 1.337 droplets, 3.1 ± 1.792 droplets, 3.2 ± 3.910 droplets, and 4.3 ± 2.214 droplets, respectively). The chest, abdomen, and left hand presented significantly more droplets in group X than in group O. The trunk area (chest and abdomen) was exposed to more droplets during extubations than during suctions. CONCLUSIONS During suctions, more droplets are splattered from mannequins without oral airways than from those with oral airways. The right and left hands were the most contaminated areas in group O. Moreover, the abdomen, right hand, left forearm, and left hand presented a lot of droplets in group X. In addition, extubations contaminate wider areas (the head, neck, chest and abdomen) of an HCW than suctions.
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Affiliation(s)
- Jiyeon Park
- Department of Anesthesiology and Pain Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Anesthesiology and Pain Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Min-Ying Su
- Department of Radiological Sciences, University of California, Irvine, CA
| | - Keum Nae Kang
- Department of Anesthesiology and Pain Medicine, National Police Hospital, Seoul, Republic of Korea
| | - Ae Sook Kim
- Department of Anesthesiology and Pain Medicine, Catholic Kwandong University, College of Medicine, International St. Mary's Hospital, Incheon, Republic of Korea
| | - Jin Hee Ahn
- Department of Anesthesiology and Pain Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunah Cho
- Department of Anesthesiology and Pain Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jun-Ho Lee
- Department of Anesthesiology and Pain Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Young Uk Kim
- Department of Radiological Sciences, University of California, Irvine, CA; Department of Anesthesiology and Pain Medicine, Catholic Kwandong University, College of Medicine, International St. Mary's Hospital, Incheon, Republic of Korea.
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18
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Digital Droplet-PCR for Quantification of Viable Campylobacter jejuni and Campylobacter coli in Chicken Meat Rinses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The EU commission established Regulation (2017/1495) in 2017 to reduce Campylobacter on chicken skin and to decrease the number of human cases of campylobacteriosis attributable to the consumption of poultry meat. A Process Hygiene Criterion based on colony-forming unit data was set to a maximum of 1000 CFU Campylobacter spp. per gram chicken neck skin at slaughterhouses. Confronted with stressors, including cold, oxidative stress or antibiotic treatment, live cells may enter into a viable but non-cultivable state (VBNC) and lose the ability to grow, in reference to the plate count ISO 10272-2:2017 method, but still possess the potential to recover and cause infections under favorable conditions. In this study, a droplet digital PCR combined with the intercalating dye propidium monoazide (PMA) was established for quantification of C. coli and C. jejuni in chicken meat rinses. The PMA was used to inactivate DNA from dead cells in this technique. This method was successfully validated against the reference method according to ISO 16140-2:2016 for accuracy and relative trueness. Additionally, it presented a 100% selectivity for Campylobacter jejuni and C. coli. Moreover, the technical measurement uncertainty was determined according to ISO 19036:2019, and the applicability of ddPCR for quantifying C. coli and C. jejuni in chicken meat rinses was investigated on naturally contaminated samples from slaughterhouses and supermarkets. Results obtained from this study demonstrated a strong correlation to qPCR as well as the classical microbiological reference method.
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19
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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20
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Lee SS, Kim S, Yoo HM, Lee DH, Bae YK. Development of SARS-CoV-2 packaged RNA reference material for nucleic acid testing. Anal Bioanal Chem 2022; 414:1773-1785. [PMID: 34958396 PMCID: PMC8711077 DOI: 10.1007/s00216-021-03846-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
Nucleic acid tests to detect the SARS-CoV-2 virus have been performed worldwide since the beginning of the COVID-19 pandemic. For the quality assessment of testing laboratories and the performance evaluation of molecular diagnosis products, reference materials (RMs) are required. In this work, we report the production of a lentiviral SARS-CoV-2 RM containing approximately 12 kilobases of its genome including common diagnostics targets such as RdRp, N, E, and S genes. The RM was measured with multiple assays using two different digital PCR platforms. To measure the homogeneity and stability of the lentiviral SARS-CoV-2 RM, reverse transcription droplet digital PCR (RT-ddPCR) was used with in-house duplex assays. The copy number concentration of each target gene in the extracted RNA solution was then converted to that of the RM solution. Their copy number values are measured to be from 1.5 × 105 to 2.0 × 105 copies/mL. The RM has a between-bottle homogeneity of 4.80-8.23% and is stable at 4 °C for 1 week and at -70 °C for 6 months. The lentiviral SARS-CoV-2 RM closely mimics real samples that undergo identical pre-analytical processes for SARS-CoV-2 molecular testing. By offering accurate reference values for the absolute copy number of viral target genes, the developed RM can be used to improve the reliability of SARS-CoV-2 molecular testing.
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Affiliation(s)
- Sang-Soo Lee
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea
| | - Seil Kim
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon, 34113, Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Hee Min Yoo
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Da-Hye Lee
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea.
| | - Young-Kyung Bae
- Bio-Metrology Group, Korea Research Institute of Standards and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, Korea.
