1
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Anyaduba TD, Otoo JA, Schlappi TS. Picoliter Droplet Generation and Dense Bead-in-Droplet Encapsulation via Microfluidic Devices Fabricated via 3D Printed Molds. MICROMACHINES 2022; 13:1946. [PMID: 36363966 PMCID: PMC9695966 DOI: 10.3390/mi13111946] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Picoliter-scale droplets have many applications in chemistry and biology, such as biomolecule synthesis, drug discovery, nucleic acid quantification, and single cell analysis. However, due to the complicated processes used to fabricate microfluidic channels, most picoliter (pL) droplet generation methods are limited to research in laboratories with cleanroom facilities and complex instrumentation. The purpose of this work is to investigate a method that uses 3D printing to fabricate microfluidic devices that can generate droplets with sizes <100 pL and encapsulate single dense beads mechanistically. Our device generated monodisperse droplets as small as ~48 pL and we demonstrated the usefulness of this droplet generation technique in biomolecule analysis by detecting Lactobacillus acidophillus 16s rRNA via digital loop-mediated isothermal amplification (dLAMP). We also designed a mixer that can be integrated into a syringe to overcome dense bead sedimentation and found that the bead-in-droplet (BiD) emulsions created from our device had <2% of the droplets populated with more than 1 bead. This study will enable researchers to create devices that generate pL-scale droplets and encapsulate dense beads with inexpensive and simple instrumentation (3D printer and syringe pump). The rapid prototyping and integration ability of this module with other components or processes can accelerate the development of point-of-care microfluidic devices that use droplet-bead emulsions to analyze biological or chemical samples with high throughput and precision.
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Affiliation(s)
- Tochukwu D. Anyaduba
- Keck Graduate Institute, Riggs School of Applied Life Sciences, Claremont, CA 91711, USA
- Abbott Rapid Diagnostics, 4545 Towne Center Ct, La Jolla, San Diego, CA 92121, USA
| | - Jonas A. Otoo
- Keck Graduate Institute, Riggs School of Applied Life Sciences, Claremont, CA 91711, USA
| | - Travis S. Schlappi
- Keck Graduate Institute, Riggs School of Applied Life Sciences, Claremont, CA 91711, USA
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2
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Miglietta L, Xu K, Chhaya P, Kreitmann L, Hill-Cawthorne K, Bolt F, Holmes A, Georgiou P, Rodriguez-Manzano J. Adaptive Filtering Framework to Remove Nonspecific and Low-Efficiency Reactions in Multiplex Digital PCR Based on Sigmoidal Trends. Anal Chem 2022; 94:14159-14168. [PMID: 36190816 PMCID: PMC9583074 DOI: 10.1021/acs.analchem.2c01883] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022]
Abstract
Real-time digital polymerase chain reaction (qdPCR) coupled with machine learning (ML) methods has shown the potential to unlock scientific breakthroughs, particularly in the field of molecular diagnostics for infectious diseases. One promising application of this emerging field explores single fluorescent channel PCR multiplex by extracting target-specific kinetic and thermodynamic information contained in amplification curves, also known as data-driven multiplexing. However, accurate target classification is compromised by the presence of undesired amplification events and not ideal reaction conditions. Therefore, here, we proposed a novel framework to identify and filter out nonspecific and low-efficient reactions from qdPCR data using outlier detection algorithms purely based on sigmoidal trends of amplification curves. As a proof-of-concept, this framework is implemented to improve the classification performance of the recently reported data-driven multiplexing method called amplification curve analysis (ACA), using available published data where the ACA is demonstrated to screen carbapenemase-producing organisms in clinical isolates. Furthermore, we developed a novel strategy, named adaptive mapping filter (AMF), to adjust the percentage of outliers removed according to the number of positive counts in qdPCR. From an overall total of 152,000 amplification events, 116,222 positive amplification reactions were evaluated before and after filtering by comparing against melting peak distribution, proving that abnormal amplification curves (outliers) are linked to shifted melting distribution or decreased PCR efficiency. The ACA was applied to assess classification performance before and after AMF, showing an improved sensitivity of 1.2% when using inliers compared to a decrement of 19.6% when using outliers (p-value < 0.0001), removing 53.5% of all wrong melting curves based only on the amplification shape. This work explores the correlation between the kinetics of amplification curves and the thermodynamics of melting curves, and it demonstrates that filtering out nonspecific or low-efficient reactions can significantly improve the classification accuracy for cutting-edge multiplexing methodologies.
