1
|
Guo Y, Zhang X, Zhang H, Liu Y, Shi J, Meng H, Chen X, Lan Q, Zhu B. Application of microfluidic technologies in forensic analysis. Electrophoresis 2023; 44:1725-1743. [PMID: 37857551 DOI: 10.1002/elps.202200268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 10/21/2023]
Abstract
The application of microfluidic technology in forensic medicine has steadily expanded over the last two decades due to the favorable features of low cost, rapidity, high throughput, user-friendliness, contamination-free, and minimum sample and reagent consumption. In this context, bibliometric methods were adopted to visualize the literature information contained in the Science Citation Index Expanded from 1989 to 2022, focusing on the co-occurrence analysis of forensic and microfluidic topics. A deep interpretation of the literature was conducted based on co-occurrence results, in which microfluidic technologies and their applications in forensic medicine, particularly forensic genetics, were elaborated. The purpose of this review is to provide an impartial evaluation of the utilization of microfluidic technology in forensic medicine. Additionally, the challenges and future trends of implementing microfluidic technology in forensic genetics are also addressed.
Collapse
Affiliation(s)
- Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, P. R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yaoshun Liu
- Ankang Hospital of Traditional Chinese Medicine, Ankang, Shaanxi, P. R. China
| | - Jianfeng Shi
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Xin Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, P. R. China
| |
Collapse
|
2
|
Turiello R, Nouwairi RL, Landers JP. Taking the microfluidic approach to nucleic acid analysis in forensics: Review and perspectives. Forensic Sci Int Genet 2023; 63:102824. [PMID: 36592574 DOI: 10.1016/j.fsigen.2022.102824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Forensic laboratories are universally acknowledged as being overburdened, underfunded, and in need of improved analytical methods to expedite investigations, decrease the costs associated with nucleic acid (NA) analysis, and perform human identification (HID) at the point of need (e.g., crime scene, booking station, etc.). In response, numerous research and development (R&D) efforts have resulted in microfluidic tools that automate portions of the forensic genetic workflow, including DNA extraction, amplification, and short tandem repeat (STR) typing. By the early 2000 s, reports from the National Institute of Justice (NIJ) anticipated that microfluidic 'swab-in-profile-out' systems would be available for use at the crime scene by 2015 and the FBI's 2010 'Rapid DNA' Initiative, approved by Congress in 2017, directed this effort by guiding the development and implementation of maturing systems. At present, few fully-automated microfluidic DNA technologies are commercially available for forensic HID and their adoption by agencies interested in identification has been limited. In practice, the integration of complex laboratory processes to produce one autonomous unit, along with the highly variable nature of forensic input samples, resulted in systems that are more expensive per sample and not comparable to gold-standard identification methods in terms of sensitivity, reproducibility, and multiplex capability. This Review and Perspective provides insight into the contributing factors to this outcome; namely, we focus on the complications associated with the tremendous undertaking that is developing a sample-in-answer-out platform for HID. For context, we also describe the intricate forensic landscape that contributes to a nuanced marketplace, not easily distilled down to cases of simple supply and demand. Moving forward and considering the trade-offs associated with developing methods to compete, sometimes directly, with conventional ones, we recommend a focus shift for microfluidics developers toward the creation of innovative solutions for emerging applications in the field to increase the bandwidth of the forensic investigative toolkit. Likewise, we urge case working personnel to reframe how they conceptualize the currently available Rapid DNA tools; rather than comparing these microfluidic methods to gold-standard procedures, take advantage of their rapid and integrated modes for those situations requiring expedited identifications in an informed manner.
Collapse
|
3
|
Nouwairi RL, Cunha LL, Turiello R, Scott O, Hickey J, Thomson S, Knowles S, Chapman JD, Landers JP. Ultra-rapid real-time microfluidic RT-PCR instrument for nucleic acid analysis. LAB ON A CHIP 2022; 22:3424-3435. [PMID: 35959772 PMCID: PMC9474628 DOI: 10.1039/d2lc00495j] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The polymerase chain reaction (PCR) is paramount in nucleic acid amplification testing, and for many assays, the use of PCR or qPCR is considered the 'gold standard'. While instrumentation for executing PCR has advanced over the last two decades, a growing interest in point-of-need testing has highlighted the deficit that exists for 'rapid PCR' systems. Here, we describe a field-forward prototype instrument capable of ultra-fast thermal cycling for real-time PCR amplification of DNA and RNA. The custom-designed, injection-molded microfluidic chips interface with a novel mechatronic system to complete 40 cycles of real-time PCR in under 10 minutes, an 84% reduction in time compared to a standard 50 minute assay. Such rapid amplification is enabled by two thermoelectric Peltiers capable of efficiently heating and cooling the sample at 12 and 10 °C s-1, respectively. Judicious selection and strategic placement of the thermal cyclers and fluorescence detector relative to the microchip enable synchronized thermal cycling and fluorescence monitoring, further reducing time-to-result. Robust amplification and detection of DNA and RNA targets empowers laboratories to achieve rapid, actionable information in endless applications.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - James P Landers
- University of Virginia, USA.