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
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21
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Digital Microfluidic qPCR Cartridge for SARS-CoV-2 Detection. MICROMACHINES 2022; 13:mi13020196. [PMID: 35208320 PMCID: PMC8874717 DOI: 10.3390/mi13020196] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023]
Abstract
Point-of-care (POC) tests capable of individual health monitoring, transmission reduction, and contact tracing are especially important in a pandemic such as the coronavirus disease 2019 (COVID-19). We develop a disposable POC cartridge that can be mass produced to detect the SARS-CoV-2 N gene through real-time quantitative polymerase chain reaction (qPCR) based on digital microfluidics (DMF). Several critical parameters are studied and improved, including droplet volume consistency, temperature uniformity, and fluorescence intensity linearity on the designed DMF cartridge. The qPCR results showed high accuracy and efficiency for two primer-probe sets of N1 and N2 target regions of the SARS-CoV-2 N gene on the DMF cartridge. Having multiple droplet tracks for qPCR, the presented DMF cartridge can perform multiple tests and controls at once.
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22
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Tran TM, Kim SC, Modavi C, Abate AR. Robotic automation of droplet microfluidics. BIOMICROFLUIDICS 2022; 16:014102. [PMID: 35145570 PMCID: PMC8816516 DOI: 10.1063/5.0064265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet microfluidics with commercial fluid-handling robotics. The workflows incorporate common microfluidic devices including droplet generators, mergers, and sorters and utilize the robot's native capabilities for thermal control, incubation, and plate scanning. The ability to automate microfluidic devices using commercial fluid handling will speed up the integration of these methods into biological workflows.
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Affiliation(s)
- Tuan M. Tran
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Samuel C. Kim
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
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23
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O'Malley K, McNamara P, McDonald W. Antibiotic resistance genes in an urban stream before and after a state fair. JOURNAL OF WATER AND HEALTH 2021; 19:885-894. [PMID: 34874897 DOI: 10.2166/wh.2021.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global spread of antibiotic resistance genes (ARGs) concomitant with a decrease in antibiotic effectiveness is a major public health issue. While research has demonstrated the impact of various urban sources, such as wastewater treatment plant (WWTP) effluent, stormwater runoff, and industrial discharge on ARG abundance in receiving waters, the impact of short-term gatherings such as state fairs is not comprehensively understood. The objective of this research was to explore the impact of a 2-week Wisconsin State Fair gathering - over 1.1 million visitors and 7,100 farm animals - on the abundance of the ARG blaTEM, the integrase of the class 1 integron (intI1), a marker for horizontal gene transfer, and the 16S rRNA gene, a marker for total biomass, in an urban stream receiving runoff from the state fair. Stream samples downstream of the state fair were taken before and after the event and quantified via a droplet digital polymerase chain reaction. The absolute abundance of all genes was significantly higher (p<0.05) following the event. This research showcases the prevalence and persistence of ARG contamination in an urban stream before and after a state fair gathering, suggesting that short-term events can be a significant source of ARGs into the environment.
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Affiliation(s)
- Kassidy O'Malley
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
| | - Patrick McNamara
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
| | - Walter McDonald
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA E-mail:
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24
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Milavec M, Cleveland MH, Bae YK, Wielgosz RI, Vonsky M, Huggett JF. Metrological framework to support accurate, reliable, and reproducible nucleic acid measurements. Anal Bioanal Chem 2021; 414:791-806. [PMID: 34738220 PMCID: PMC8568362 DOI: 10.1007/s00216-021-03712-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
Nucleic acid analysis is used in many areas of life sciences such as medicine, food safety, and environmental monitoring. Accurate, reliable measurements of nucleic acids are crucial for maximum impact, yet users are often unaware of the global metrological infrastructure that exists to support these measurements. In this work, we describe international efforts to improve nucleic acid analysis, with a focus on the Nucleic Acid Analysis Working Group (NAWG) of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM). The NAWG is an international group dedicated to improving the global comparability of nucleic acid measurements; its primary focus is to support the development and maintenance of measurement capabilities and the dissemination of measurement services from its members: the National Metrology Institutes (NMIs) and Designated Institutes (DIs). These NMIs and DIs provide DNA and RNA measurement services developed in response to the needs of their stakeholders. The NAWG members have conducted cutting edge work over the last 20 years, demonstrating the ability to support the reliability, comparability, and traceability of nucleic acid measurement results in a variety of sectors.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Megan H Cleveland
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Robert I Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Maxim Vonsky
- D.I. Mendeleev Institute for Metrology, Moskovsky pr., 19, Saint-Petersburg, 190005, Russian Federation
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK.,School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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Jerič Kokelj B, Štalekar M, Vencken S, Dobnik D, Kogovšek P, Stanonik M, Arnol M, Ravnikar M. Feasibility of Droplet Digital PCR Analysis of Plasma Cell-Free DNA From Kidney Transplant Patients. Front Med (Lausanne) 2021; 8:748668. [PMID: 34692738 PMCID: PMC8531215 DOI: 10.3389/fmed.2021.748668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patients' plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
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Affiliation(s)
- Barbara Jerič Kokelj
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Miha Arnol
- Department of Nephrology, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Suoranta T, Laham-Karam N, Ylä-Herttuala S. Optimized Protocol for Accurate Titration of Adeno-Associated Virus Vectors. Hum Gene Ther 2021; 32:1270-1279. [PMID: 33560161 DOI: 10.1089/hum.2020.318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Adeno-associated virus (AAV) is currently the most popular gene delivery vector for in vivo gene therapy. However, variability in titration methods between different laboratories affects the reproducibility of experiments and evaluation of safety and efficacy in clinical trials. We describe an optimized protocol for AAV titration, including quantitative PCR (qPCR) standard preparation and quantitation and treatment of AAV samples before qPCR and droplet digital PCR (ddPCR) titration. During the protocol development, we observed that quantitation of the qPCR standard was dependent on its conformation and that A260-based quantitation overestimated the plasmid copy numbers, introducing significant error. Linearized, free inverted terminal repeat (free-ITR), and supercoiled standards were compared with enhanced green fluorescent protein (EGFP), SV40p(A), and AAV2-ITR qPCR assays and we found that using the AAV2-ITR assay together with either linearized or supercoiled standard led to overestimation of the titers, while EGFP and SV40p(A) assays were more accurate with the linearized standard. Finally, we compared extraction of AAV1, AAV2, AAV5, AAV6, AAV8, and AAV9 genomes by heat denaturation, proteinase K treatment, and kit extraction. Kit extraction, which contained proteinase K treatment in denaturing buffer before spin-column purification, significantly increased the titers acquired for all the serotypes in both qPCR and ddPCR. These improvements resulted in an accurate quantitation of the ATCC reference standard and in a robust and reliable protocol for AAV titration.