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Affiliation(s)
- Luca Miglietta
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K.
| | - Ke Xu
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K.
| | - Priya Chhaya
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K.
| | - Louis Kreitmann
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
| | - Kerri Hill-Cawthorne
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
| | - Frances Bolt
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
| | - Alison Holmes
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
| | - Pantelis Georgiou
- Department
of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, LondonSW7 2AZ, U.K.
| | - Jesus Rodriguez-Manzano
- Department
of Infectious Disease, Faculty of Medicine, Imperial College London, LondonW12 0NN, U.K.
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3
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Xue Y, Luo X, Pang X, Zhou J, Wang J. Optimizing the performance of digital loop-mediated isothermal amplification. Anal Biochem 2021; 631:114371. [PMID: 34509442 DOI: 10.1016/j.ab.2021.114371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Digital loop-mediated isothermal amplification (dLAMP) is attractive for the detection of nucleic acid due to its superior characteristics including isothermal amplification, absolute quantification, and single-molecule sensitivity. However, dLAMP suffers from the inaccurate quantification caused by low digital efficiency, which means only part of loaded template molecules could be amplified. We here developed a prehybridization-induced enhancement (PIE) strategy which could improve digital efficiency about 2-40 times without any new primer or additional operation. This work provides new insight into understanding the reaction dynamic of dLAMP. The PIE strategy could be applied to the other digital amplification methods.
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Affiliation(s)
- Yingying Xue
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xinyi Luo
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xueyuan Pang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Jianhua Zhou
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China
| | - Jiasi Wang
- School of Biomedical Engineering, Sun Yat-sen University, Shenzhen, 518107, China.
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4
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Moniri A, Miglietta L, Malpartida-Cardenas K, Pennisi I, Cacho-Soblechero M, Moser N, Holmes A, Georgiou P, Rodriguez-Manzano J. Amplification Curve Analysis: Data-Driven Multiplexing Using Real-Time Digital PCR. Anal Chem 2020; 92:13134-13143. [PMID: 32946688 DOI: 10.1021/acs.analchem.0c02253] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Information about the kinetics of PCR reactions is encoded in the amplification curve. However, in digital PCR (dPCR), this information is typically neglected by collapsing each amplification curve into a binary output (positive/negative). Here, we demonstrate that the large volume of raw data obtained from real-time dPCR instruments can be exploited to perform data-driven multiplexing in a single fluorescent channel using machine learning methods, by virtue of the information in the amplification curve. This new approach, referred to as amplification curve analysis (ACA), was shown using an intercalating dye (EvaGreen), reducing the cost and complexity of the assay and enabling the use of melting curve analysis for validation. As a case study, we multiplexed 3 carbapenem-resistant genes to show the impact of this approach on global challenges such as antimicrobial resistance. In the presence of single targets, we report a classification accuracy of 99.1% (N = 16188), which represents a 19.7% increase compared to multiplexing based on the final fluorescent intensity. Considering all combinations of amplification events (including coamplifications), the accuracy was shown to be 92.9% (N = 10383). To support the analysis, we derived a formula to estimate the occurrence of coamplification in dPCR based on multivariate Poisson statistics and suggest reducing the digital occupancy in the case of multiple targets in the same digital panel. The ACA approach takes a step toward maximizing the capabilities of existing real-time dPCR instruments and chemistries, by extracting more information from data to enable data-driven multiplexing with high accuracy. Furthermore, we expect that combining this method with existing probe-based assays will increase multiplexing capabilities significantly. We envision that once emerging point-of-care technologies can reliably capture real-time data from isothermal chemistries, the ACA method will facilitate the implementation of dPCR outside of the lab.
