1
|
Shin JC, Jeong JY, Son SG, Choi SH, Nam HC, Yoon TH, Kim HJ, Choi DG, Lee H, Lee U, Yang SM, Kang I, Jung DY, Lee HW, Lee MK, Lee TJ, Kim G, Park HO, Lee SW. Developing centrifugal force real-time digital PCR for detecting extremely low DNA concentration. Sci Rep 2024; 14:11522. [PMID: 38769102 DOI: 10.1038/s41598-024-62199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Digital PCR (dPCR) is a technique for absolute quantification of nucleic acid molecules. To develop a dPCR technique that enables more accurate nucleic acid detection and quantification, we established a novel dPCR apparatus known as centrifugal force real-time dPCR (crdPCR). This system is efficient than other systems with only 2.14% liquid loss by dispensing samples using centrifugal force. Moreover, we applied a technique for analyzing the real-time graph of the each micro-wells and distinguishing true/false positives using artificial intelligence to mitigate the rain, a persistent issue with dPCR. The limits of detection and quantification were 1.38 and 4.19 copies/μL, respectively, showing a two-fold higher sensitivity than that of other comparable devices. With the integration of this new technology, crdPCR will significantly contribute to research on next-generation PCR targeting absolute micro-analysis.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ukyeol Lee
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | - Il Kang
- RevoSketch Inc., Daejeon, Republic of Korea
| | | | | | - Moon-Keun Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Tae Jae Lee
- Center for Nano Bio Development, National NanoFab Center (NNFC), Daejeon, Republic of Korea
| | - Geehong Kim
- Nano-Convergence Systems Research Division, Korea Institute of Machinery & Materials, Daejeon, Republic of Korea
| | - Han-Oh Park
- Bioneer Corporation, Daejeon, Republic of Korea
| | | |
Collapse
|
2
|
Zhang H, Liu X, Wang X, Yan Z, Xu Y, Gaňová M, Řezníček T, Korabečná M, Neuzil P. SPEED: an integrated, smartphone-operated, handheld digital PCR Device for point-of-care testing. Microsyst Nanoeng 2024; 10:62. [PMID: 38770032 PMCID: PMC11102901 DOI: 10.1038/s41378-024-00689-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/14/2024] [Accepted: 03/04/2024] [Indexed: 05/22/2024]
Abstract
This study elaborates on the design, fabrication, and data analysis details of SPEED, a recently proposed smartphone-based digital polymerase chain reaction (dPCR) device. The dPCR chips incorporate partition diameters ranging from 50 μm to 5 μm, and these partitions are organized into six distinct blocks to facilitate image processing. Due to the superior thermal conductivity of Si and its potential for mass production, the dPCR chips were fabricated on a Si substrate. A temperature control system based on a high-power density Peltier element and a preheating/cooling PCR protocol user interface shortening the thermal cycle time. The optical design employs four 470 nm light-emitting diodes as light sources, with filters and mirrors effectively managing the light emitted during PCR. An algorithm is utilized for image processing and illumination nonuniformity correction including conversion to a monochromatic format, partition identification, skew correction, and the generation of an image correction mask. We validated the device using a range of deoxyribonucleic acid targets, demonstrating its potential applicability across multiple fields. Therefore, we provide guidance and verification of the design and testing of the recently proposed SPEED device.
Collapse
Affiliation(s)
- Haoqing Zhang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
- The Key Laboratory of Biomedical Information Engineering of the Ministry of Education; School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710049 PR China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi’an Jiaotong University, Xi’an, 710049 PR China
| | - Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| | - Xinlu Wang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| | - Zhiqiang Yan
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi’an, Shaanxi 710072 PR China
| | - Ying Xu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| | - Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300 Brno, Czech Republic
| | - Tomáš Řezníček
- ITD Tech S.R.O, Osvoboditelu, 1005, 735 81 Bohumín, Czech Republic
| | - Marie Korabečná
- Institute of Biology and Medical Genetics; First Faculty of Medicine, Charles University and General University Hospital of Prague, Albertov 4, 12800 Prague, Czech Republic
| | - Pavel Neuzil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace; School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, Shaanxi 710072 PR China
| |
Collapse
|
3
|
Wang J, Lyu X, Zhang X, Wang S, Zeng W, Yang T, Wang B, Luo G. An approach for integrating droplet generation and detection in digital polymerase chain reaction applications based on a bifunctional microfluidic cross-structure. Talanta 2024; 267:125240. [PMID: 37778182 DOI: 10.1016/j.talanta.2023.125240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023]
Abstract
Digital polymerase chain reaction (dPCR) is an approach for absolute nucleic acid quantification with high sensitivity. Although several successful commercial dPCR devices have been developed to date, further miniaturizing device dimensions, decreasing cross-contamination, and improving automation level are still research highlights. In this study, we developed a fully contamination-free dPCR detection chip with fluorescence flow cytometry and micro droplet approach. A bifunctional cross-structure (BFCS) was designed to realize monodisperse sample droplet generation in forward flow and droplet detection in backward flow with simple pneumatic control and fixed chip position. In order to improve droplet detection efficiency and accuracy, droplets morphology and sequence pattern during microfluidic droplet generation and backward flow droplet detection at the same cross-structure were observed and analyzed under different pneumatic pressures. In addition, during backward flow droplet detection, an optimized declination angle of the chip was applied to increase droplet reflux rates. For the validation of PCR performance, temperature changing processes during PCR cycles were achieved by heating the monodispersed droplet array with a customized PCR amplification device. The fluorescence signal of each droplet right after passing the cross-structure was excitated and detected. The absolute quantification ability of our integrated dPCR microfluidic chip utilizing flow fluorescence cytometry was tested and verified with Influenza A virus gene (from 7.5 copies/μL to 30000 copies/μL). Thus, our platform provides a novel and integrated approach for ddPCR analysis.
