1
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Hosokawa K, Ohmori H. Digital PCR using a simple PDMS microfluidic chip and standard laboratory equipment. ANAL SCI 2023; 39:2067-2074. [PMID: 37710081 DOI: 10.1007/s44211-023-00425-2] [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: 07/18/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
Digital PCR (dPCR) enables sensitive and precise quantification of template nucleic acid without calibration. However, dPCR is not yet in widespread use, probably due to the need for expensive specialized instruments. In this paper, we describe a dPCR system using a simple microfluidic chip and common laboratory tools. The microfluidic chip consists of two parts: a PDMS part with 24,840 × 0.25 nL microwells and a PDMS-coated flat glass plate. Human RNase P gene was adopted as the model template. Commercial products of human genomic DNA and real-time PCR reagents were mixed to make a PCR mixture. The PCR mixture was confined to the microwells by the PDMS degas-driven liquid control technique. The thermal cycling was performed on a common well-type thermal cycler with a minor modification. During the thermal cycling, evaporation of the PCR mixture was prevented with a handmade water holder. In the fluorescence image, bright (positive) microwells and dim (negative) ones were clearly discriminated. The number of the positive microwells was counted using software, and was used for estimation of the template concentration in the sample based on the theory of the Poisson distribution. The estimated concentrations well agreed with the input template concentrations in the range from 1.32 copies/µL to 13 200 copies/µL. The techniques presented in this paper will pave the way for facile dPCR in a broad range of laboratories without the need for expensive instruments.
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Affiliation(s)
- Kazuo Hosokawa
- Materials Fabrication Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Hitoshi Ohmori
- Materials Fabrication Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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2
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Chen S, Sun Y, Fan F, Chen S, Zhang Y, Zhang Y, Meng X, Lin JM. Present status of microfluidic PCR chip in nucleic acid detection and future perspective. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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3
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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: 37] [Impact Index Per Article: 18.5] [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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4
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Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Cao L, Guo X, Mao P, Ren Y, Li Z, You M, Hu J, Tian M, Yao C, Li F, Xu F. A Portable Digital Loop-Mediated Isothermal Amplification Platform Based on Microgel Array and Hand-Held Reader. ACS Sens 2021; 6:3564-3574. [PMID: 34606243 DOI: 10.1021/acssensors.1c00603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Digital polymerase chain reaction (dPCR) has found widespread applications in molecular diagnosis of various diseases owing to its sensitive single-molecule detection capability. However, the existing dPCR platforms rely on the auxiliary procedure to disperse DNA samples, which needs complicated operation, expensive apparatus, and consumables. Besides, the complex and costly dPCR readers also impede the applications of dPCR for point-of-care testing (POCT). Herein, we developed a portable digital loop-mediated isothermal amplification (dLAMP) platform, integrating a microscale hydrogel (microgel) array chip for sample partition, a miniaturized heater for DNA amplification, and a hand-held reader for digital readout. In the platform, the chip with thousands of isolated microgels holds the capability of self-absorption and partition of DNA samples, thus avoiding auxiliary equipment and professional personnel operations. Using the integrated dLAMP platform, λDNA templates have been quantified with a good linear detection range of 2-1000 copies/μL and a detection limit of 1 copy/μL. As a demonstration, the epidermal growth factor receptor L858R gene mutation, a crucial factor for the susceptibility of the tyrosine kinase inhibitor in non-small-cell lung cancer treatment, has been accurately identified by the dLAMP platform with a spiked plasma sample. This work shows that the developed dLAMP platform provides a low-cost, facile, and user-friendly solution for the absolute quantification of DNA, showing great potential for the POCT of nucleic acids.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiaojin Guo
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
- Department of Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Ping Mao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Yulin Ren
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Jie Hu
- Suzhou DiYinAn Biotechnology Company Ltd., Suzhou 215000, China
| | - Miao Tian
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Fei Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an 710049, China
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6
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McCarthy Riley BF, Ward CL, Linz TH. Influence of microfabrication on digital PCR performance in bead-based microwell array assays. Anal Bioanal Chem 2020; 412:6917-6926. [PMID: 32772126 DOI: 10.1007/s00216-020-02822-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 11/25/2022]
Abstract