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Affiliation(s)
- Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Luca Miglietta
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Ivana Pennisi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London W2 1NY, U.K
| | - Miguel Cacho-Soblechero
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Alison Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, U.K.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London W12 0NN, U.K
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5
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Rodriguez-Manzano J, Moser N, Malpartida-Cardenas K, Moniri A, Fisarova L, Pennisi I, Boonyasiri A, Jauneikaite E, Abdolrasouli A, Otter JA, Bolt F, Davies F, Didelot X, Holmes A, Georgiou P. Rapid Detection of Mobilized Colistin Resistance using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System. Sci Rep 2020; 10:8448. [PMID: 32439986 PMCID: PMC7242339 DOI: 10.1038/s41598-020-64612-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/13/2020] [Indexed: 11/30/2022] Open
Abstract
The increasing prevalence of antimicrobial resistance is a serious threat to global public health. One of the most concerning trends is the rapid spread of Carbapenemase-Producing Organisms (CPO), where colistin has become the last-resort antibiotic treatment. The emergence of colistin resistance, including the spread of mobilized colistin resistance (mcr) genes, raises the possibility of untreatable bacterial infections and motivates the development of improved diagnostics for the detection of colistin-resistant organisms. This work demonstrates a rapid response for detecting the most recently reported mcr gene, mcr−9, using a portable and affordable lab-on-a-chip (LoC) platform, offering a promising alternative to conventional laboratory-based instruments such as real-time PCR (qPCR). The platform combines semiconductor technology, for non-optical real-time DNA sensing, with a smartphone application for data acquisition, visualization and cloud connectivity. This technology is enabled by using loop-mediated isothermal amplification (LAMP) as the chemistry for targeted DNA detection, by virtue of its high sensitivity, specificity, yield, and manageable temperature requirements. Here, we have developed the first LAMP assay for mcr−9 - showing high sensitivity (down to 100 genomic copies/reaction) and high specificity (no cross-reactivity with other mcr variants). This assay is demonstrated through supporting a hospital investigation where we analyzed nucleic acids extracted from 128 carbapenemase-producing bacteria isolated from clinical and screening samples and found that 41 carried mcr−9 (validated using whole genome sequencing). Average positive detection times were 6.58 ± 0.42 min when performing the experiments on a conventional qPCR instrument (n = 41). For validating the translation of the LAMP assay onto a LoC platform, a subset of the samples were tested (n = 20), showing average detection times of 6.83 ± 0.92 min for positive isolates (n = 14). All experiments detected mcr−9 in under 10 min, and both platforms showed no statistically significant difference (p-value > 0.05). When sample preparation and throughput capabilities are integrated within this LoC platform, the adoption of this technology for the rapid detection and surveillance of antimicrobial resistance genes will decrease the turnaround time for DNA detection and resistotyping, improving diagnostic capabilities, patient outcomes, and the management of infectious diseases.
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Affiliation(s)
- Jesus Rodriguez-Manzano
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom. .,Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom.
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Lenka Fisarova
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Ivana Pennisi
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Adhiratha Boonyasiri
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Alireza Abdolrasouli
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jonathan A Otter
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,Imperial College Healthcare NHS Trust, St Mary's Hospital, London, United Kingdom
| | - Frances Bolt
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Frances Davies
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Alison Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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6
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Bao Y, Jiang Y, Xiong E, Tian T, Zhang Z, Lv J, Li Y, Zhou X. CUT-LAMP: Contamination-Free Loop-Mediated Isothermal Amplification Based on the CRISPR/Cas9 Cleavage. ACS Sens 2020; 5:1082-1091. [PMID: 32242409 DOI: 10.1021/acssensors.0c00034] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive and widely used gene amplification technique. However, high amplification efficiency and amplification products containing multiple inverted repeats make the LAMP reaction extremely vulnerable to false-positive amplification caused by contamination. Herein, a contamination-free LAMP (CUT-LAMP) assisted by the CRISPR/Cas9 cleavage with superior reliability and durability has been reported. The core of CUT-LAMP is the engineering of the forward or backward inner primer in the target-independent region, which makes the LAMP products contain a protospacer adjacent motif (PAM) site for the CRISPR/Cas9 recognition. For the CUT-LAMP reaction, cross-contamination can be efficiently cleaved by the corresponding Cas9/sgRNA, but the target gene can get rid of digestion due to the lack of a PAM site near the recognition region. CUT-LAMP shows impressive contamination resistance but does not significantly increase procedure complexity; thus, it represents a simple and versatile toolkit facilitating the adoption by open- and closed-tube detection format.
