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Lee SM, Balakrishnan HK, Doeven EH, Yuan D, Guijt RM. Chemical Trends in Sample Preparation for Nucleic Acid Amplification Testing (NAAT): A Review. BIOSENSORS 2023; 13:980. [PMID: 37998155 PMCID: PMC10669371 DOI: 10.3390/bios13110980] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
Nucleic acid amplification testing facilitates the detection of disease through specific genomic sequences and is attractive for point-of-need testing (PONT); in particular, the early detection of microorganisms can alert early response systems to protect the public and ecosystems from widespread outbreaks of biological threats, including infectious diseases. Prior to nucleic acid amplification and detection, extensive sample preparation techniques are required to free nucleic acids and extract them from the sample matrix. Sample preparation is critical to maximize the sensitivity and reliability of testing. As the enzymatic amplification reactions can be sensitive to inhibitors from the sample, as well as from chemicals used for lysis and extraction, avoiding inhibition is a significant challenge, particularly when minimising liquid handling steps is also desirable for the translation of the assay to a portable format for PONT. The reagents used in sample preparation for nucleic acid testing, covering lysis and NA extraction (binding, washing, and elution), are reviewed with a focus on their suitability for use in PONT.
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Affiliation(s)
- Soo Min Lee
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
| | - Hari Kalathil Balakrishnan
- Department of Chemical Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Egan H. Doeven
- School of Life and Environmental Sciences, Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia;
| | - Dan Yuan
- School of Mechanical and Mining Engineering, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Rosanne M. Guijt
- Centre for Regional and Rural Futures (CeRRF), Deakin University, Locked Bag 20000, Geelong, VIC 3220, Australia
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2
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Li C, McCrone S, Warrick JW, Andes DR, Hite Z, Volk CF, Rose WE, Beebe DJ. Under-oil open microfluidic systems for rapid phenotypic antimicrobial susceptibility testing. LAB ON A CHIP 2023; 23:2005-2015. [PMID: 36883560 PMCID: PMC10581760 DOI: 10.1039/d3lc00066d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Antimicrobial susceptibility testing (AST) remains the cornerstone of effective antimicrobial selection and optimization in patients. Despite recent advances in rapid pathogen identification and resistance marker detection with molecular diagnostics (e.g., qPCR, MALDI-TOF MS), phenotypic (i.e., microbial culture-based) AST methods - the gold standard in hospitals/clinics - remain relatively unchanged over the last few decades. Microfluidics-based phenotypic AST has been growing fast in recent years, aiming for rapid (i.e., turnaround time <8 h), high-throughput, and automated species identification, resistance detection, and antibiotics screening. In this pilot study, we describe the application of a multi-liquid-phase open microfluidic system, named under-oil open microfluidic systems (UOMS), to achieve a rapid phenotypic AST. UOMS provides an open microfluidics-based solution for rapid phenotypic AST (UOMS-AST) by implementing and recording a pathogen's antimicrobial activity in micro-volume testing units under an oil overlay. UOMS-AST allows free physical access (e.g., by standard pipetting) to the system and label-free, single-cell resolution optical access. UOMS-AST can accurately and rapidly determine antimicrobial activities [including susceptibility/resistance breakpoint and minimum inhibitory concentration (MIC)] from nominal sample/bacterial cells in a system aligned with clinical laboratory standards where open systems and optical microscopy are predominantly adopted. Further, we combine UOMS-AST with a cloud lab data analytic technique for real-time image analysis and report generation to provide a rapid (<4 h) sample-to-report turnaround time, shedding light on its utility as a versatile (e.g., low-resource setting and manual laboratory operation, or high-throughput automated system) phenotypic AST platform for hospital/clinic use.
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Affiliation(s)
- Chao Li
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sue McCrone
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jay W. Warrick
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David R. Andes
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary Hite
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cecilia F. Volk
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Warren E. Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Beebe
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
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3
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Juang DS, Juang TD, Dudley DM, Newman CM, Accola MA, Rehrauer WM, Friedrich TC, O'Connor DH, Beebe DJ. Oil immersed lossless total analysis system for integrated RNA extraction and detection of SARS-CoV-2. Nat Commun 2021; 12:4317. [PMID: 34262053 PMCID: PMC8280165 DOI: 10.1038/s41467-021-24463-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic exposed difficulties in scaling current quantitative PCR (qPCR)-based diagnostic methodologies for large-scale infectious disease testing. Bottlenecks include lengthy multi-step processes for nucleic acid extraction followed by qPCR readouts, which require costly instrumentation and infrastructure, as well as reagent and plastic consumable shortages stemming from supply chain constraints. Here we report an Oil Immersed Lossless Total Analysis System (OIL-TAS), which integrates RNA extraction and detection onto a single device that is simple, rapid, cost effective, and requires minimal supplies and infrastructure to perform. We validated the performance of OIL-TAS using contrived SARS-CoV-2 viral particle samples and clinical nasopharyngeal swab samples. OIL-TAS showed a 93% positive predictive agreement (n = 57) and 100% negative predictive agreement (n = 10) with clinical SARS-CoV-2 qPCR assays in testing clinical samples, highlighting its potential to be a faster, cheaper, and easier-to-deploy alternative for infectious disease testing. Bottlenecks in qPCR-based COVID-19 diagnostics include the lengthy multistep process and reagent shortages. Here the authors report OIL-TAS which integrates RNA extraction and detection into a single device.