Digital PCR (dPCR) is a highly sensitive analytical technique used to quantify DNA targets. Detection sensitivity can be further enhanced by capturing target sequences onto beads for preconcentration and sample cleanup prior to analysis in microfluidic microwell arrays. However, robust digital analysis requires individual beads to be interrogated within individual wells. Fabricating microwells with dimensions ≤ 3 μm is challenging, and the high surface area-to-volume ratio of the wells leaves PCR susceptible to inhibition stemming from materials used during device processing. This report describes the development of a microfabrication procedure to create ultralow-volume wells (100 fL) for bead-based dPCR and characterize the effects of microprocessing materials on assay performance. Standard microfabrication protocols used for creating microelectronics resulted in devices with nanoscopic debris originating from photoresists used during processing. A model dPCR assay was developed to characterize the effects of this debris, which revealed variable PCR inhibition. Debris within microwells attenuated digital and analog assay signals to a greater extent than debris on the device surface. Spatial heterogeneity of debris across devices was quantified to characterize regional PCR inhibition and intra- and inter-device variability. Ultimately, a fabrication procedure was developed to create pristine microfluidic arrays using dual processes to remove positive resist and forgoing use of negative resist entirely, which enabled robust amplification with digital signals matching theoretical predictions. Results from this work catalog the unique performance artifacts from device microfabrication and provide a guide for future studies seeking to conduct robust, high-sensitivity bead-based dPCR assays. Graphical abstract.
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Affiliation(s)
| | - Cassandra L Ward
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA.
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7
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Yin J, Zou Z, Yin F, Liang H, Hu Z, Fang W, Lv S, Zhang T, Wang B, Mu Y. A Self-Priming Digital Polymerase Chain Reaction Chip for Multiplex Genetic Analysis. ACS NANO 2020; 14:10385-10393. [PMID: 32794742 DOI: 10.1021/acsnano.0c04177] [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] [Indexed: 06/11/2023]
Abstract
Digital PCR (polymerase chain reaction) is a powerful and attractive tool for the quantification of nucleic acids. However, the multiplex detection capabilities of this system are limited or require expensive instrumentation and reagents, all of which can hinder multiplex detection goals. Here, we propose strategies toward solving these issues regarding digital PCR. We designed and tested a self-priming digital PCR chip containing 6-plex detection capabilities using monochrome fluorescence, which has six detection areas and four-layer structures. This strategy achieved multiplex digital detection by the use of self-priming to preintroduce the specific reaction mix to a certain detection area. This avoids competition when multiple primer pairs coexist, allowing for multiplexing in a shorter time while using less reagents and low-cost instruments. This also prevents the digital PCR chip from experiencing long sample introduction time and evaporation. For further validation, this multiplex digital PCR chip was used to detect five types of EGFR (epidermal growth factor receptor) gene mutations in 15 blood samples from lung cancer patients. We conclude that this technique can precisely quantify EGFR mutations in high-performance diagnostics. This multiplex digital detection chip is a simple and inexpensive test intended for liquid biopsies. It can be applied and used in prenatal diagnostics, the monitoring of residual disease, rapid pathogen detection, and many other procedures.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Zheyu Zou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Fangfang Yin
- Weifang People's Hospital, Weifang 261000, China
| | - Hongxiao Liang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Zhenming Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Weibo Fang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130000, China
| | - Tao Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Ben Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
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8
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Jiang Y, Manz A, Wu W. Fully automatic integrated continuous-flow digital PCR device for absolute DNA quantification. Anal Chim Acta 2020; 1125:50-56. [DOI: 10.1016/j.aca.2020.05.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 01/09/2023]
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9
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Padmanabhan S, Han JY, Nanayankkara I, Tran K, Ho P, Mesfin N, White I, DeVoe DL. Enhanced sample filling and discretization in thermoplastic 2D microwell arrays using asymmetric contact angles. BIOMICROFLUIDICS 2020; 14:014113. [PMID: 32095199 PMCID: PMC7028432 DOI: 10.1063/1.5126938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/09/2020] [Indexed: 05/04/2023]
Abstract