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Affiliation(s)
- Yijuan Bao
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Yongzhong Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, P. R. China
| | - Erhu Xiong
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Tian Tian
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
| | - Zhenzhen Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Jing Lv
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, P. R. China
| | - Yang Li
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, P. R. China
| | - Xiaoming Zhou
- College of Biophotonics & School of Life Sciences, South China Normal University, Guangzhou 510631, P. R. China
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7
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Yuan H, Chao Y, Shum HC. Droplet and Microchamber-Based Digital Loop-Mediated Isothermal Amplification (dLAMP). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904469. [PMID: 31899592 DOI: 10.1002/smll.201904469] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/22/2019] [Indexed: 05/15/2023]
Abstract
Digital loop-mediated isothermal amplification (dLAMP) refers to compartmentalizing nucleic acids and LAMP reagents into a large number of individual partitions, such as microchambers and droplets. This compartmentalization enables dLAMP to be an excellent platform to quantify the absolute number of the target nucleic acids. Owing to its low requirement for instrumentation complexity, high specificity, and strong tolerance to inhibitors in the nucleic acid samples, dLAMP has been recognized as a simple and accurate technique to quantify pathogenic nucleic acid. Herein, the general process of dLAMP techniques is summarized, the current dLAMP techniques are categorized, and a comprehensive discussion on different types of dLAMP techniques is presented. Also, the challenges of the current dLAMP are illustrated together with the possible strategies to address these challenges. In the end, the future directions of the dLAMP developments, including multitarget detection, multisample detection, and processing nucleic acid extraction are outlined. With recently significant advances in dLAMP, this technology has the potential to see more widespread use beyond the laboratory in the future.
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Affiliation(s)
- Hao Yuan
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, Hong Kong
| | - Youchuang Chao
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, Hong Kong
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8
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Malpartida-Cardenas K, Miscourides N, Rodriguez-Manzano J, Yu LS, Moser N, Baum J, Georgiou P. Quantitative and rapid Plasmodium falciparum malaria diagnosis and artemisinin-resistance detection using a CMOS Lab-on-Chip platform. Biosens Bioelectron 2019; 145:111678. [PMID: 31541787 PMCID: PMC7224984 DOI: 10.1016/j.bios.2019.111678] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 08/01/2019] [Accepted: 09/04/2019] [Indexed: 12/16/2022]
Abstract
Early and accurate diagnosis of malaria and drug-resistance is essential to effective disease management. Available rapid malaria diagnostic tests present limitations in analytical sensitivity, drug-resistance testing and/or quantification. Conversely, diagnostic methods based on nucleic acid amplification stepped forwards owing to their high sensitivity, specificity and robustness. Nevertheless, these methods commonly rely on optical measurements and complex instrumentation which limit their applicability in resource-poor, point-of-care settings. This paper reports the specific, quantitative and fully-electronic detection of Plasmodium falciparum, the predominant malaria-causing parasite worldwide, using a Lab-on-Chip platform developed in-house. Furthermore, we demonstrate on-chip detection of C580Y, the most prevalent single-nucleotide polymorphism associated to artemisinin-resistant malaria. Real-time non-optical DNA sensing is facilitated using Ion-Sensitive Field-Effect Transistors, fabricated in unmodified complementary metal-oxide-semiconductor (CMOS) technology, coupled with loop-mediated isothermal amplification. This work holds significant potential for the development of a fully portable and quantitative malaria diagnostic that can be used as a rapid point-of-care test.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, UK
| | - Nicholas Miscourides
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, UK
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, UK.
| | - Ling-Shan Yu
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, UK
| | - Nicolas Moser
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, UK
| | - Jake Baum
- Department of Life Sciences, Imperial College London, UK
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering, Imperial College London, UK
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9
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Moniri A, Rodriguez-Manzano J, Malpartida-Cardenas K, Yu LS, Didelot X, Holmes A, Georgiou P. Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves. Anal Chem 2019; 91:7426-7434. [PMID: 31056898 PMCID: PMC6551572 DOI: 10.1021/acs.analchem.9b01466] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Real-time PCR is a highly sensitive
and powerful technology for
the quantification of DNA and has become the method of choice in microbiology,
bioengineering, and molecular biology. Currently, the analysis of
real-time PCR data is hampered by only considering a single feature
of the amplification profile to generate a standard curve. The current
“gold standard” is the cycle-threshold (Ct) method which is known to provide poor quantification
under inconsistent reaction efficiencies. Multiple single-feature
methods have been developed to overcome the limitations of the Ct method; however, there is an unexplored area
of combining multiple features in order to benefit from their joint
information. Here, we propose a novel framework that combines existing
standard curve methods into a multidimensional standard curve. This
is achieved by considering multiple features together such that each
amplification curve is viewed as a point in a multidimensional space.