- MicroGEM International, PLC, USA
| |
Collapse
|
4
|
Nelson DA, Thompson BL, Scott A, Nouwairi R, Birch C, DuVall JA, Roux DL, Li J, Root BE, Landers JP. Rapid, inexpensive fabrication of electrophoretic microdevices for fluorescence detection. Electrophoresis 2022; 43:1746-1754. [PMID: 35656648 PMCID: PMC9544361 DOI: 10.1002/elps.202200090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel A. Nelson
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | | | - An‐Chi Scott
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | - Renna Nouwairi
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | - Christopher Birch
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | | | - Delphine Le Roux
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | - Jingyi Li
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | - Brian E. Root
- Department of Chemistry University of Virginia Charlottesville Virginia USA
| | - James P. Landers
- Department of Chemistry University of Virginia Charlottesville Virginia USA
- Department of Mechanical Engineering University of Virginia Charlottesville Virginia USA
- Department of Pathology University of Virginia Charlottesville Virginia USA
| |
Collapse
|
5
|
Furutani S, Furutani N, Kawai Y, Nakayama A, Nagai H. Rapid DNA Sequencing Technology Based on the Sanger Method for Bacterial Identification. SENSORS (BASEL, SWITZERLAND) 2022; 22:2130. [PMID: 35336302 PMCID: PMC8955868 DOI: 10.3390/s22062130] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Antimicrobial resistance, a global health concern, has been increasing due to inappropriate use of antibacterial agents. To facilitate early treatment of sepsis, rapid bacterial identification is imperative to determine appropriate antibacterial agent for better therapeutic outcomes. In this study, we developed a rapid PCR method, rapid cycle sequencing, and microchip electrophoresis, which are the three elemental technologies for DNA sequencing based on the Sanger sequencing method, for bacterial identification. We achieved PCR amplification within 13 min and cycle sequencing within 14 min using a rapid thermal cycle system applying microfluidic technology. Furthermore, DNA analysis was completed in 14 min by constructing an algorithm for analyzing and performing microchip electrophoresis. Thus, the three elemental Sanger-based DNA sequencing steps were accomplished within 41 min. Development of a rapid purification process subsequent to PCR and cycle sequence using a microchip would help realize the identification of causative bacterial agents within one hour, and facilitate early treatment of sepsis.
Collapse
Affiliation(s)
- Shunsuke Furutani
- Advanced Photonics and Biosensing Open Innovation Laboratory (Photo-BIO OIL), National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (S.F.); (N.F.)
| | - Nozomi Furutani
- Advanced Photonics and Biosensing Open Innovation Laboratory (Photo-BIO OIL), National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (S.F.); (N.F.)
| | - Yasuyuki Kawai
- Department of Emergency and Critical Care Medicine, Nara Medical University, 840 Shijo, Kashihara 634-8522, Nara, Japan;
| | - Akifumi Nakayama
- Department of Medical Technology, School of Health Sciences, Gifu University of Medical Science, 795-1 Ichihiraga, Seki 501-3892, Gifu, Japan;
| | - Hidenori Nagai
- Advanced Photonics and Biosensing Open Innovation Laboratory (Photo-BIO OIL), National Institute of Advanced Industrial Science and Technology (AIST), 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (S.F.); (N.F.)
| |
Collapse
|
6
|
Robust and easy-to-use microchip electrophoresis within sub-millimeter channels for fast and highly efficient separation. Talanta 2021; 235:122747. [PMID: 34517615 DOI: 10.1016/j.talanta.2021.122747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 11/20/2022]
Abstract
Microchip capillary electrophoresis (MCE) is a powerful technique for rapid separation; however, its acceptance in routine laboratories is still limited. Compromises caused by the efforts for solving different problems, such as reducing its cost of fabrication and ensuring high separation efficiency, undermine the competitiveness of this technology compared to other separation techniques. Contrary to the conventional pursuit of narrow microchannels, this study investigated the suitability of microchips with channels at the sub-millimeter level, targeting the simplification of the overall operation, cost reduction, and robustness improvement. To this effect, we considered the influence of pressurized flow and Joule heating on the separation. The suppression of pressurized flow with viscous solutions was confirmed through a combination of simulations and experimental results, indicating that the buffer viscosity was enough for successful separation. We fabricated channels of 200 μm × 230 μm using computer numerical controlled (CNC) machining and obtained theoretical plate numbers of 4.8 × 105 m-1 and 5.3 × 105 m-1 for fluorescein isothiocyanate (FITC) labeled small molecules and DNA fragments, respectively, with a buffer viscosity of 168 mPa s (0.5 % hydroxypropyl methylcellulose, HPMC). These values are comparable with that of narrow-bore microchips. Furthermore, we did not observe any deleterious effects with low-conductivity buffers. We investigated the rapid and highly sensitive detection of mycoplasma contamination and the real samples of circulating cell-free DNA (cfDNA), which gave a limit of detection (LOD) as low as 2.3 ng mL-1. Owing to the significant reduction in cost, ease of operation, and fast separation capabilities demonstrated in this work, MCE can be a viable alternative to the usual slab gel electrophoresis running in most biological laboratories.