Sample filling and discretization within thermoplastic 2D microwell arrays is investigated toward the development of low cost disposable microfluidics for passive sample discretization. By using a high level of contact angle asymmetry between the filling channel and microwell surfaces, a significant increase in the range of well geometries that can be successfully filled is revealed. The performance of various array designs is characterized numerically and experimentally to assess the impact of contact angle asymmetry and device geometry on sample filling and discretization, resulting in guidelines to ensure robust microwell filling and sample isolation over a wide range of well dimensions. Using the developed design rules, reliable and bubble-free sample filling and discretization is achieved in designs with critical dimensions ranging from 20 μm to 800 μm. The resulting devices are demonstrated for discretized nucleic acid amplification by performing loop-mediated isothermal amplification for the detection of the mecA gene associated with methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- S. Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - J. Y. Han
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. Nanayankkara
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - K. Tran
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - P. Ho
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - N. Mesfin
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. White
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - D. L. DeVoe
- Author to whom correspondence should be addressed:. Tel.: +1-301-405-8125
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10
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Zhou X, Ravichandran GC, Zhang P, Yang Y, Zeng Y. A microfluidic alternating-pull-push active digitization method for sample-loss-free digital PCR. LAB ON A CHIP 2019; 19:4104-4116. [PMID: 31720646 PMCID: PMC6894176 DOI: 10.1039/c9lc00932a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Digital polymerase chain reaction (dPCR) is a powerful tool for genetic analysis, providing superior sensitivity and accuracy. In many applications that demand minuscule reaction volumes, such as single cell analysis, efficient and reproducible sample handling and digitization is pivotal for accurate absolute quantification of targets, but remains a significant technical challenge. In this paper, we described a robust and flexible microfluidic alternating-pull-push active digitization (μAPPAD) strategy that confers close to 100% sample digitization efficiency for microwell-based dPCR. Our strategy employs pneumatic valve control to periodically manipulate air pressure inside the chip to greatly facilitate the vacuum-driven partition of solution into microwells, enabling efficient digitization of a small-volume solution with significantly reduced volume variability. The μAPPAD method was evaluated on both tandem-channel and parallel-channel chips, which achieved a digitization efficiency of 99.5 ± 0.3% and 94.6 ± 0.9% within 10.5 min and 2 min, respectively. To assess the analytical performance of the μAPPAD chip, we calibrated it for absolution dPCR quantitation of λDNA across a range of concentrations. The results obtained with our chip matched well with the theoretical curve computed from Poisson statistics. Compared to the existing methods for highly efficient sample digitization, not only does our technology greatly reduce the constraints on microwell geometries and channel design, but also benefits from the intrinsic amenability of the pneumatic valve technique with device integration and automation. Thus we envision that the μAPPAD technology will provide a scalable and widely adaptable platform to promote the development of advanced lab-on-a-chip systems integrating microscale sample processing with dPCR for a broad scope of applications, such as single cell analysis of tumor heterogeneity and genetic profiling of circulating exosomes directly in clinical samples.
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Affiliation(s)
- Xin Zhou
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | | | - Peng Zhang
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | - Yang Yang
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA.
| | - Yong Zeng
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA. and University of Kansas Cancer Center, Kansas City, KS 66160, USA
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11
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Xu Z, Qiao Y, Tu J. Microfluidic Technologies for cfDNA Isolation and Analysis. MICROMACHINES 2019; 10:mi10100672. [PMID: 31623361 PMCID: PMC6843514 DOI: 10.3390/mi10100672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/27/2019] [Accepted: 09/29/2019] [Indexed: 12/18/2022]
Abstract
Cell-free DNA (cfDNA), which promotes precision oncology, has received extensive concern because of its abilities to inform genomic mutations, tumor burden and drug resistance. The absolute quantification of cfDNA concentration has been proved as an independent prognostic biomarker of overall survival. However, the properties of low abundance and high fragmentation hinder the isolation and further analysis of cfDNA. Microfluidic technologies and lab-on-a-chip (LOC) devices provide an opportunity to deal with cfDNA sample at a micrometer scale, which reduces required sample volume and makes rapid isolation possible. Microfluidic platform also allow for high degree of automation and high-throughput screening without liquid transfer, where rapid and precise examination and quantification could be performed at the same time. Microfluidic technologies applied in cfDNA isolation and analysis are limited and remains to be further explored. This paper reviewed the existing and potential applications of microfluidic technologies in collection and enrichment of cfDNA, quantification, mutation detection and sequencing library construction, followed by discussion of future perspectives.