Collapse
Affiliation(s)
- Jinxian Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xin Lyu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaoliang Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Shun Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wen Zeng
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Tianhang Yang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Bidou Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou ZhongKe Medical Device Industry Development Co., Ltd., Suzhou, 215163, China.
| | - Gangyin Luo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou ZhongKe Medical Device Industry Development Co., Ltd., Suzhou, 215163, China.
| |
Collapse
|
4
|
Hu W, Zhu Y, Tang Q, Ji X, Wang L, Ou W, Li G, Wu L, Cong H, Qin Y. Facile prepared microfluidic chip for multiplexed digital RT-qPCR test. Biotechnol J 2024; 19:e2300273. [PMID: 37702130 DOI: 10.1002/biot.202300273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/14/2023]
Abstract
The chip-based digital polymerase chain reaction (PCR) is an indispensable technique for amplifying and quantifying nucleic acids, which has been widely employed in molecular diagnostics at both fundamental and clinical levels. However, the previous designs have yet to achieve widespread application due to limitations in complex chip fabrication, pretreatment procedures, special surface properties, and low throughput. This study presents a facile digital microfluidic chip driven by centrifugal force for digital PCR analysis. Interestingly, regardless of the hydrophilicity or hydrophobicity of the inner chip surface, an efficient digitization process can be achieved. PCR reagents introduced into the inlet can be allocated to 9600 microchambers and subsequently isolated by the immiscible phase (silicone oil). The centrifugal priming approach offers a facile means to achieve high-throughput analysis. The design was further employed for the quantification of nucleic acids using digital PCR. The calculated result exhibited a strong correlation with the measured value at the concentrations from 1 copy/μL to 1000 copies/μL (R2 = 0.99). Additionally, the chip also allowed digital multiplexed analysis, thereby indicating its potential for multi-target detection applications.
Collapse
Affiliation(s)
- Wenqi Hu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, P. R. China
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, P. R. China
| | - Yidan Zhu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, P. R. China
| | - Qu Tang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, P. R. China
| | - Xiaolei Ji
- Nantong Center for Disease Control and Prevention, Nantong, Jiangsu, P. R. China
| | - Lei Wang
- Nantong Egens Biotechnology Co., Ltd, Nantong, Jiangsu, P. R. China
| | - Weijun Ou
- Nantong Egens Biotechnology Co., Ltd, Nantong, Jiangsu, P. R. China
| | - Guo Li
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, P. R. China
| | - Li Wu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, P. R. China
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, P. R. China
| | - Hui Cong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, P. R. China
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu, P. R. China
- Department of Blood Transfusion, Affiliated Hospital of Nantong University, Nantong, Jiangsu, P. R. China
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, P. R. China
| |
Collapse
|
5
|
Liu X, Wang X, Zhang H, Yan Z, Gaňová M, Lednický T, Řezníček T, Xu Y, Zeng W, Korabečná M, Neužil P. Smartphone integrated handheld (SPEED) digital polymerase chain reaction device. Biosens Bioelectron 2023; 232:115319. [PMID: 37087984 DOI: 10.1016/j.bios.2023.115319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
We demonstrate a smartphone integrated handheld (SPEED) digital polymerase chain reaction (dPCR) device for point-of-care application. The device has dimensions of ≈100 × 200 × 35 mm3 and a weight of ≈400 g. It can perform 45 PCR cycles in ≈49 min. The device also features integrated, miniaturized modules for thermal cycling, image taking, and wireless data communication. These functions are controlled by self-developed Android-based applications. The only consumable is the developed silicon-based dPCR chip, which has the potential to be recycled. The device's precision and accuracy are comparable with commercial dPCR machines. We have verified the SPEED dPCR prototype's utility in the testing of severe acute respiratory syndrome coronavirus 2, the detection of cancer-associated gene sequences, and the confirmations of Down syndrome diagnoses. Due to its low upfront capital investment, as well as its nominal running cost, we envision that the SPEED dPCR device will help to perform cancer screenings and non-invasive prenatal tests for the general population. It will also aid in the timely identification and monitoring of infectious disease testing, thereby expediting alerts with respect to potential emerging pandemics.