Collapse
|
7
|
Microchip for continuous DNA analysis based on gel electrophoresis coupled with co-injection of size markers and in-channel staining. Anal Bioanal Chem 2021; 413:5685-5694. [PMID: 34345950 DOI: 10.1007/s00216-021-03560-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
A continuous-flow microchip enabling high-accuracy DNA analysis was developed. Serial consecutive analysis for multiple amplified DNA samples was demonstrated. The sample segments were continuously introduced to the microchip from the PCR device which was interfaced to the microchip through capillary tubing. Electrokinetic co-injection of the DNA samples with size marker enabled reproducible and reliable injection of the DNAs into the gel-filled separation channel providing accurate size determination of the DNA samples. Cross-contamination between serially introduced DNA samples was minimized by plugging a washing solution segment following the previous sample segment between two sample plugs. Using this microchip, continuous separation of multiple samples was performed without any inconvenient and labor-intensive sample preparation steps such as sample mixing, staining, and gel loading which are necessary for conventional gel electrophoresis. It has taken about 4 min to separate single DNA sample and taken 37 min for three serially injected samples which implies that this microchip can be a platform device for fast as well as highly accurate DNA analysis.
Collapse
|
8
|
Sun C, Liu L, Vasudevan HN, Chang KC, Abate AR. Accurate Bulk Quantitation of Droplet Digital Polymerase Chain Reaction. Anal Chem 2021; 93:9974-9979. [PMID: 34252272 PMCID: PMC8829825 DOI: 10.1021/acs.analchem.1c00877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Droplet digital PCR
provides superior accuracy for nucleic acid
quantitation. The requirement of microfluidics to generate and analyze
the emulsions, however, is a barrier to its adoption, particularly
in low resource settings or clinical laboratories. Here, we report
a novel method to prepare ddPCR droplets by vortexing and readout
of the results by bulk analysis of recovered amplicons. We demonstrate
the approach by accurately quantitating SARS-CoV-2 sequences using
entirely bulk processing and no microfluidics. Our approach for quantitating
reactions should extend to all digital assays that generate amplicons,
including digital PCR and LAMP conducted in droplets, microchambers,
or nanoliter wells. More broadly, our approach combines important
attributes of ddPCR, including enhanced accuracy and robustness to
inhibition, with the high-volume sample processing ability of quantitative
PCR.
Collapse
Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Harish N Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94158, United States
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| |
Collapse
|
9
|
Bacillus thuringiensis Cells Selectively Captured by Phages and Identified by Surface Enhanced Raman Spectroscopy Technique. MICROMACHINES 2021; 12:mi12020100. [PMID: 33498471 PMCID: PMC7909556 DOI: 10.3390/mi12020100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/11/2022]
Abstract
In this work, the results on the detection and identification of Bacillus thuringiensis (Bt) cells by using surface-enhanced Raman spectroscopy (SERS) are presented. Bt has been chosen as a harmless surrogate of the pathogen Bacillus anthracis (Ba) responsible for the deadly Anthrax disease, because of their genetic similarities. Drops of 200 μL of Bt suspensions, with concentrations 102 CFU/mL, 104 CFU/mL, 106 CFU/mL, were deposited on a SERS chip and sampled after water evaporation. To minimize the contribution to the SERS data given by naturally occurring interferents present in a real scenario, the SERS chip was functionalized with specific phage receptors BtCS33, that bind Bt (or Ba) cells to the SERS surface and allow to rinse the chip removing unwanted contaminants. Different chemometric approaches were applied to the SERS data to classify spectra from Bt-contaminated and uncontaminated areas of the chip: Principal Component Regression (PCR), Partial Least Squares Regression (PLSR) and Data Driven Soft Independent Modeling of Class Analogy (DD-SIMCA). The first two was tested and trained by using data from both contaminated and un-contaminated chips, the last was trained by using data from un-contaminated chips only and tested with all the available data. All of them were able to correctly classify the SERS spectra with great accuracy, the last being suitable for an automated recognition procedure.
Collapse
|
10
|
Sun C, Liu L, Vasudevan HN, Chang KC, Abate AR. Accurate bulk quantitation of droplet digital PCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.13.424628. [PMID: 33469578 PMCID: PMC7814815 DOI: 10.1101/2021.01.13.424628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Droplet digital PCR provides superior accuracy in nucleic acid quantitation. The requirement of microfluidics to generate and analyze the emulsions, however, is a barrier to its adoption, particularly in low resource or clinical settings. Here, we report a novel method to prepare ddPCR droplets by vortexing and readout the results by bulk analysis of recovered amplicons. We demonstrate the approach by accurately quantitating SARS-CoV-2 sequences using entirely bulk processing and no microfluidics. Our approach for quantitating reactions should extend to all digital assays that generate amplicons, including digital PCR and LAMP conducted in droplets, microchambers, or nanoliter wells. More broadly, our approach combines important attributes of ddPCR, including enhanced accuracy and robustness to inhibition, with the high-volume sample processing ability of quantitative PCR.