Contrary to only considering a single-feature, in the multidimensional
space, data points do not fall exactly on the standard curve, which
enables a similarity measure between amplification curves based on
distances between data points. We show that this framework expands
the capabilities of standard curves in order to optimize quantification
performance, provide a measure of how suitable an amplification curve
is for a standard, and thus automatically detect outliers and increase
the reliability of quantification. Our aim is to provide an affordable
solution to enhance existing diagnostic settings through maximizing
the amount of information extracted from conventional instruments.
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Affiliation(s)
- Ahmad Moniri
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London SW7 2AZ , U.K
| | - Jesus Rodriguez-Manzano
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London SW7 2AZ , U.K
| | - Kenny Malpartida-Cardenas
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London SW7 2AZ , U.K
| | - Ling-Shan Yu
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London SW7 2AZ , U.K
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics , University of Warwick , Coventry CV4 7AL , U.K
| | - Alison Holmes
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance , Imperial College London , Hammersmith Hospital Campus, London W12 0NN , U.K
| | - Pantelis Georgiou
- Centre for Bio-Inspired Technology, Department of Electrical and Electronic Engineering , Imperial College London , London SW7 2AZ , U.K
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10
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Rolando J, Jue E, Schoepp NG, Ismagilov RF. Real-Time, Digital LAMP with Commercial Microfluidic Chips Reveals the Interplay of Efficiency, Speed, and Background Amplification as a Function of Reaction Temperature and Time. Anal Chem 2019; 91:1034-1042. [PMID: 30565936 PMCID: PMC6322147 DOI: 10.1021/acs.analchem.8b04324] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022]
Abstract
Real-time, isothermal, digital nucleic acid amplification is emerging as an attractive approach for a multitude of applications including diagnostics, mechanistic studies, and assay optimization. Unfortunately, there is no commercially available and affordable real-time, digital instrument validated for isothermal amplification; thus, most researchers have not been able to apply digital, real-time approaches to isothermal amplification. Here, we generate an approach to real-time digital loop-mediated isothermal amplification (LAMP) using commercially available microfluidic chips and reagents and open-source components. We demonstrate this approach by testing variables that influence LAMP reaction speed and the probability of detection. By analyzing the interplay of amplification efficiency, background, and speed of amplification, this real-time digital method enabled us to test enzymatic performance over a range of temperatures, generating high-precision kinetic and end-point measurements. We were able to identify the unique optimal temperature for two polymerase enzymes while accounting for amplification efficiency, nonspecific background, and time to threshold. We validated this digital LAMP assay and pipeline by performing a phenotypic antibiotic susceptibility test on 17 archived clinical urine samples from patients diagnosed with urinary tract infections. We provide all the necessary workflows to perform digital LAMP using standard laboratory equipment and commercially available materials. This real-time digital approach will be useful to others in the future to understand the fundamentals of isothermal chemistries, including which components determine amplification fate, reaction speed, and enzymatic performance. Researchers can also adapt this pipeline, which uses only standard equipment and commercial components, to quickly study and optimize assays using precise, real-time digital quantification, accelerating development of critically needed diagnostics.
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Affiliation(s)
- Justin
C. Rolando
- Division
of Chemistry & Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 210-41, Pasadena, California, 91125, United States
| | - Erik Jue
- Division
of Biology & Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 210-41, Pasadena, California 91125 United States
| | - Nathan G. Schoepp
- Division
of Chemistry & Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 210-41, Pasadena, California, 91125, United States
| | - Rustem F. Ismagilov
- Division
of Chemistry & Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 210-41, Pasadena, California, 91125, United States
- Division
of Biology & Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Mail Code 210-41, Pasadena, California 91125 United States
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11
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Schoepp NG, Schlappi TS, Curtis MS, Butkovich SS, Miller S, Humphries RM, Ismagilov RF. Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples. Sci Transl Med 2018; 9:9/410/eaal3693. [PMID: 28978750 DOI: 10.1126/scitranslmed.aal3693] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/30/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022]
Abstract
Rapid antimicrobial susceptibility testing (AST) is urgently needed for informing treatment decisions and preventing the spread of antimicrobial resistance resulting from the misuse and overuse of antibiotics. To date, no phenotypic AST exists that can be performed within a single patient visit (30 min) directly from clinical samples. We show that AST results can be obtained by using digital nucleic acid quantification to measure the phenotypic response of Escherichia coli present within clinical urine samples exposed to an antibiotic for 15 min. We performed this rapid AST using our ultrafast (~7 min) digital real-time loop-mediated isothermal amplification (dLAMP) assay [area under the curve (AUC), 0.96] and compared the results to a commercial (~2 hours) digital polymerase chain reaction assay (AUC, 0.98). The rapid dLAMP assay can be used with SlipChip microfluidic devices to determine the phenotypic antibiotic susceptibility of E. coli directly from clinical urine samples in less than 30 min. With further development for additional pathogens, antibiotics, and sample types, rapid digital AST (dAST) could enable rapid clinical decision-making, improve management of infectious diseases, and facilitate antimicrobial stewardship.