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Affiliation(s)
- Tuisku Suoranta
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.,Heart Center, Kuopio University Hospital, Kuopio, Finland.,Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
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28
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Huggett JF. The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clin Chem 2021; 66:1012-1029. [PMID: 32746458 DOI: 10.1093/clinchem/hvaa125] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022]
Abstract
Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.
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Zhao S, Zhang Z, Hu F, Wu J, Peng N. Massive droplet generation for digital PCR via a smart step emulsification chip integrated in a reaction tube. Analyst 2021; 146:1559-1568. [PMID: 33533355 DOI: 10.1039/d0an01841d] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Step emulsification (SE) devices coupled with parallel generation nozzles are widely used in the production of large-scale monodisperse droplets, especially for droplet-based digital polymerase chain reaction (ddPCR) analysis. Although current ddPCR systems based on the SE method can provide a fully enclosed ddPCR scheme, high demands on chip fabrication and system control will increase testing costs and reduce its flexibility in ddPCR analysis. In this study, a compact SE device, integrating a smart SE chip into a reaction tube, was developed to prepare large-scale water-in-fluorinated-oil droplets for ddPCR analysis. The SE chip contained dozens of droplet-generation nozzles. By adjusting the nozzle height of the SE chip, monodisperse droplets in a picolitre to nanolitre vloume could be prepared at a production rate of tens to hundreds of microlitres per minute. Subsequently, we utilized such an integrated SE device to prepare monodisperse droplets for ddPCR experiments. The volume of PCR reagent and the number of droplets could be flexibly adjusted according to the requirements of the ddPCR analysis. The quantitative results showed that emulsions prepared by the SE device could achieve ddPCR detection with high accuracy, good repeatability, and an adaptive dynamic range, which also demonstrated the robustness and reliability of such devices in the droplet preparation. Thus, this compact SE device provides an inexpensive, flexible, and simplified droplet preparation method for digital PCR quantitative analysis.
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Affiliation(s)
- Shuhao Zhao
- State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an, 710054, Shaanxi, China.
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Zhou H, Liu D, Ma L, Ma T, Xu T, Ren L, Li L, Xu S. A SARS-CoV-2 Reference Standard Quantified by Multiple Digital PCR Platforms for Quality Assessment of Molecular Tests. Anal Chem 2021; 93:715-721. [PMID: 33289545 PMCID: PMC7737535 DOI: 10.1021/acs.analchem.0c03996] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/24/2020] [Indexed: 01/03/2023]
Abstract
The outbreak of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. A reference standard with a well-characterized concentration or titer is of the utmost importance for the study of limit of detection (LoD), which is a crucial feature for a diagnostic assay. Although several reference standards of plasmids or synthetic RNA have already been announced, a reference standard for inactivated virus particles with an accurate concentration is still needed to evaluate the complete procedure. Here, we performed a collaborative study to estimate the NAT-detectable units as a viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6 × 105 ± 6.5 × 104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.
