1
|
Bruijns B, Knotter J, Tiggelaar R. A Systematic Review on Commercially Available Integrated Systems for Forensic DNA Analysis. SENSORS (BASEL, SWITZERLAND) 2023; 23:1075. [PMID: 36772114 PMCID: PMC9919030 DOI: 10.3390/s23031075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of aspects, such as performance, time-to-result, ease-of-use, portability, and costs (per analysis run) of these three (modified) rapid DNA analysis systems, are considered. Despite their advantages and developmental progress, major steps still have to be made before rapid systems can be broadly applied at crime scenes for full DNA profiling. Aspects in particular that need (further) improvement are portability, performance, the possibility to analyze a (wider) variety of (complex) forensic samples, and (cartridge) costs. Moreover, steps forward regarding ease-of-use and time-to-result will benefit the broader use of commercial rapid DNA systems. In fact, it would be a profit if rapid DNA systems could be used for full DNA profile generation as well as indicative analyses that can give direction to forensic investigators which will speed up investigations.
Collapse
Affiliation(s)
- Brigitte Bruijns
- Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H. Tromplaan 28, 7513 AB Enschede, The Netherlands
- Politieacademie, Arnhemseweg 348, 7334 AC Apeldoorn, The Netherlands
| | - Jaap Knotter
- Technologies for Criminal Investigations, Saxion University of Applied Sciences, M.H. Tromplaan 28, 7513 AB Enschede, The Netherlands
- Politieacademie, Arnhemseweg 348, 7334 AC Apeldoorn, The Netherlands
| | - Roald Tiggelaar
- NanoLab Cleanroom, MESA+ Institute, University of Twente, Drienerlolaan 5, 7500 AE Enschede, The Netherlands
| |
Collapse
|
2
|
Yang J, Kidd M, Nordquist AR, Smith SD, Hurth C, Modlin IM, Zenhausern F. A Sensitive, Portable Microfluidic Device for SARS-CoV-2 Detection from Self-Collected Saliva. Infect Dis Rep 2021; 13:1061-1077. [PMID: 34940407 PMCID: PMC8701218 DOI: 10.3390/idr13040097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Since the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in December 2019, the spread of SARS-CoV2 infection has been escalating rapidly around the world. In order to provide more timely access to medical intervention, including diagnostic tests and medical treatment, the FDA authorized multiple test protocols for diagnostic tests from nasopharyngeal swab, saliva, urine, bronchoalveolar lavage and fecal samples. The traditional diagnostic tests for this novel coronavirus 2019 require standard processes of viral RNA isolation, reverse transcription of RNA to cDNA, then real-time quantitative PCR with the RNA templates extracted from the patient samples. Recently, many reports have demonstrated a direct detection of SARS-Co-V2 genomic material from saliva samples without any RNA isolation step. To make the rapid detection of SARS-Co-V2 infection more accessible, a point-of-care type device was developed for SARS-CoV-2 detection. Herein, we report a portable microfluidic-based integrated detection-analysis system for SARS-CoV-2 nucleic acids detection directly from saliva samples. The saliva cartridge is self-contained and capable of microfluidic evaluation of saliva, from heating, mixing with the primers to multiplex real-time quantitative polymerase chain reaction, detecting SARS-CoV-2 with different primer sets and internal control. The approach has a detection sensitivity of 1000 copies/mL of SARS-CoV-2 RNA or virus, with consistency and automation, from saliva sample-in to result-out.
Collapse
Affiliation(s)
- Jianing Yang
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Mark Kidd
- WREN Laboratories, Branford, CT 06405, USA; (M.K.); (I.M.M.)
| | - Alan R. Nordquist
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Stanley D. Smith
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Cedric Hurth
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| | - Irvin M. Modlin
- WREN Laboratories, Branford, CT 06405, USA; (M.K.); (I.M.M.)