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Affiliation(s)
- Nathan G Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Travis S Schlappi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Curtis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Slava S Butkovich
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Shelley Miller
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA 90095, USA
| | - Romney M Humphries
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA 90095, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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12
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Zhao Y, Chen F, Qin J, Wei J, Wu W, Zhao Y. Engineered Janus probes modulate nucleic acid amplification to expand the dynamic range for direct detection of viral genomes in one microliter crude serum samples. Chem Sci 2018; 9:392-397. [PMID: 29629109 PMCID: PMC5868314 DOI: 10.1039/c7sc03994h] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/27/2017] [Indexed: 11/21/2022] Open
Abstract
The viral genome load in diverse clinical samples varies over several orders of magnitude (e.g. 1-104 copies per μL), thus a dynamic range-extended and sensitive analysis method is highly desired. However, existing well-developed nucleic acid amplification systems always suffer from either a limited dynamic range or modest sensitivity for analysis of these samples. Herein, we propose a general engineered Janus probe to modulate the thermodynamics and kinetic properties of the amplification reaction. Through rational regulation, the Janus system improves the performance by both reducing the background and enhancing the signal, expanding the operative dynamic range by 2 orders of magnitude. This proposed approach achieves a detection limit for hepatitis B virus (HBV) DNA of down to 3 copies and can be successfully applied for direct quantification of the HBV genome in one microliter crude serum samples without any pretreatment. The results are consistent with clinical diagnosis and hold considerable potential to discriminate healthy volunteers and patients at different disease stages. Whereas, following the same operation, the representative well-developed system provided serious false-negative results using such trace amounts of samples from clinically confirmed positive patients.
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Affiliation(s)
- Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Qin
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Wenhua Wu
- Department of Infectious Disease , The Second Affiliated Hospital of Medical College , Xi'an Jiaotong University , Xiwu Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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13
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Abstract
Digital nucleic acid amplification (Digital NAA) quantifies nucleic acid by compartmentalizing a sample of DNA or RNA into a large number of discrete partitions and performing parallel nucleic acid amplification, such as polymerase chain reaction (PCR) or isothermal amplification reactions. With the counts of positive wells, total number of wells, and volumes of wells, the concentration of the target nucleic acid in the sample can be quantified. Digital NAA is considered increasingly powerful for ultra-sensitive detection and accurate quantification of nucleic acid for biological research and potentially medical diagnostics. Here, we describe glass SlipChip devices to perform digital NAA without cumbersome manual manipulation or complex fluidic control systems.
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Affiliation(s)
- Feng Shen
- SlipChip Corporation, 230 Constitution Drive, Menlo Park, CA, 94025, USA.
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14
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Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices. PLoS One 2016; 11:e0163060. [PMID: 27760148 PMCID: PMC5070811 DOI: 10.1371/journal.pone.0163060] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/01/2016] [Indexed: 11/25/2022] Open
Abstract
Nucleic acid amplification tests that are coupled with a digital readout enable the absolute quantification of single molecules, even at ultralow concentrations. Digital methods are robust, versatile and compatible with many amplification chemistries including isothermal amplification, making them particularly invaluable to assays that require sensitive detection, such as the quantification of viral load in occult infections or detection of sparse amounts of DNA from forensic samples. A number of microfluidic platforms are being developed for carrying out digital amplification. However, the mechanistic investigation and optimization of digital assays has been limited by the lack of real-time kinetic information about which factors affect the digital efficiency and analytical sensitivity of a reaction. Commercially available instruments that are capable of tracking digital reactions in real-time are restricted to only a small number of device types and sample-preparation strategies. Thus, most researchers who wish to develop, study, or optimize digital assays rely on the rate of the amplification reaction when performed in a bulk experiment, which is now recognized as an unreliable predictor of digital efficiency. To expand our ability to study how digital reactions proceed in real-time and enable us to optimize both the digital efficiency and analytical sensitivity of digital assays, we built a custom large-format digital real-time amplification instrument that can accommodate a wide variety of devices, amplification chemistries and sample-handling conditions. Herein, we validate this instrument, we provide detailed schematics that will enable others to build their own custom instruments, and we include a complete custom software suite to collect and analyze the data retrieved from the instrument. We believe assay optimizations enabled by this instrument will improve the current limits of nucleic acid detection and quantification, improving our fundamental understanding of single-molecule reactions and providing advancements in practical applications such as medical diagnostics, forensics and environmental sampling.