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Affiliation(s)
- Haiwei Zhou
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Donglai Liu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Liang Ma
- Department of Biomedical Devices, Bioland
Laboratory (Guangzhou Regenerative Medicine and Health Guangdong
Laboratory), Guangzhou 510320, China
| | - Tingting Ma
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Tingying Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
| | - Lili Ren
- Institute of Pathogen Biology, Chinese
Academy of Medical Sciences & Peking Union Medical College, Beijing
100730, China
| | - Liang Li
- Biotechnology Research Institute, Chinese
Academy of Agricultural Sciences, Beijing 100081,
China
| | - Sihong Xu
- Division II of In Vitro Diagnostics for Infectious
Diseases, Institute for In Vitro Diagnostics Control, National Institutes for
Food and Drug Control, Beijing 100050, China
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Zhu K, Suttner B, Pickering A, Konstantinidis KT, Brown J. A novel droplet digital PCR human mtDNA assay for fecal source tracking. WATER RESEARCH 2020; 183:116085. [PMID: 32750535 PMCID: PMC7495096 DOI: 10.1016/j.watres.2020.116085] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 05/22/2023]
Abstract
Human mitochondrial DNA provides a promising target for fecal source tracking because it is unique and intrinsic to humans. We developed a TaqMan chemistry assay, hCYTB484, targeting the cytochrome b gene of the human mitochondrial genome on a droplet digital PCR (ddPCR) platform and compared the performance of hCYTB484 with the HF183/BacR287 assay, a widely used assay targeting human-associated Bacteroides. For both assays, we defined the analytical limit of detection and analytical lower limit of quantification using frequency of detection and imprecision goals, respectively. We then established these analytical limits using empirical ddPCR data, presenting a novel approach to determining the analytical lower limit of quantification. We evaluated assay sensitivity using individual human feces from US, Bangladesh, and Mozambique and evaluated assay specificity using cow, pig, chicken, and goat samples collected from the US. To compare assay performance across a range of thresholds, we utilized receiver operating characteristic curves. The hCYTB484 marker was detected and quantifiable in 100% of the human feces from the 3 geographical distant regions whereas the HF183/BacR287 marker was detectable and quantifiable in 51% and 31% (respectively) of human feces samples. The hCYTB484 marker also was more specific (97%), having fewer detections in pig, chicken, and goat samples than the HF183/BacR287 marker (80%). The higher performance of the hCYTB484 marker in individual feces from geographically distant regions is desirable in the detection of fecal pollution from sources to which fewer individuals contribute, such as the non-sewered forms of sanitation (e.g. pit latrines and septic tanks) that serve most of Earth's population and carry the highest risk of exposure to fecal-oral pathogens.
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Affiliation(s)
- Kevin Zhu
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brittany Suttner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Amy Pickering
- Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | | | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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32
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Li J, Li L, Zhang L, Zhang X, Li X, Zhai S, Gao H, Li Y, Wu G, Wu Y. Development of a certified genomic DNA reference material for detection and quantification of genetically modified rice KMD. Anal Bioanal Chem 2020; 412:7007-7016. [PMID: 32740822 DOI: 10.1007/s00216-020-02834-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/09/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Qualitative and quantitative detection of genetically modified products is inseparable from the application of reference materials (RMs). In this study, a batch of genomic DNA (gDNA) certified reference materials (CRMs) was developed using genetically modified rice Kemingdao (KMD) homozygotes as the raw material. The gDNA CRMs in this batch showed good homogeneity; the minimum sample intake was determined to be 2 μL. The stability study showed that transportation by cold chain is preferable, no significant degradation trend was observed during a 12-month period when storing the gDNA CRMs at 4 °C and - 20 °C, and the number of freeze-thaw cycles cannot exceed 10. The property values of the copy number ratio of transgene and endogenous gene and the copy number concentration for gDNA CRMs were determined by a collaborative characterization of eight laboratories using the duplex KMD/PLD droplet digital PCR (ddPCR) assays. The uncertainty components of characterization, potential between-unit heterogeneity, and potential degradation during long-term storage were combined to estimate the expanded uncertainty of the certified value with a coverage factor k of 2.0. The certified value of copy number ratio for KMD gDNA CRM is 0.99 ± 0.05, and that of copy number concentration is (1.76 ± 0.10) × 105 copies/μL. Compared to the gDNA CRMs in availability, this batch of KMD gDNA CRMs is assigned accurate property values and can be directly used for qualitative and quantitative detection of GMOs as well as evaluation of the parameters of analytical methods with no need of further DNA concentration measurement. Graphical abstract.
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Affiliation(s)
- Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Zhang
- School of Life Science, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Xiujie Zhang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs P. R. China, Beijing, 100025, China.
| | - Xiaying Li
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs P. R. China, Beijing, 100025, China
| | - Shanshan Zhai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Hongfei Gao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Yunjing Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Gang Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
| | - Yuhua Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
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Villamil C, Calderon MN, Arias MM, Leguizamon JE. Validation of Droplet Digital Polymerase Chain Reaction for Salmonella spp. Quantification. Front Microbiol 2020; 11:1512. [PMID: 32733415 PMCID: PMC7358645 DOI: 10.3389/fmicb.2020.01512] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023] Open
Abstract
Salmonellosis is a foodborne disease caused by Salmonella spp. Although cell culture is the gold standard for its identification, validated molecular methods are becoming an alternative, because of their rapidity, selectivity, and specificity. A simplex and duplex droplet digital polymerase chain reaction (ddPCR)-based method for the identification and quantification of Salmonella using ttr, invA, hilA, spaQ, and siiA gene sequences was validated. The method has high specificity, working interval between 8 and 8,000 cp/μL in ddPCR reaction, a limit of detection of 0.5 copies/μL, and precision ranging between 5 and 10% measured as a repeatability standard deviation. The relative standard measurement uncertainty was between 2 and 12%. This tool will improve food safety in national consumption products and will increase the competitiveness in agricultural product trade.