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Affiliation(s)
- Zheyun Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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13
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Gao W, Zhang X, Yuan H, Wang Y, Zhou H, Jin H, Jia C, Jin Q, Cong H, Zhao J. EGFR point mutation detection of single circulating tumor cells for lung cancer using a micro-well array. Biosens Bioelectron 2019; 139:111326. [PMID: 31129389 DOI: 10.1016/j.bios.2019.111326] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/26/2019] [Accepted: 05/13/2019] [Indexed: 01/06/2023]
Abstract
In view of their critical function in metastasis, characterization of single circulating tumor cells (CTCs) can provide important clinical information to monitor tumor progression and guide personal therapy. Single-cell genetic analysis methods based on microfluidics have some inherent shortcomings such as complicated operation, low throughput, and expensive equipment requirements. To overcome these barriers, we developed a simple and open micro-well array containing 26,208 units for either nuclear acids or single-cell genetic analysis. Through modification of the polydimethylsiloxane surface and optimization of chip packaging, we addressed protein adsorption and solution evaporation for PCR amplification on a chip. In the detection of epidermal growth factor receptor (EGFR) exon gene 21, this micro-well array demonstrated good linear correlation at a DNA concentration from 1 × 101 to 1 × 105 copies/μL (R2 = 0.9877). We then successfully integrated cell capture, lysis, PCR amplification, and signal read-out on the micro-well array, enabling the rapid and simple genetic analysis of single cells. This device was used to detect duplex EGFR mutation genes of lung cancer cell lines (H1975 and A549 cells) and normal leukocytes, demonstrating the ability to perform high-throughput, massively parallel duplex gene analysis at the single-cell level. Different types of point mutations (EGFR-L858R mutation or EGFR-T790M mutation) were detected in single H1975 cells, further validating the significance of single-cell level gene detection. In addition, this method showed a good performance in the heterogeneity detection of individual CTCs from lung cancer patients, required for micro-invasive cancer monitoring and treatment selection.
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Affiliation(s)
- Wanlei Gao
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China; State Key Laboratories of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Xiaofen Zhang
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226000, China
| | - Haojun Yuan
- State Key Laboratories of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Yanmin Wang
- State Key Laboratories of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Hongbo Zhou
- State Key Laboratories of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Han Jin
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chunping Jia
- State Key Laboratories of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Qinghui Jin
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Hui Cong
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226000, China.
| | - Jianlong Zhao
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China
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14
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Lin X, Huang X, Urmann K, Xie X, Hoffmann MR. Digital Loop-Mediated Isothermal Amplification on a Commercial Membrane. ACS Sens 2019; 4:242-249. [PMID: 30604619 PMCID: PMC6350201 DOI: 10.1021/acssensors.8b01419] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
In
this work, we report digital loop-mediated isothermal amplification
(LAMP) or reverse-transcription LAMP (RT-LAMP) on a commercial membrane,
without the need for complex chip fabrication or use of specialized
equipment. Due to the pore size distribution, the theoretical error
for digital LAMP on these membranes was analyzed, using a combination
of Random Distribution Model and Multivolume Theory. A facile peel-off
process was developed for effective droplet formation on the commercial
track-etched polycarbonate (PCTE) membrane. Each pore functions as
an individual nanoreactor for single DNA amplification. Absolute quantification
of bacteria genomic DNA was realized with a dynamic range from 11
to 1.1 × 105 copies/μL. One-step digital RT-LAMP
was also successfully performed on the membrane for the quantification
of MS2 virus in wastewater. With the introduction of new probes, the
positive pores can be easily distinguished from negative ones with
100 times difference in fluorescence intensities. Finally, the cost
of a disposable membrane is less than $0.10/piece, which, to the best
of our knowledge, is the most inexpensive way to perform digital LAMP.