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA; (A.R.N.); (S.D.S.); (C.H.)
| |
Collapse
|
3
|
Yang J, Hurth C, Nordquist A, Smith S, Zenhausern F. Integrated Microfluidic System for Rapid DNA Fingerprint Analysis: A Miniaturized Integrated DNA Analysis System (MiDAS)-Swab Sample-In to DNA Profile-Out. Methods Mol Biol 2019; 1906:207-224. [PMID: 30488395 DOI: 10.1007/978-1-4939-8964-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A fully automated rapid DNA analysis system requires integrating several operational elements performing multiple steps onto one single microfluidic platform. The functions to include on the microfluidic platform consist of substrate lysis, lysate DNA extraction, single or multiplexed PCR amplification, amplicon separation, and product readout. Here we describe a fully automated integrated system for forensic short tandem repeat (STR) analysis of reference samples, achieving buccal swab-in and DNA profile-out.
Collapse
Affiliation(s)
- Jianing Yang
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
| | - Cedric Hurth
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Alan Nordquist
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Stan Smith
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| |
Collapse
|
4
|
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
|
5
|
Kim YT, Heo HY, Oh SH, Lee SH, Kim DH, Seo TS. Microchip-based forensic short tandem repeat genotyping. Electrophoresis 2015; 36:1728-37. [DOI: 10.1002/elps.201400477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 03/06/2015] [Accepted: 04/20/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyun Young Heo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Shin Hye Oh
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Seung Hwan Lee
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Do Hyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| |
Collapse
|
6
|
A miniature quantitative PCR device for directly monitoring a sample processing on a microfluidic rapid DNA system. Biomed Microdevices 2015; 16:905-14. [PMID: 25106501 DOI: 10.1007/s10544-014-9895-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We report a microfluidic device and measurement method to perform real-time PCR (or qPCR) in a miniaturized configuration for on-chip implementation using reaction volumes of less than 20 μL. The qPCR bioreactor is designed as a module to be embedded in an automated sample-in/profile-out system for rapid DNA biometrics or human identification. The PCR mixture is excited with a 505 nm diode-pumped solid-state laser (DPSSL) and the fluorescence build-up is measured using optical fibers directly embedded to the sidewalls of the microfluidic qPCR bioreactor. We discuss manufacturing and operating parameters necessary to adjust the internal surface conditions and temperature profiles of the bioreactor and to optimize the yield and quality of the PCR reaction for the amplification of 62 bp hTERT intron fragments using the commercial Quantifiler® kit (Life Technologies, Carlsbad, CA) commonly accepted for genotyping analysis. We designed a microfluidic device suitable for continuously processing a specimen by efficiently mixing the reagents from the kit to a set volume of DNA template on chip. Our approach relies on a calibration curve for the specific device using control DNA. We successfully applied this method to determine the concentration of genomic DNA extracted from a buccal swab on separate microfluidic devices which are operated upstream the qPCR device and perform buccal swab lysis and buccal DNA extraction. A precise correlation between the amount determined on chip and that obtained using a commercial cycler is demonstrated.
Collapse
|
7
|
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: 46] [Impact Index Per Article: 5.1] [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
|
8
|
Neužil P, Campos CDM, Wong CC, Soon JBW, Reboud J, Manz A. From chip-in-a-lab to lab-on-a-chip: towards a single handheld electronic system for multiple application-specific lab-on-a-chip (ASLOC). LAB ON A CHIP 2014; 14:2168-2176. [PMID: 24828468 DOI: 10.1039/c4lc00310a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present a portable, battery-operated and application-specific lab-on-a-chip (ASLOC) system that can be easily configured for a wide range of lab-on-a-chip applications. It is based on multiplexed electrical current detection that serves as the sensing system. We demonstrate different configurations to perform most detection schemes currently in use in LOC systems, including some of the most advanced such as nanowire-based biosensing, surface plasmon resonance sensing, electrochemical detection and real-time PCR. The complete system is controlled by a single chip and the collected information is stored in situ, with the option of transferring the data to an external display by using a USB interface. In addition to providing a framework for truly portable real-life developments of LOC systems, we envisage that this system will have a significant impact on education, especially since it can easily demonstrate the benefits of integrated microanalytical systems.
Collapse
Affiliation(s)
- P Neužil
- KIST Europe Forschungsgesellschaft mbH, Campus E7 1, DE-66 123 Saarbrücken, Germany.
| | | | | | | | | | | |
Collapse
|