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Affiliation(s)
- Carolina Villamil
- Departamento de Química, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Maria Mercedes Arias
- Grupo de Metrología en Bioanálisis, Instituto Nacional de Metrología, Bogota, Colombia
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Cao WW, He DS, Chen ZJ, Zuo YZ, Chen X, Chang YL, Zhang ZG, Ye L, Shi L. Development of a droplet digital PCR for detection and quantification of porcine epidemic diarrhea virus. J Vet Diagn Invest 2020; 32:572-576. [PMID: 32552416 DOI: 10.1177/1040638720924753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Porcine epidemic diarrhea, a disease caused by porcine epidemic diarrhea virus (PEDV), results in large economic losses to the global swine industry. To manage this disease effectively, it is essential to detect PEDV early and accurately. We developed a sensitive and accurate droplet digital PCR (ddPCR) assay to detect PEDV. The optimal primer-to-probe concentration and melting temperature were identified as 300:200 nM and 59.2°C, respectively. The specificity of the ddPCR assay was confirmed by negative test results for common swine pathogens. The detection limit for the ddPCR was 0.26 copies/μL, which is a 5.7-fold increase in sensitivity compared to that of real-time PCR (rtPCR). Both ddPCR and rtPCR assays exhibited good linearity, although ddPCR provided higher sensitivity for clinical detection compared to that of rtPCR. Our ddPCR methodology provides a promising tool for evaluating the PEDV viral load when used for clinical testing, particularly for detecting samples with low-copy viral loads.
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Affiliation(s)
- Wei W Cao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Dong S He
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Zhen J Chen
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Yu Z Zuo
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Xun Chen
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Yan L Chang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Zhi G Zhang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China (Cao, Z.J. Chen, X. Chen, Chang, Shi, Ye); College of Veterinary Medicine, South China Agricultural University, Guangzhou, China (He); College of Animal Science and Technology, Agricultural University of Hebei, Baoding, China (Zuo); State Key Laboratory of Food Safety Technology for Meat Products and Synergetic Innovation Center of Food Safety and Nutrition, Xiamen Yinxiang Group, Xiamen, China (Zhang, Shi)
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Sesen M, Whyte G. Image-Based Single Cell Sorting Automation in Droplet Microfluidics. Sci Rep 2020; 10:8736. [PMID: 32457421 PMCID: PMC7250914 DOI: 10.1038/s41598-020-65483-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
The recent boom in single-cell omics has brought researchers one step closer to understanding the biological mechanisms associated with cell heterogeneity. Rare cells that have historically been obscured by bulk measurement techniques are being studied by single cell analysis and providing valuable insight into cell function. To support this progress, novel upstream capabilities are required for single cell preparation for analysis. Presented here is a droplet microfluidic, image-based single-cell sorting technique that is flexible and programmable. The automated system performs real-time dual-camera imaging (brightfield & fluorescent), processing, decision making and sorting verification. To demonstrate capabilities, the system was used to overcome the Poisson loading problem by sorting for droplets containing a single red blood cell with 85% purity. Furthermore, fluorescent imaging and machine learning was used to load single K562 cells amongst clusters based on their instantaneous size and circularity. The presented system aspires to replace manual cell handling techniques by translating expert knowledge into cell sorting automation via machine learning algorithms. This powerful technique finds application in the enrichment of single cells based on their micrographs for further downstream processing and analysis.
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Affiliation(s)
- Muhsincan Sesen
- Heriot-Watt University, Institute of Biological Chemistry, Biophysics and Bioengineering, Edinburgh, EH14 4AS, United Kingdom
- Imperial College London, Department of Bioengineering, London, SW7 2AZ, United Kingdom
| | - Graeme Whyte
- Heriot-Watt University, Institute of Biological Chemistry, Biophysics and Bioengineering, Edinburgh, EH14 4AS, United Kingdom.
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36
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Chang YJ, Yang HW, Yao LH, Yang WT. Droplet-Based Immunosensor for Simultaneous Immunoassays of Multiplex Histidine-Tagged Proteins. SLAS Technol 2020; 25:132-139. [DOI: 10.1177/2472630319879647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Oliveira B, Veigas B, Fernandes AR, Águas H, Martins R, Fortunato E, Baptista PV. Fast Prototyping Microfluidics: Integrating Droplet Digital Lamp for Absolute Quantification of Cancer Biomarkers. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1624. [PMID: 32183359 PMCID: PMC7146133 DOI: 10.3390/s20061624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022]
Abstract
Microfluidic (MF) advancements have been leveraged toward the development of state-of-the-art platforms for molecular diagnostics, where isothermal amplification schemes allow for further simplification of DNA detection and quantification protocols. The MF integration with loop-mediated isothermal amplification (LAMP) is today the focus of a new generation of chip-based devices for molecular detection, aiming at fast and automated nucleic acid analysis. Here, we combined MF with droplet digital LAMP (ddLAMP) on an all-in-one device that allows for droplet generation, target amplification, and absolute quantification. This multilayer 3D chip was developed in less than 30 minutes by using a low-cost and extremely adaptable production process that exploits direct laser writing technology in "Shrinky-dinks" polystyrene sheets. ddLAMP and target quantification were performed directly on-chip, showing a high correlation between target concentration and positive droplet score. We validated this integrated chip via the amplification of targets ranging from five to 500,000 copies/reaction. Furthermore, on-chip amplification was performed in a 10 µL volume, attaining a limit of detection of five copies/µL under 60 min. This technology was applied to quantify a cancer biomarker, c-MYC, but it can be further extended to any other disease biomarker.