The membrane system offers opportunities for point-of-care users or
common laboratories to perform digital quantification, single cell
analysis, or other bioassays in an inexpensive, flexible, and simplified
way.
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Affiliation(s)
- Xingyu Lin
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
| | - Xiao Huang
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
| | - Katharina Urmann
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
| | - Xing Xie
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Michael R. Hoffmann
- Linde + Robinson Laboratories, California Institute of Technology, Pasadena, California 91125, United States
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15
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Lin X, Huang X, Zhu Y, Urmann K, Xie X, Hoffmann MR. Asymmetric Membrane for Digital Detection of Single Bacteria in Milliliters of Complex Water Samples. ACS NANO 2018; 12:10281-10290. [PMID: 30211534 PMCID: PMC6202633 DOI: 10.1021/acsnano.8b05384] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/13/2018] [Indexed: 05/22/2023]
Abstract
In this work, we introduce an asymmetric membrane as a simple and robust nanofluidic platform for digital detection of single pathogenic bacteria directly in 10 mL of unprocessed environmental water samples. The asymmetric membrane, consisting of uniform micropores on one side and a high density of vertically aligned nanochannels on the other side, was prepared within 1 min by a facile method. The single membrane covers all the processing steps from sample concentration, purification, and partition to final digital loop-mediated isothermal amplification (LAMP). By simple filtration, bacteria were enriched and partitioned inside the micropores, while inhibitors typically found in the environmental samples ( i.e., proteins, heavy metals, and organics) were washed away through the nanochannels. Meanwhile, large particles, indigenous plankton, and positively charged pollutants in the samples were excluded by using a sacrificial membrane stacked on top. After initial filtration, modified LAMP reagents, including NaF and lysozyme, were loaded onto the membrane. Each pore in the asymmetric membrane functioned as an individual nanoreactor for selective, rapid, and efficient isothermal amplification of single bacteria, generating a bright fluorescence for direct counting. Even though high levels of inhibitors were present, absolute quantification of Escherichia coli and Salmonella directly in an unprocessed environmental sample (seawater and pond water) was achieved within 1 h, with sensitivity down to single cell and a dynamic range of 0.3-10000 cells/mL. The simple and low-cost analysis platform described herein has an enormous potential for the detection of pathogens, exosomes, stem cells, and viruses as well as single-cell heterogeneity analysis in environmental, food, and clinical research.
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Affiliation(s)
- Xingyu Lin
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xiao Huang
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Yanzhe Zhu
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Katharina Urmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
| | - Xing Xie
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Michael R. Hoffmann
- Linde
+ Robinson Laboratories, California Institute
of Technology, Pasadena, California 91125, United States
- E-mail:
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16
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Li X, Zhang D, Zhang H, Guan Z, Song Y, Liu R, Zhu Z, Yang C. Microwell Array Method for Rapid Generation of Uniform Agarose Droplets and Beads for Single Molecule Analysis. Anal Chem 2018; 90:2570-2577. [PMID: 29350029 DOI: 10.1021/acs.analchem.7b04040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with preselectable diameters ranging from 20 to 100 μm can be produced with relative standard deviations less than 3.5%. The array-based droplet generation method was used to perform digital PCR for absolute DNA quantitation. The array-based droplet isolation and sol-gel switching property of agarose enable formation of stable beads by chilling the droplet array at -20 °C, thus, maintaining the monoclonality of each droplet and facilitating the selective retrieval of desired droplets. The monoclonality of droplets was demonstrated by DNA sequencing and FACS analysis, suggesting the robustness and flexibility of the approach for single molecule amplification and analysis. We believe our approach will lead to new possibilities for a great variety of applications, such as single-cell gene expression studies, aptamer selection, and oligonucleotide analysis.