Collapse
Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Harish N. Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|
11
|
Abstract
Reducing the risk of (cross-)contamination, improving the chain of custody, providing fast analysis times and options of direct analysis at crime scenes: these requirements within forensic DNA analysis can be met upon using microfluidic devices. To become generally applied in forensics, the most important requirements for microfluidic devices are: analysis time, method of DNA detection and biocompatibility of used materials. In this work an overview is provided about biosensing of DNA, by DNA profiling via standard short tandem repeat (STR) analysis or by next generation sequencing. The material of which a forensic microfluidic device is made is crucial: it should for example not inhibit DNA amplification and its thermal conductivity and optical transparency should be suitable for achieving fast analysis. The characteristics of three materials frequently used materials, i.e., glass, silicon and PDMS, are given, in addition to a promising alternative, viz. cyclic olefin copolymer (COC). New experimental findings are presented about the biocompatibility of COC and the use of COC chips for multiple displacement amplification and real-time monitoring of DNA amplification.
Collapse
|
12
|
Chen R, Lu X, Li M, Chen G, Deng Y, Du F, Dong J, Huang X, Cui X, Tang Z. Polymerase Chain Reaction using "V" Shape Thermal Cycling Program. Theranostics 2019; 9:1572-1579. [PMID: 31037124 PMCID: PMC6485190 DOI: 10.7150/thno.31986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/14/2019] [Indexed: 11/05/2022] Open
Abstract
Polymerase chain reaction (PCR) is the most commonly used technique in molecular biology and diagnostics. To achieve faster PCR reaction time, two strategies were employed by previous studies. That includes improving the thermal ramp rate by developing novel devices to reduce the time wasted on temperature transitions and cutting the holding time in every step, which could even lead to compromise in amplification efficiency. Hence the need to further improve the technique. Methods: A different way to achieve fast DNA amplification is developed by using the previously thought wasted time spent on heating and cooling the samples to finish the amplification. That means the holding time of the three procedures are omitted and this could be carried out on the ordinary PCR thermal cyclers. Results: 2/3 of the amplification time is easily saved, compared to the conventionally used method. Additionally, the reaction time could be further reduced by using longer primers with higher melting temperature (Tm). The record time of the "V" shape Polymerase chain reaction (VPCR) conducted on ordinary PCR machine for amplification of a 98 bp fragment is 8 min. Furthermore, VPCR still retains the merits of traditional PCR technique, including specificity, sensitivity, generality, and compatibility with quantitative detection. Conclusion: It is confirmed that the three procedures of PCR could be completed during the dynamic heating and cooling process when the cyclers are run at a moderate thermal ramp rate. As VPCR described here is based on the current PCR system, it could be implemented in any biological Lab immediately and provide great convenience to the people working in the field of life science and human health.
Collapse
|
13
|
Khan M, Mao S, Li W, Lin J. Microfluidic Devices in the Fast‐Growing Domain of Single‐Cell Analysis. Chemistry 2018; 24:15398-15420. [DOI: 10.1002/chem.201800305] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Mashooq Khan
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry, & Chemical Biology Tsinghua University Beijing 100084 China
| | - Sifeng Mao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry, & Chemical Biology Tsinghua University Beijing 100084 China
| | - Weiwei Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry, & Chemical Biology Tsinghua University Beijing 100084 China
| | - Jin‐Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry, & Chemical Biology Tsinghua University Beijing 100084 China
| |
Collapse
|
14
|
Han J, Gan W, Zhuang B, Sun J, Zhao L, Ye J, Liu Y, Li CX, Liu P. A fully integrated microchip system for automated forensic short tandem repeat analysis. Analyst 2018; 142:2004-2012. [PMID: 28513665 DOI: 10.1039/c7an00295e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection. The entire STR analysis can be completed in about two hours without any human intervention. Since the 15-plex STR system has a more stringent requirement for PCR efficiency, we optimized the structure of the plastic DNA extraction and amplification chip, in which the reaction chamber was formed by sandwiching a hollow structure layer with two blank cover layers, to reduce the adsorption of PCR reagents to the surfaces. In addition, PCR additives, bovine serum albumin, poly(ethylene glycol), and more magnesium chloride were included into the on-chip multiplex STR system. The limit-of-detection study demonstrated that our microsystem was able to produce full 15-plex STR profiles from 3.75 ng standard K562 DNA. Buccal swab and whole blood samples were also successfully typed by our system, validating the feasibility of performing rapid DNA typing in a "sample-in-answer-out" manner for on-site forensic human identification.