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15
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Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF. Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure. Angew Chem Int Ed Engl 2016; 55:9557-61. [PMID: 27357747 PMCID: PMC5215780 DOI: 10.1002/anie.201602763] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/05/2016] [Indexed: 01/11/2023]
Abstract
Rapid antimicrobial susceptibility testing (AST) would decrease misuse and overuse of antibiotics. The "holy grail" of AST is a phenotype-based test that can be performed within a doctor visit. Such a test requires the ability to determine a pathogen's susceptibility after only a short antibiotic exposure. Herein, digital PCR (dPCR) was employed to test whether measuring DNA replication of the target pathogen through digital single-molecule counting would shorten the required time of antibiotic exposure. Partitioning bacterial chromosomal DNA into many small volumes during dPCR enabled AST results after short exposure times by 1) precise quantification and 2) a measurement of how antibiotics affect the states of macromolecular assembly of bacterial chromosomes. This digital AST (dAST) determined susceptibility of clinical isolates from urinary tract infections (UTIs) after 15 min of exposure for all four antibiotic classes relevant to UTIs. This work lays the foundation to develop a rapid, point-of-care AST and strengthen global antibiotic stewardship.
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Affiliation(s)
- Nathan G Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Travis S Schlappi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Matthew S Curtis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Romney M Humphries
- Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA, 90095, USA
| | - Janet A Hindler
- Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA, 90095, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
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16
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Schoepp NG, Khorosheva EM, Schlappi TS, Curtis MS, Humphries RM, Hindler JA, Ismagilov RF. Digital Quantification of DNA Replication and Chromosome Segregation Enables Determination of Antimicrobial Susceptibility after only 15 Minutes of Antibiotic Exposure. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602763] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Nathan G. Schoepp
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Eugenia M. Khorosheva
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Travis S. Schlappi
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Matthew S. Curtis
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
| | - Romney M. Humphries
- Pathology and Laboratory Medicine; University of California, Los Angeles; 10888 Le Conte Avenue, Brentwood Annex Los Angeles CA 90095 USA
| | - Janet A. Hindler
- Pathology and Laboratory Medicine; University of California, Los Angeles; 10888 Le Conte Avenue, Brentwood Annex Los Angeles CA 90095 USA
| | - Rustem F. Ismagilov
- Division of Chemistry and Chemical Engineering; California Institute of Technology; 1200 E. California Blvd. Pasadena CA 91125 USA
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17
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Rodriguez-Manzano J, Karymov MA, Begolo S, Selck DA, Zhukov D, Jue E, Ismagilov RF. Reading Out Single-Molecule Digital RNA and DNA Isothermal Amplification in Nanoliter Volumes with Unmodified Camera Phones. ACS NANO 2016; 10:3102-13. [PMID: 26900709 PMCID: PMC4819493 DOI: 10.1021/acsnano.5b07338] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Digital single-molecule technologies are expanding diagnostic capabilities, enabling the ultrasensitive quantification of targets, such as viral load in HIV and hepatitis C infections, by directly counting single molecules. Replacing fluorescent readout with a robust visual readout that can be captured by any unmodified cell phone camera will facilitate the global distribution of diagnostic tests, including in limited-resource settings where the need is greatest. This paper describes a methodology for developing a visual readout system for digital single-molecule amplification of RNA and DNA by (i) selecting colorimetric amplification-indicator dyes that are compatible with the spectral sensitivity of standard mobile phones, and (ii) identifying an optimal ratiometric image-process for a selected dye to achieve a readout that is robust to lighting conditions and camera hardware and provides unambiguous quantitative results, even for colorblind users. We also include an analysis of the limitations of this methodology, and provide a microfluidic approach that can be applied to expand dynamic range and improve reaction performance, allowing ultrasensitive, quantitative measurements at volumes as low as 5 nL. We validate this methodology using SlipChip-based digital single-molecule isothermal amplification with λDNA as a model and hepatitis C viral RNA as a clinically relevant target. The innovative combination of isothermal amplification chemistry in the presence of a judiciously chosen indicator dye and ratiometric image processing with SlipChip technology allowed the sequence-specific visual readout of single nucleic acid molecules in nanoliter volumes with an unmodified cell phone camera. When paired with devices that integrate sample preparation and nucleic acid amplification, this hardware-agnostic approach will increase the affordability and the distribution of quantitative diagnostic and environmental tests.