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Affiliation(s)
- Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Dongfeng Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Huimin Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China.,The MOE Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, People's Republic of China
| | - Ruochen Liu
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey United States
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University , Xiamen 361005, People's Republic of China
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17
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Zhou X, Zhou X, Zheng B. Stacking chip for quantitative bioanalysis. Talanta 2017; 175:483-487. [PMID: 28842021 DOI: 10.1016/j.talanta.2017.07.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 11/17/2022]
Abstract
This paper describes a microwell-based microdevice for performing quantitative bioanalysis. This microdevice combined the passive pumping by degassed polydimethylsiloxane (PDMS) with serial operations including solution dispensing, plates splitting and plates stacking. We name this microdevice "stacking chip". To use the stacking chip in quantitative bioanalysis, nanoliter solutions were first dispensed into the microwells through the degassed PDMS microchannels. Next, we split the microwell and microchannel plates assisted by the application of one drop of silicone oil, which resulted in a microwell array containing the reagent solutions. Microreactor arrays were formed by stacking the two microwell arrays containing the reagent solutions. With this microdevice, the enzymatic kinetics of alkaline phosphatase during the dissociation of the fluorescein diphosphate was measured and analyzed by the Michaelis-Menten model. The stacking chip is simple to fabricate and operate, and amenable to automation for high throughput analysis.
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Affiliation(s)
- Xiaohu Zhou
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuechang Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
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18
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Sposito AJ, DeVoe DL. Staggered trap arrays for robust microfluidic sample digitization. LAB ON A CHIP 2017; 17:4105-4112. [PMID: 29090708 DOI: 10.1039/c7lc00846e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A sample digitization method that exploits the controlled pinning of fluid at geometric discontinuities within an array of staggered microfluidic traps is presented. The staggered trap design enables reliable sample filling within high aspect ratio microwells, even when employing substrate materials such as thermoplastics that are not gas permeable. A simple geometric model is developed to predict the impact of device geometry on sample filling and discretization, and validated experimentally using fabricated cyclic olefin polymer devices. Using the developed design guidelines, a 768-element staggered trap array is demonstrated, with reliable passive loading and discretization achieved within 5 min. The resulting discretization platform offers a simplified workflow with flexible trap design, reliable discretization, and repeatable operation using low-cost thermoplastic substrates.
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Affiliation(s)
- A J Sposito
- Department of Mechanical Engineering, University of Maryland, College Park, MD, USA.
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19
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Zhu Q, Xu Y, Qiu L, Ma C, Yu B, Song Q, Jin W, Jin Q, Liu J, Mu Y. A scalable self-priming fractal branching microchannel net chip for digital PCR. LAB ON A CHIP 2017; 17:1655-1665. [PMID: 28418438 DOI: 10.1039/c7lc00267j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR has been widely used in many bioresearch fields, such as next generation sequencing, single cell analysis, gene editing detection and so on. However, existing digital PCR methods still have some disadvantages, including high cost, sample loss, and complicated operation. In this work, we develop an exquisite scalable self-priming fractal branching microchannel net digital PCR chip. This chip with a special design inspired by natural fractal-tree systems has an even distribution and 100% compartmentalization of the sample without any sample loss, which is not available in existing chip-based digital PCR methods. A special 10 nm nano-waterproof layer was created to prevent the solution from evaporating. A vacuum pre-packaging method called self-priming reagent introduction is used to passively drive the reagent flow into the microchannel nets, so that this chip can realize sequential reagent loading and isolation within a couple of minutes, which is very suitable for point-of-care detection. When the number of positive microwells stays in the range of 100 to 4000, the relative uncertainty is below 5%, which means that one panel can detect an average of 101 to 15 374 molecules by the Poisson distribution. This chip is proved to have an excellent ability for single molecule detection and quantification of low expression of hHF-MSC stem cell markers. Due to its potential for high throughput, high density, low cost, lack of sample and reagent loss, self-priming even compartmentalization and simple operation, we envision that this device will significantly expand and extend the application range of digital PCR involving rare samples, liquid biopsy detection and point-of-care detection with higher sensitivity and accuracy.
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Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.
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