Collapse
Affiliation(s)
- Junping Han
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Anazawa T, Yamazaki M. An ultra-small, multi-point, and multi-color photo-detection system with high sensitivity and high dynamic range. LAB ON A CHIP 2017; 17:4231-4242. [PMID: 29115316 DOI: 10.1039/c7lc01070b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although multi-point, multi-color fluorescence-detection systems are widely used in various sciences, they would find wider applications if they are miniaturized. Accordingly, an ultra-small, four-emission-point and four-color fluorescence-detection system was developed. Its size (space between emission points and a detection plane) is 15 × 10 × 12 mm, which is three-orders-of-magnitude smaller than that of a conventional system. Fluorescence from four emission points with an interval of 1 mm on the same plane was respectively collimated by four lenses and split into four color fluxes by four dichroic mirrors. Then, a total of sixteen parallel color fluxes were directly input into an image sensor and simultaneously detected. The emission-point plane and the detection plane (the image-sensor surface) were parallel and separated by a distance of only 12 mm. The developed system was applied to four-capillary array electrophoresis and successfully achieved Sanger DNA sequencing. Moreover, compared with a conventional system, the developed system had equivalent high fluorescence-detection sensitivity (lower detection limit of 17 pM dROX) and 1.6-orders-of-magnitude higher dynamic range (4.3 orders of magnitude).
Collapse
|
16
|
Basha IHK, Ho ETW, Yousuff CM, Hamid NHB. Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies. MICROMACHINES 2017; 8:E266. [PMID: 30400456 PMCID: PMC6190060 DOI: 10.3390/mi8090266] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/30/2017] [Accepted: 07/16/2017] [Indexed: 12/21/2022]
Abstract
Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
Collapse
Affiliation(s)
- Ismail Hussain Kamal Basha
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Eric Tatt Wei Ho
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Caffiyar Mohamed Yousuff
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Nor Hisham Bin Hamid
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| |
Collapse
|
17
|
Mao S, Zhang Y, Zhang W, Zeng H, Nakajima H, Lin JM, Uchiyama K. Convection-Diffusion Layer in an “Open Space” for Local Surface Treatment and Microfabrication using a Four-Aperture Microchemical Pen. Chemphyschem 2017; 18:2357-2363. [DOI: 10.1002/cphc.201700577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Sifeng Mao
- Department of Chemistry; Beijing Key Laboratory of Microanalytical Methods and Instrumentation; The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology; Tsinghua University; Beijing 100084 China
- Department of Applied Chemistry; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minamiohsawa Hachioji Tokyo 192-0397 Japan
| | - Yong Zhang
- Department of Applied Chemistry; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minamiohsawa Hachioji Tokyo 192-0397 Japan
| | - Weifei Zhang
- Department of Applied Chemistry; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minamiohsawa Hachioji Tokyo 192-0397 Japan
| | - Hulie Zeng
- Department of Applied Chemistry; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minamiohsawa Hachioji Tokyo 192-0397 Japan
| | - Hizuru Nakajima
- Department of Applied Chemistry; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minamiohsawa Hachioji Tokyo 192-0397 Japan
| | - Jin-Ming Lin
- Department of Chemistry; Beijing Key Laboratory of Microanalytical Methods and Instrumentation; The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology; Tsinghua University; Beijing 100084 China
| | - Katsumi Uchiyama
- Department of Applied Chemistry; Graduate School of Urban Environmental Sciences; Tokyo Metropolitan University; Minamiohsawa Hachioji Tokyo 192-0397 Japan
| |
Collapse
|
18
|
Qin Y, Zhang L, Li S, Zhao J, Huang Y, Zhao S, Liu YM. A microchip electrophoresis-based fluorescence signal amplification strategy for highly sensitive detection of biomolecules. Chem Commun (Camb) 2017; 53:455-458. [PMID: 27966686 DOI: 10.1039/c6cc08911a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have developed a microchip electrophoresis (MCE)-based fluorescence signal amplification strategy as a universal MCE method for the detection of trace biomolecules. This strategy exhibits high sensitivity and specificity for target molecules, and has been applied for the detection of interferon-gamma (IFN-γ) in human plasma with satisfactory results.
Collapse
Affiliation(s)
- Yingfeng Qin
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Shuting Li
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Jingjin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Yong Huang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China.
| | - Yi-Ming Liu
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St., Jackson, MS 39217, USA
| |
Collapse
|
19
|
Anazawa T, Uchiho Y, Yokoi T, Chalkidis G, Yamazaki M. A simple and highly sensitive spectroscopic fluorescence-detection system for multi-channel plastic-microchip electrophoresis based on side-entry laser-beam zigzag irradiation. LAB ON A CHIP 2017; 17:2235-2242. [PMID: 28585967 DOI: 10.1039/c7lc00448f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A five-color fluorescence-detection system for eight-channel plastic-microchip electrophoresis was developed. In the eight channels (with effective electrophoretic lengths of 10 cm), single-stranded DNA fragments were separated (with single-base resolution up to 300 bases within 10 min), and seventeen-loci STR genotyping for forensic human identification was successfully demonstrated. In the system, a side-entry laser beam is passed through the eight channels (eight A channels), with alternately arrayed seven sacrificial channels (seven B channels), by a technique called "side-entry laser-beam zigzag irradiation." Laser-induced fluorescence from the eight A channels and Raman-scattered light from the seven B channels are then simultaneously, uniformly, and spectroscopically detected, in the direction perpendicular to the channel array plane, through a transmission grating and a CCD camera. The system is therefore simple and highly sensitive. Because the microchip is fabricated by plastic-injection molding, it is inexpensive and disposable and thus suitable for actual use in various fields.