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18
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Khorosheva EM, Karymov MA, Selck DA, Ismagilov RF. Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP. Nucleic Acids Res 2016; 44:e10. [PMID: 26358811 PMCID: PMC4737171 DOI: 10.1093/nar/gkv877] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 08/14/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions.
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Affiliation(s)
- Eugenia M Khorosheva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Mikhail A Karymov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - David A Selck
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
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19
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Nyan DC, Swinson KL. A method for rapid detection and genotype identification of hepatitis C virus 1-6 by one-step reverse transcription loop-mediated isothermal amplification. Int J Infect Dis 2015; 43:30-36. [PMID: 26686938 DOI: 10.1016/j.ijid.2015.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/26/2015] [Accepted: 12/05/2015] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Hepatitis C virus (HCV) is probably the leading cause of liver cirrhosis and hepatocellular carcinoma globally. Diagnostic tools conventionally used for the detection and identification of HCV infection are technically demanding, time-consuming, and costly for resource-limited environments. This study reports the development of the first rapid loop-mediated reverse transcription isothermal amplification assay that rapidly detects and identifies HCV genotypes in blood components. METHODS RNA extracted from donor plasma and serum specimens was applied to a one-step reverse transcription loop-mediated isothermal amplification reaction performed with HCV-specific oligonucleotides. Reactions were conducted at 63.5 °C for 30-60 min. The diagnostic characteristics of the assay were investigated and validated with clinical specimens. RESULTS Electrophoretic analysis of amplification revealed detection and identification of HCV genotypes 1-6. Positive amplification revealed unique ladder-like banding patterns that identified each HCV genotype. The assay demonstrated a sensitivity of 91.5% and specificity of 100%. Rapid naked-eye detection of HCV infection was facilitated by observation of an intense fluorescent glow of amplified targets under UV illumination. CONCLUSION These diagnostic characteristics highlight the potential utility of this assay for the rapid detection and genotype identification of HCV infection in field and point-of-care settings in endemic regions and resource-limited environments.
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Affiliation(s)
- Dougbeh-Chris Nyan
- Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Kevin L Swinson
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
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20
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Begolo S, Zhukov DV, Selck DA, Li L, Ismagilov RF. The pumping lid: investigating multi-material 3D printing for equipment-free, programmable generation of positive and negative pressures for microfluidic applications. LAB ON A CHIP 2014; 14:4616-28. [PMID: 25231706 PMCID: PMC10773560 DOI: 10.1039/c4lc00910j] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Equipment-free pumping is a challenging problem and an active area of research in microfluidics, with applications for both laboratory and limited-resource settings. This paper describes the pumping lid method, a strategy to achieve equipment-free pumping by controlled generation of pressure. Pressure was generated using portable, lightweight, and disposable parts that can be integrated with existing microfluidic devices to simplify workflow and eliminate the need for pumping equipment. The development of this method was enabled by multi-material 3D printing, which allows fast prototyping, including composite parts that combine materials with different mechanical properties (e.g. both rigid and elastic materials in the same part). The first type of pumping lid we describe was used to produce predictable positive or negative pressures via controlled compression or expansion of gases. A model was developed to describe the pressures and flow rates generated with this approach and it was validated experimentally. Pressures were pre-programmed by the geometry of the parts and could be tuned further even while the experiment was in progress. Using multiple lids or a composite lid with different inlets enabled several solutions to be pumped independently in a single device. The second type of pumping lid, which relied on vapor-liquid equilibrium to generate pressure, was designed, modeled, and experimentally characterized. The pumping lid method was validated by controlling flow in different types of microfluidic applications, including the production of droplets, control of laminar flow profiles, and loading of SlipChip devices. We believe that applying the pumping lid methodology to existing microfluidic devices will enhance their use as portable diagnostic tools in limited resource settings as well as accelerate adoption of microfluidics in laboratories.
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Affiliation(s)
- Stefano Begolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.
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