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Affiliation(s)
- Duane S Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Terry D Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Christina M Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - William M Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI, USA
| | - Thomas C Friedrich
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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4
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Lin Q, Huang Z, Ye X, Yang B, Fang X, Liu B, Chen H, Kong J. Lab in a tube: Isolation, extraction, and isothermal amplification detection of exosomal long noncoding RNA of gastric cancer. Talanta 2021; 225:122090. [PMID: 33592799 DOI: 10.1016/j.talanta.2021.122090] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 12/19/2022]
Abstract
Tumor-derived exosomes that inherit molecular information on parental cells hold great promise for cancer diagnostics. Currently, two main technical challenges, time-consuming and labor-intensive isolation of exosome and nucleic acid extraction with limited recovery that have restricted the detection of ultralow abundance exosomal nucleic acids. Here, we proposed a simple, efficient and "lab in a tube" system for the detection of exosomal nucleic acids, which fully integrated exosomes enrichment using immunomagnetic beads (IMB) (10 min), fast exosomes lysis based on NP-40 lysate (5 min) and sensitive loop-mediated isothermal amplification (LAMP) in a tube. This method was demonstrated by detecting two exosomal long noncoding RNA biomarkers of gastric cancer (HOTTIP and lncRNA-GC1) with a dynamic detection ranging from 300 ng/μL to 10 ng/μL, and the detection limit of LAMP was 10 ng/μL. Additionally, this platform exhibited good performance in the analysis of exosomal HOTTIP RNA directly in human serum samples, which has the potential for detection of low-abundance exosomal nucleic acid biomarkers from cancers.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China
| | - Zhipeng Huang
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China
| | - Xin Ye
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China
| | - Bin Yang
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China
| | - Baohong Liu
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China; Shanghai Stomatological Hospital, Shanghai, 200438, PR China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China.
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, PR China.
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Ohashi T, Kuyama H. Magnetic particle transport through organogel - an application to DNA extraction. Anal Biochem 2020; 611:113932. [PMID: 32891594 DOI: 10.1016/j.ab.2020.113932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/23/2022]
Abstract
An observation that magnetic particles are transported through organogel encouraged us to investigate its feasibility of liquid-phase displacement in DNA extraction using magnetic particles. Organogel for this study was prepared from a gelator, 12-hydroxystearic acid (12-HSA), and an apolar solvent, methylphenylsilicone oil. The organogel is a gel-like solid material with hydrophobic and elastic properties. These properties, hydrophobicity, and elasticity were demonstrated to be advantageous for liquid compartmentalization and efficient liquid-phase displacement. The extracted DNA with using the organogel device was successfully detected off-chip by conventional real-time PCR.
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Affiliation(s)
- Tetsuo Ohashi
- Technology Research Laboratory, Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto, 619-0237, Japan.
| | - Hiroki Kuyama
- Technology Research Laboratory, Shimadzu Corporation, 3-9-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto, 619-0237, Japan
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6
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Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Emaus MN, Anderson JL. Allelic discrimination between circulating tumor DNA fragments enabled by a multiplex-qPCR assay containing DNA-enriched magnetic ionic liquids. Anal Chim Acta 2020; 1124:184-193. [PMID: 32534671 DOI: 10.1016/j.aca.2020.04.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/24/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Multiplex amplification of DNA can be highly valuable in circulating tumor DNA (ctDNA) analysis due to the sheer number of potential mutations. However, commercial ctDNA extraction methods struggle to preconcentrate low concentrations of DNA and require multiple sample handling steps. Recently, magnetic ionic liquids (MILs) have been used to extract DNA and were integrated with a quantitative polymerase chain reaction (qPCR). However, in previous studies, DNA could not be preconcentrated from plasma and only one fragment could be amplified per reaction. In this study, MILs were utilized as DNA extraction solvents and directly integrated into a multiplex-qPCR buffer to simultaneously amplify wild-type KRAS, G12S KRAS, and wild-type BRAF, three clinically-relevant genes whose mutation status can affect the success of anti-EGFR therapy. DNA was desorbed from the MIL solvent during a multiplex-PCR without having a significant effect on the amplification efficiency, and allelic discrimination of single-nucleotide polymorphisms could still be achieved. Enrichment factors over 35 for all three sequences were achieved from Tris buffer using the [N8,8,8,Bz+][Ni(hfacac)3-]) and [P6,6,6,14+][Ni(Phtfacac)3-] MILs. DNA could still be preconcentrated from 2-fold diluted human plasma using the [N8,8,8,Bz+][Ni(hfacac)3-] MIL. Extractions from undiluted plasma were reproducible with the [P6,6,6,14+][Ni(Phtfacac)3-] MIL although DNA was not preconcentrated with enrichment factors around 0.6 for all three fragments. Compared to commercial DNA extraction methods (i.e., silica-based spin columns and magnetic beads), the MIL-based extraction achieved higher enrichment factors in Tris buffer and plasma. The ability of the MIL-based dispersive liquid-liquid microextraction (DLLME) direct-multiplex-qPCR method to simultaneously achieve high enrichment factors of multiple DNA fragments from human plasma is highly promising in the field of ctDNA detection.
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Affiliation(s)
- Miranda N Emaus
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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