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Affiliation(s)
- Beatriz Oliveira
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Bruno Veigas
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Hugo Águas
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Rodrigo Martins
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Elvira Fortunato
- i3N|CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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One-Step Reverse-Transcription Digital PCR for Reliable Quantification of Different Pepino Mosaic Virus Genotypes. PLANTS 2020; 9:plants9030326. [PMID: 32143472 PMCID: PMC7154864 DOI: 10.3390/plants9030326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 01/05/2023]
Abstract
In recent years, pepino mosaic virus (PepMV) has rapidly evolved from an emerging virus to an endemic pathogen, as it causes significant loses to tomato crops worldwide. At present, the main control strategy for prevention of PepMV disease in tomato production remains based on strict hygiene measures. To prevent damage caused by PepMV, cross-protection is used in some countries. Reliable characterisation, detection and quantification of the pathogen are vital for disease control. At present, reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) is generally used for this purpose. However, quantitative use of RT-qPCR is linked to standardised reference materials, which are not available for PepMV. In addition, many factors can influence RT-qPCR efficiencies and lead to lower accuracy of the quantification. In this study, well-characterised PepMV-genotype-specific RT-qPCR assays were transferred to two digital PCR (dPCR) platforms. dPCR-based assays allow absolute quantification without the need for standard curves, and due to the binary nature of the reaction, dPCR also overcomes many of the other drawbacks of RT-qPCR. We have shown that these newly developed and validated PepMV-genotype-specific dPCR assays are suitable candidates for higher-order methods for quantification of PepMV RNA, as they show lower measurement variability, with sensitivity and specificity comparable to RT-qPCR.
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Byrnes SA, Huynh T, Chang TC, Anderson CE, McDermott JJ, Oncina CI, Weigl BH, Nichols KP. Wash-Free, Digital Immunoassay in Polydisperse Droplets. Anal Chem 2020; 92:3535-3543. [DOI: 10.1021/acs.analchem.9b02526] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samantha A. Byrnes
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Toan Huynh
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Tim C. Chang
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Caitlin E. Anderson
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - James J. McDermott
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Ciela I. Oncina
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Bernhard H. Weigl
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
| | - Kevin P. Nichols
- Center for In Vitro Diagnostics, Intellectual Ventures Laboratory, Bellevue, Washington 98007, United States
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40
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Lowenthal MS, Quittman E, Phinney KW. Absolute Quantification of RNA or DNA Using Acid Hydrolysis and Mass Spectrometry. Anal Chem 2019; 91:14569-14576. [PMID: 31638773 DOI: 10.1021/acs.analchem.9b03625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate, traceable quantification of ribonucleotide or deoxyribonucleotide oligomers is achievable using acid hydrolysis and isotope dilution mass spectrometry (ID-MS). In this work, formic acid hydrolysis is demonstrated to generate stoichiometric release of nucleobases from intact oligonucleotides, which then can be measured by ID-MS, facilitating true and precise absolute quantification of RNA, short linearized DNA, or genomic DNA. Surrogate nucleobases are quantified with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow, using multiple reaction monitoring (MRM). Nucleobases were chromatographically resolved using a novel cation-exchange separation, incorporating a pH gradient. Trueness of this quantitative assay is estimated from agreement among the surrogate nucleobases and by comparison to concentrations provided for commercial materials or Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST). Comparable concentration estimates using NanoDrop spectrophotometry or established from droplet-digital polymerase chain reaction (ddPCR) techniques agree well with the results. Acid hydrolysis-ID-LC-MS/MS provides excellent quantitative selectivity and accuracy while enabling traceability to mass unit. Additionally, this approach can be uniquely useful for quantifying modified nucleobases or mixtures.
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Affiliation(s)
- Mark S Lowenthal
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Eva Quittman
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
| | - Karen W Phinney
- Biomolecular Measurement Division , National Institute of Standards and Technology , 100 Bureau Drive, Stop 8314 , Gaithersburg , Maryland 20899 , United States
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41
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Eun HS, Chun K, Song IS, Oh CH, Seong IO, Yeo MK, Kim KH. High nuclear NADPH oxidase 4 expression levels are correlated with cancer development and poor prognosis in hepatocellular carcinoma. Pathology 2019; 51:579-585. [PMID: 31443922 DOI: 10.1016/j.pathol.2019.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 11/30/2022]
Abstract
NADPH oxidase (NOX) is a key source of reactive oxygen species (ROS). This study aimed to verify NOX2 and NOX4 expression levels in hepatocellular carcinoma (HCC). A total of 134 matched pairs of HCC cells and non-tumour hepatocytes from 134 patients were examined by immunohistochemical staining, and the association of NOX2 and NOX4 expression with clinicopathological parameters was analysed. Western blotting in four HCC cell lines and reverse transcription digital droplet polymerase chain reaction (RT-ddPCR) in 20 pairs of HCC and non-tumour tissue samples were also performed to detect NOX4. Cytoplasmic NOX2 and nuclear NOX4 expression levels were shown by immunohistochemistry to be higher in HCC cells than in non-tumour hepatocytes (p<0.001 each). The western blotting results for NOX4 in four HCC cell lines were consistent with the immunohistochemical results. Increased cytoplasmic expression of NOX2 and NOX4 in HCC cells was significantly correlated with liver cirrhosis (p<0.001 and p<0.031, respectively). However, decreased cytoplasmic expression of NOX2 and NOX4 was significantly correlated with advanced pathological TNM stage (p<0.029 and p<0.007, respectively). Multivariate analysis with clinicopathological parameters showed that high nuclear and low cytoplasmic NOX4 expression levels are correlated with short overall survival (p=0 .021). Our findings imply that cytoplasmic NOX2 and nuclear NOX4 expression is upregulated during HCC development. In particular, NOX4 translocation into the nucleus may affect the development and progression of HCC. NOX2 and NOX4 could be diagnostic markers and have therapeutic implications in HCC.