Collapse
Affiliation(s)
- Xiaocheng Liu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Xinlu Wang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Haoqing Zhang
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Ministry of Education Key Laboratory of Biomedical Information Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Zhiqiang Yan
- School of Marine Science and Technology, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, PR China
| | - Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic
| | - Tomáš Lednický
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, 61300, Brno, Czech Republic
| | - Tomáš Řezníček
- ITD Tech s.r.o, Osvoboditelu 1005, 735 81, Bohumín, Czech Republic
| | - Ying Xu
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Wen Zeng
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital of Prague, Albertov 4, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Ministry of Education Key Laboratory of Micro and Nano Systems for Aerospace, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi, 710072, PR China; Faculty of Electrical Engineering, Brno University of Technology, Technická 3058/10, 61600, Brno, Czech Republic.
| |
Collapse
|
6
|
Iida T, Ando J, Shinoda H, Makino A, Yoshimura M, Murai K, Mori M, Takeuchi H, Noda T, Nishimasu H, Watanabe R. Compact wide-field femtoliter-chamber imaging system for high-speed and accurate digital bioanalysis. Lab Chip 2023; 23:684-691. [PMID: 36255223 DOI: 10.1039/d2lc00741j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The femtoliter-chamber array is a bioanalytical platform that enables highly sensitive and quantitative analysis of biological reactions at the single-molecule level. This feature has been considered a key technology for "digital bioanalysis" in the biomedical field; however, its versatility is limited by the need for a large and expensive setup such as a fluorescence microscope, which requires a long time to acquire the entire image of a femtoliter-chamber array. To address these issues, we developed a compact and inexpensive wide-field imaging system (COWFISH) that can acquire fluorescence images with a large field of view (11.8 mm × 7.9 mm) and a high spatial resolution of ∼ 3 μm, enabling high-speed analysis of sub-million femtoliter chambers in 20 s. Using COWFISH, we demonstrated a CRISPR-Cas13a-based digital detection of viral RNA of SARS-CoV-2 with an equivalent detection sensitivity (limit of detection: 480 aM) and a 10-fold reduction in total imaging time, as compared to confocal fluorescence microscopy. In addition, we demonstrated the feasibility of COWFISH to discriminate between SARS-CoV-2-positive and -negative clinical specimens with 95% accuracy, showing its application in COVID-19 diagnosis. Therefore, COWFISH can serve as a compact and inexpensive imaging system for high-speed and accurate digital bioanalysis, paving a way for various biomedical applications, such as diagnosis of viral infections.
Collapse
Affiliation(s)
| | - Jun Ando
- Cluster for Pioneering Research, RIKEN, Japan.
| | | | | | | | - Kazue Murai
- Cluster for Pioneering Research, RIKEN, Japan.
| | - Makiko Mori
- Cluster for Pioneering Research, RIKEN, Japan.
| | - Hiroaki Takeuchi
- Department of Molecular Virology, Tokyo Medical and Dental University, Japan
| | - Takeshi Noda
- Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Japan
- RCAST, The University of Tokyo, Japan
| | | |
Collapse
|
7
|
Lee YS, Choi JW, Kang T, Chung BG. Deep Learning-Assisted Droplet Digital PCR for Quantitative Detection of Human Coronavirus. Biochip J 2023; 17:112-9. [PMID: 36687365 DOI: 10.1007/s13206-023-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/15/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023]
Abstract
Since coronavirus disease 2019 (COVID-19) pandemic rapidly spread worldwide, there is an urgent demand for accurate and suitable nucleic acid detection technology. Although the conventional threshold-based algorithms have been used for processing images of droplet digital polymerase chain reaction (ddPCR), there are still challenges from noise and irregular size of droplets. Here, we present a combined method of the mask region convolutional neural network (Mask R-CNN)-based image detection algorithm and Gaussian mixture model (GMM)-based thresholding algorithm. This novel approach significantly reduces false detection rate and achieves highly accurate prediction model in a ddPCR image processing. We demonstrated that how deep learning improved the overall performance in a ddPCR image processing. Therefore, our study could be a promising method in nucleic acid detection technology.
Collapse
|
8
|
Zhang H, Laššáková S, Yan Z, Wang X, Šenkyřík P, Gaňová M, Chang H, Korabecna M, Neuzil P. Digital polymerase chain reaction duplexing method in a single fluorescence channel. Anal Chim Acta 2022; 1238:340243. [DOI: 10.1016/j.aca.2022.340243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022]
|