Collapse
Affiliation(s)
| | | | | | | | - Motohiro Yamazaki
- Hitachi High-Technologies Corporation, Science & Medical Systems Business Group, Japan
| |
Collapse
|
20
|
Wang Y, Gan N, Zhou Y, Li T, Hu F, Cao Y, Chen Y. Novel label-free and high-throughput microchip electrophoresis platform for multiplex antibiotic residues detection based on aptamer probes and target catalyzed hairpin assembly for signal amplification. Biosens Bioelectron 2017; 97:100-106. [PMID: 28578167 DOI: 10.1016/j.bios.2017.05.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/21/2023]
Abstract
Novel label-free and multiplex aptasensors have been developed for simultaneous detection of several antibiotics based on a microchip electrophoresis (MCE) platform and target catalyzed hairpin assembly (CHA) for signal amplification. Kanamycin (Kana) and oxytetracycline (OTC) were employed as models for testing the system. These aptasensors contained six DNA strands termed as Kana aptamer-catalysis strand (Kana apt-C), Kana inhibit strand (Kana inh), OTC aptamer-catalysis strand (OTC apt-C), OTC inhibit strand (OTC inh), hairpin structures H1 and H2 which were partially complementary. Upon the addition of Kana or OTC, the binding event of aptamer and target triggered the self-assembly between H1 and H2, resulting in the formation of many H1-H2 complexes. They could show strong signals which represented the concentration of Kana or OTC respectively in the MCE system. With the help of the well-designed and high-quality CHA amplification, the assay could yield 300-fold amplified signal comparing that from non-amplified system. Under optimal conditions, this assay exhibited a linear correlation in the ranges from 0.001ngmL-1 to 10ngmL-1, with the detection limits of 0.7pgmL-1 and 0.9pgmL-1 (S/N=3) toward Kana and OTC, respectively. The platform has the following advantages: firstly, the aptamer probes can be fabricated easily without labeling signal tags for MCE detection; Secondly, the targets can just react with probes and produce the amplified signal in one-pot. Finally, the targets can be simultaneously detected within 10min in different channels, thus high-throughput measurement can be achieved. Based on this work, it is estimated that this detection platform will be universally served as a simple, sensitive and portable platform for antibiotic contaminants detection in biological and environmental samples.
Collapse
Affiliation(s)
- Ye Wang
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Ning Gan
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - You Zhou
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Tianhua Li
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Futao Hu
- Faculty of Marine, Ningbo University, Ningbo 315211, China
| | - Yuting Cao
- Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Yinji Chen
- Department of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210000, China
| |
Collapse
|
21
|
Chemiluminescence noncompetitive immunoassay based on microchip electrophoresis for the determination of β-subunit of human chorionic gonadotropin. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1053:42-47. [DOI: 10.1016/j.jchromb.2017.03.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/23/2017] [Accepted: 03/26/2017] [Indexed: 11/15/2022]
|
22
|
Roche PJR, Najih M, Lee SS, Beitel LK, Carnevale ML, Paliouras M, Kirk AG, Trifiro MA. Real time plasmonic qPCR: how fast is ultra-fast? 30 cycles in 54 seconds. Analyst 2017; 142:1746-1755. [PMID: 28443837 DOI: 10.1039/c7an00304h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polymerase Chain Reaction (PCR) is a critical tool for biological research investigators but recently it also has been making a significant impact in clinical, veterinary and agricultural applications. Plasmonic PCR, which employs the very efficient heat transfer of optically irradiated metallic nanoparticles, is a simple and powerful methodology to drive PCR reactions. The scalability of next generation plasmonic PCR technology will introduce various forms of PCR applications ranging from small footprint portable point of care diagnostic devices to large footprint central laboratory multiplexing devices. In a significant advance, we have introduced a real time plasmonic PCR and explored the ability of ultra-fast cycling compatible with both label-free and fluorescence-based monitoring of amplicon production. Furthermore, plasmonic PCR has been substantially optimized to now deliver a 30 cycle PCR in 54 seconds, with a detectable product. The advances described here will have an immediate impact on the further development of the use of plasmonic PCR playing a critical role in rapid point of care diagnostics.
Collapse
Affiliation(s)
- Philip J R Roche
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Mohamed Najih
- Department of Electrical and Computer Engineering, McGill University, Montreal, Quebec, Canada.
| | - Seung S Lee
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Lenore K Beitel
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Matthew L Carnevale
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Miltiadis Paliouras
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada. and Department of Medicine, McGill University, Montreal, QC, Canada
| | - Andrew G Kirk
- Department of Electrical and Computer Engineering, McGill University, Montreal, Quebec, Canada.