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Affiliation(s)
- Hyuk Soo Eun
- Department of Internal Medicine, Chungnam National University Hospital, Jung-gu, Daejeon, Republic of Korea; Department of Internal Medicine, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea
| | - Kwangsik Chun
- Department of Surgery, Chungnam National University Hospital, Jung-gu, Daejeon, Republic of Korea; Department of Surgery, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea
| | - In-Sang Song
- Department of Surgery, Chungnam National University Hospital, Jung-gu, Daejeon, Republic of Korea; Department of Surgery, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea
| | - Cheong-Hae Oh
- Department of Internal Medicine, Chungnam National University Hospital, Jung-gu, Daejeon, Republic of Korea; Department of Internal Medicine, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea
| | - In-Ock Seong
- Department of Pathology, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea
| | - Kyung-Hee Kim
- Department of Pathology, Chungnam National University School of Medicine, Jung-gu, Daejeon, Republic of Korea.
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42
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Cao W, Li Y, Chen X, Chang Y, Li L, Shi L, Bai W, Ye L. Species identification and quantification of silver pomfret using the droplet digital PCR assay. Food Chem 2019; 302:125331. [PMID: 31404867 DOI: 10.1016/j.foodchem.2019.125331] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 11/30/2022]
Abstract
Adulteration of the high-value silver pomfret (Pampus argenteus) is a serious problem worldwide, necessitating accurate identification and quantification of the species. In this study, optimisation of the digital droplet PCR (ddPCR) assay for the identification and quantification of the silver pomfret was carried out. The primer and probe concentrations, melting temperature, and PCR cycle number were optimised by combining single-factor experiments with an orthogonal experimental design. The absolute limits of detection and quantification of the ddPCR were 2copies/μl and 21 copies/μl, respectively. Its sensitivity was 0.1% for meat mixtures and 0.5% for DNA mixtures. The ddPCR was 156 times more sensitive than the real-time PCR, although both methods had similar specificities. However, the overall time needed to complete the ddPCR method was twice that of the real-time PCR. Notwithstanding, the ddPCR methodology established in this study can be a valuable tool for addressing species adulteration issues.
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Affiliation(s)
- Weiwei Cao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yiming Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510641, Guangdong, China
| | - Xun Chen
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yanlei Chang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China.
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43
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Dobnik D, Kogovšek P, Jakomin T, Košir N, Tušek Žnidarič M, Leskovec M, Kaminsky SM, Mostrom J, Lee H, Ravnikar M. Accurate Quantification and Characterization of Adeno-Associated Viral Vectors. Front Microbiol 2019; 10:1570. [PMID: 31379763 PMCID: PMC6650692 DOI: 10.3389/fmicb.2019.01570] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
One of the main challenges in the gene therapy viral vector development is to establish an optimized process for its large scale production. This requires optimization for upstream and downstream processes as well as methods that enable the step-by step analytical characterization of the virus, the results of which inform the iterative refinement of production for yield, purity and potency. The biggest problem here is a plethora of viral vector formulations, many of which interfere with analytical techniques. We took adeno-associated virus (AAV) as an example and showed benefits of combined use of molecular methods and transmission electron microscopy (TEM) for viral vectors' characterization and quantification. Results of the analyses showed that droplet digital PCR (ddPCR) performs better than quantitative real-time PCR (qPCR), in terms of robustness and assay variance, and this was especially relevant for partially purified (in-process) samples. Moreover, we demonstrate the importance of sample preparation prior to PCR analysis. We evaluated viral structure, presence of aggregates and impurities with TEM analysis and found that these impacted the differences in viral titers observed by qPCR and ddPCR and could be altered by sample preparation. These results serve as a guide for the establishment of the analytical methods required to provide measures of identity and purity for AAV viral vectors.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tjaša Jakomin
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nejc Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Stephen M Kaminsky
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Janet Mostrom
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Hyunmi Lee
- Belfer Gene Therapy Core Facility, Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, United States
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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44
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Emslie KR, H McLaughlin JL, Griffiths K, Forbes-Smith M, Pinheiro LB, Burke DG. Droplet Volume Variability and Impact on Digital PCR Copy Number Concentration Measurements. Anal Chem 2019; 91:4124-4131. [PMID: 30775910 DOI: 10.1021/acs.analchem.8b05828] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Digital polymerase chain reaction (dPCR) is increasingly being adopted by reference material producers and metrology institutes for value assignment, and for homogeneity and stability studies of nucleic acid reference materials. A reference method procedure should fulfill several requirements, and the uncertainty and biases should be completely understood. A bias in target concentration when inaccurate droplet volume is used in the droplet dPCR measurement equation has previously been documented. In this study, we characterize both intrawell and interwell droplet volume variability using optical microscopy and determine the impact of these two sources of variability on target concentration estimates. A small optical distortion across the image was measured which, without correction, biased droplet volume measurements. Longitudinal monitoring of interwell droplet volume over 39 weeks using several lots of Mastermix demonstrated a mean droplet volume of 0.786 nL and intermediate precision of 1.7%. The frequency distribution of intrawell droplet volumes varied. Some wells displayed a skewed distribution which resulted in a small bias in estimated target concentration for a simulated dPCR with target concentrations of between 62 and 8000 copies μL-1. The size and direction of this bias was influenced by the distribution pattern of the droplet volumes within the well. The proportion of Mastermix in dPCR mix affected droplet volume. A pipetting error of 10% during mixing of the premix and Mastermix resulted in a 2.6% change in droplet volume and, consequently, a bias in concentration measurements highlighting the advantages of gravimetric preparation of dPCR mixes for high accuracy measurements.