| | - Mark A Trifiro
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada. and Department of Medicine, McGill University, Montreal, QC, Canada
| |
Collapse
|
23
|
Han JP, Sun J, Wang L, Liu P, Zhuang B, Zhao L, Liu Y, Li CX. The Optimization of Electrophoresis on a Glass Microfluidic Chip and its Application in Forensic Science. J Forensic Sci 2017; 62:1603-1612. [PMID: 28168694 DOI: 10.1111/1556-4029.13408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 10/23/2016] [Accepted: 11/29/2016] [Indexed: 11/29/2022]
Abstract
Microfluidic chips offer significant speed, cost, and sensitivity advantages, but numerous parameters must be optimized to provide microchip electrophoresis detection. Experiments were conducted to study the factors, including sieving matrices (the concentration and type), surface modification, analysis temperature, and electric field strengths, which all impact the effectiveness of microchip electrophoresis detection of DNA samples. Our results showed that the best resolution for ssDNA was observed using 4.5% w/v (7 M urea) lab-fabricated LPA gel, dynamic wall coating of the microchannel, electrophoresis temperatures between 55 and 60°C, and electrical fields between 350 and 450 V/cm on the microchip-based capillary electrophoresis (μCE) system. One base-pair resolution could be achieved in the 19-cm-length microchannel. Furthermore, both 9947A standard genomic DNA and DNA extracted from blood spots were demonstrated to be successfully separated with well-resolved DNA peaks in 8 min. Therefore, the microchip electrophoresis system demonstrated good potential for rapid forensic DNA analysis.
Collapse
Affiliation(s)
- Jun P Han
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.,Forensic Science and Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, 100102, China
| | - Jing Sun
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Le Wang
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Peng Liu
- Tsinghua University, Beijing, 100084, China
| | - Bin Zhuang
- Tsinghua University, Beijing, 100084, China
| | - Lei Zhao
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Yao Liu
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Cai X Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| |
Collapse
|
24
|
Thompson BL, Birch C, Nelson DA, Li J, DuVall JA, Le Roux D, Tsuei AC, Mills DL, Root BE, Landers JP. A centrifugal microfluidic device with integrated gold leaf electrodes for the electrophoretic separation of DNA. LAB ON A CHIP 2016; 16:4569-4580. [PMID: 27766331 DOI: 10.1039/c6lc00953k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Current conventional methods utilized for forensic DNA analysis are time consuming and labor-intensive requiring large and expensive equipment and instrumentation. While more portable Rapid DNA systems have been developed, introducing them to a working laboratory still necessitates a high cost of initiation followed by the recurrent cost of the devices. This has highlighted the need for an inexpensive, rapid and portable DNA analysis tool for human identification in a forensic setting. In order for an integrated DNA analysis system such as this to be realized, device operations must always be concluded by a rapid separation of short-tandem repeat (STR) DNA fragments. Contributing to this, we report the development of a unique, multi-level, centrifugal microdevice that can perform both reagent loading and DNA separation. The fabrication protocol was inspired by the print, cut and laminate (PCL) technique described previously by our group, and in accordance, offers a rapid and inexpensive option compared with existing approaches. The device comprises multiple polyester-toner fluidic layers, a cyclic olefin copolymer separation domain and integrated gold leaf electrodes. All materials are commercially-available and complement the PCL process in a way that permits fabrication of increasingly sought after single-use devices. All reagents, including a viscous sieving matrix, are loaded centrifugally, eliminating external pneumatic pumping, and the sample is separated in <5 minutes using an effective separation length of only 4 cm (reagent loading to completed separation, is <37 minutes). The protocol for gold leaf electrode manufacture yielded up to 30 electrodes for less than $3 (cost of a 79 mm × 79 mm gold leaf sheet) and when using a device combining these electrodes and centrifugal reagent/polymer loading, the electrophoretic separation of STR fragments with two base resolution was demonstrated. This exemplary performance makes the device an ideal candidate for further integration and development of an inexpensive, portable and rapid forensic human identification system.
Collapse
Affiliation(s)
- Brandon L Thompson
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Christopher Birch
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Daniel A Nelson
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Jingyi Li
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Jacquelyn A DuVall
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Delphine Le Roux
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - An-Chi Tsuei
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | | | - Brian E Root
- Applied Research Institute, University of Virginia, Charlottesville, VA 22904, USA
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA. and Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22904, USA and Department of Pathology, University of Virginia, Charlottesville, VA 22904, USA
| |
Collapse
|
25
|
Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
Collapse
Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
| |
Collapse
|
26
|
Microfluidic Devices for Forensic DNA Analysis: A Review. BIOSENSORS-BASEL 2016; 6:bios6030041. [PMID: 27527231 PMCID: PMC5039660 DOI: 10.3390/bios6030041] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/07/2016] [Accepted: 07/25/2016] [Indexed: 12/16/2022]
Abstract
Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10–20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.
Collapse
|
27
|
The μSCAPE System: 3-Dimensional Profiling of Microfluidic Architectural Features Using a Flatbed Scanner. Sci Rep 2016; 6:22246. [PMID: 26924294 PMCID: PMC4770298 DOI: 10.1038/srep22246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 12/16/2022] Open
Abstract
We developed a microfluidic scanner-based profile exploration system, μSCAPE, capable of generating high resolution 3D profiles of microstructure architecture in a variety of transparent substrates. The profile is obtained by scanning the dye-filled microstructure followed by absorbance calculation and the reconstruction of the optical length at each point. The power of the method was demonstrated in (1) the inspection of the variation of the cross-section of laser-ablated PDMS channel; (2) the volume of PeT chamber; and (3) the population distribution of the volumes of the micro wells in HF-etched glass and laser-ablated PDMS. The reported methods features low equipment-cost, convenient operation and large field of view (FOV), and has revealed unreported quality parameters of the tested microstructures.
Collapse
|
28
|
Zhuang B, Han J, Xiang G, Gan W, Wang S, Wang D, Wang L, Sun J, Li CX, Liu P. A fully integrated and automated microsystem for rapid pharmacogenetic typing of multiple warfarin-related single-nucleotide polymorphisms. LAB ON A CHIP 2016; 16:86-95. [PMID: 26568290 DOI: 10.1039/c5lc01094b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A fully integrated and automated microsystem consisting of low-cost, disposable plastic chips for DNA extraction and PCR amplification combined with a reusable glass capillary array electrophoresis chip in a modular-based format was successfully developed for warfarin pharmacogenetic testing. DNA extraction was performed by adopting a filter paper-based method, followed by "in situ" PCR that was carried out directly in the same reaction chamber of the chip without elution. PCR products were then co-injected with sizing standards into separation channels for detection using a novel injection electrode. The entire process was automatically conducted on a custom-made compact control and detection instrument. The limit of detection of the microsystem for the singleplex amplification of amelogenin was determined to be 0.625 ng of standard K562 DNA and 0.3 μL of human whole blood. A two-color multiplex allele-specific PCR assay for detecting the warfarin-related single-nucleotide polymorphisms (SNPs) 6853 (-1639G>A) and 6484 (1173C>T) in the VKORC1 gene and the *3 SNP (1075A>C) in the CYP2C9 gene was developed and used for validation studies. The fully automated genetic analysis was completed in two hours with a minimum requirement of 0.5 μL of input blood. Samples from patients with different genotypes were all accurately analyzed. In addition, both dried bloodstains and oral swabs were successfully processed by the microsystem with a simple modification to the DNA extraction and amplification chip. The successful development and operation of this microsystem establish the feasibility of rapid warfarin pharmacogenetic testing in routine clinical practice.
Collapse
Affiliation(s)
- Bin Zhuang
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China. and CapitalBio Corporation, Beijing, 102206, China
| | - Junping Han
- Chinese People's Public Security University, Beijing, 100038, China
| | - Guangxin Xiang
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China. and CapitalBio Corporation, Beijing, 102206, China
| | - Wupeng Gan
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China. and CapitalBio Corporation, Beijing, 102206, China
| | - Shuaiqin Wang
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Dong Wang
- CapitalBio Corporation, Beijing, 102206, China and National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, China
| | - Lei Wang
- CapitalBio Corporation, Beijing, 102206, China and National Engineering Research Center for Beijing Biochip Technology, Beijing, 102206, China
| | - Jing Sun
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Cai-Xia Li
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Peng Liu
- Department of Biomedical Engineering, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
29
|
Affiliation(s)
- Sanjin Hosic
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Shashi K. Murthy
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA
| | - Abigail N. Koppes
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| |
Collapse
|
30
|
Romsos EL, Vallone PM. Rapid PCR of STR markers: Applications to human identification. Forensic Sci Int Genet 2015; 18:90-9. [DOI: 10.1016/j.fsigen.2015.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/03/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
|
31
|
Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
Collapse
Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | | | | |
Collapse
|
32
|
Le Roux D, Root BE, Hickey JA, Scott ON, Tsuei A, Li J, Saul DJ, Chassagne L, Landers JP, de Mazancourt P. An integrated sample-in-answer-out microfluidic chip for rapid human identification by STR analysis. LAB ON A CHIP 2014; 14:4415-4425. [PMID: 25248520 DOI: 10.1039/c4lc00685b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A fully integrated microfluidic chip for human identification by short tandem repeat (STR) analysis that includes a unique enzymatic liquid preparation of the DNA, microliter non-contact PCR, and a polymer that allows a high-resolution separation within a compact microchip footprint has been developed. A heat-activated enzyme that digests biological materials is employed to generate the target yield of DNA from a buccal swab or FTA paper. The microfluidic architecture meters an aliquot of the liberated DNA and mixes it with the PCR reagents prior to non-contact IR-mediated PCR amplification. The products of PCR amplification are mixed with a sizing standard (ladder) and the 18-plex STR amplicons are separated in an effective length (Leff) of just 7 cm. The development, optimization and integration of each of these processes within the microfluidic chip are described. The device is able to generate genetic profiles in approximately 2 hours that match the profiles from the conventional processes performed using separate conventional instruments. Analysis is performed on a single plastic microchip with a size similar to that of a 96-well plate and only a few mm thick with no pretreatment of any of the functional domains. This is significant advancement in terms of ease of fabrication over glass microdevices or polymeric systems assembled from multiple components. Consequently, this fully integrated sample-in-answer-out microchip is an important step toward generation of a rapid micro-total analysis system for point-of-collection human identification based on genetic analysis.
Collapse
Affiliation(s)
- Delphine Le Roux
- Versailles - Saint Quentin en Yvelines University, 55 Avenue de Paris, 78000 Versailles, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|