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Affiliation(s)
- Kerry R Emslie
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | | | - Kate Griffiths
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | | | - Leonardo B Pinheiro
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
| | - Daniel G Burke
- National Measurement Institute , Lindfield , New South Wales 2070 , Australia
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45
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Wu Y, Li J, Li X, Zhai S, Gao H, Li Y, Zhang X, Wu G. Development and strategy of reference materials for the DNA-based detection of genetically modified organisms. Anal Bioanal Chem 2019; 411:1729-1744. [DOI: 10.1007/s00216-019-01576-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/21/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022]
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46
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Huynh T, Byrnes SA, Chang TC, Weigl BH, Nichols KP. General methods for quantitative interpretation of results of digital variable-volume assays. Analyst 2019; 144:7209-7219. [DOI: 10.1039/c9an01479a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In digital assays, devices typically require precisely controlled volumes since variation can cause biases in concentration estimates. Here, we develop methods to correct bias when compartment volumes are variable.
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Affiliation(s)
- Toan Huynh
- Intellectual Ventures Laboratory
- Bellevue
- USA
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47
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Abstract
Digital PCR-based methods, such as droplet digital PCR, are one of the best tools for determination of absolute nucleic-acid copy numbers. These techniques avoid the need for reference materials with known target concentrations. Compared to real-time PCR, they provide higher accuracy of quantification at low target concentrations, and have higher resilience to inhibitors. In this Chapter, we describe the droplet digital PCR workflow for the detection and quantification of flavescence dorée phytoplasma.
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Affiliation(s)
- Nataša Mehle
- National Institute of Biology, Ljubljana, Slovenia.
| | - Tanja Dreo
- National Institute of Biology, Ljubljana, Slovenia
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48
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Malic L, Daoud J, Geissler M, Boutin A, Lukic L, Janta M, Elmanzalawy A, Veres T. Epigenetic subtyping of white blood cells using a thermoplastic elastomer-based microfluidic emulsification device for multiplexed, methylation-specific digital droplet PCR. Analyst 2019; 144:6541-6553. [DOI: 10.1039/c9an01316d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Digital droplet PCR for epigenetic leukocyte subtyping from clinically relevant samples is implemented using a thermoplastic elastomer microfluidic droplet generator as a first step towards an economical, customizable and easily deployable system.
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Affiliation(s)
- Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Alex Boutin
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Ljuboje Lukic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Mojra Janta
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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49
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Quantification of the allergen soy (Glycine max) in food using digital droplet PCR (ddPCR). Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3182-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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50
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Yang H, Chen Z, Cao X, Li Z, Stavrakis S, Choo J, deMello AJ, Howes PD, He N. A sample-in-digital-answer-out system for rapid detection and quantitation of infectious pathogens in bodily fluids. Anal Bioanal Chem 2018; 410:7019-7030. [PMID: 30155705 DOI: 10.1007/s00216-018-1335-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/02/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022]
Abstract
A variety of automated sample-in-answer-out systems for in vitro molecular diagnostics have been presented and even commercialized. Although efficient in operation, they are incapable of quantifying targets, since quantitation based on analog analytical methods (via standard curve analysis) is complex, expensive, and challenging. To address this issue, herein, we describe an integrated sample-in-digital-answer-out (SIDAO) diagnostic system incorporating DNA extraction and digital recombinase polymerase amplification, which enables rapid and quantitative nucleic acid analysis from bodily fluids within a disposable cartridge. Inside the cartridge, reagents are pre-stored in sterilized tubes, with an automated pipetting module allowing facile liquid transfer. For digital analysis, we fabricate a simple, single-layer polydimethylsiloxane microfluidic device and develop a novel and simple sample compartmentalization strategy. Sample solution is partitioned into an array of 40,044 fL-volume microwells by sealing the microfluidic device through the application of mechanical pressure. The entire analysis is performed in a portable, fully automated instrument. We evaluate the quantitative capabilities of the system by analyzing Mycobacterium tuberculosis genomic DNA from both spiked saliva and serum samples, and demonstrate excellent analytical accuracy and specificity. This SIDAO system provides a promising diagnostic platform for quantitative nucleic acid testing at the point-of-care. Graphical abstract ᅟ.
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Affiliation(s)
- Haowen Yang
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, 4058, Basel, Switzerland
| | - Zhu Chen
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, Hunan, China.,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xiaobao Cao
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Zhiyang Li
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Sa-1-dong 1271, Ansan, 15588, South Korea
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland.
| | - Philip D Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Nongyue He
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007, Hunan, China. .,State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China.
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