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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.
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2
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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.
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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
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3
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Ren ZL, Zhang JR, Zhang XM, Liu X, Lin YF, Bai H, Wang MC, Cheng F, Liu JD, Li P, Kong L, Bo XC, Wang SQ, Ni M, Yan JW. Forensic nanopore sequencing of STRs and SNPs using Verogen's ForenSeq DNA Signature Prep Kit and MinION. Int J Legal Med 2021; 135:1685-1693. [PMID: 33950286 PMCID: PMC8098014 DOI: 10.1007/s00414-021-02604-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/14/2021] [Indexed: 11/17/2022]
Abstract
The MinION nanopore sequencing device (Oxford Nanopore Technologies, Oxford, UK) is the smallest commercially available sequencer and can be used outside of conventional laboratories. The use of the MinION for forensic applications, however, is hindered by the high error rate of nanopore sequencing. One approach to solving this problem is to identify forensic genetic markers that can consistently be typed correctly based on nanopore sequencing. In this pilot study, we explored the use of nanopore sequencing for single nucleotide polymorphism (SNP) and short tandem repeat (STR) profiling using Verogen’s (San Diego, CA, USA) ForenSeq DNA Signature Prep Kit. Thirty single-contributor samples and DNA standard material 2800 M were genotyped using the Illumina (San Diego, CA, USA) MiSeq FGx and MinION (with R9.4.1 flow cells) devices. With an optimized cutoff for allelic imbalance, all 94 identity-informative SNP loci could be genotyped reliably using the MinION device, with an overall accuracy of 99.958% (1 error among 2926 genotypes). STR typing was notably error prone, and its accuracy was locus dependent. We developed a custom-made bioinformatics workflow, and finally selected 13 autosomal STRs, 14 Y-STRs, and 4 X-STRs showing high consistency between nanopore and Illumina sequencing among the tested samples. These SNP and STR loci could be candidates for panel design for forensic analysis based on nanopore sequencing.
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Affiliation(s)
- Zi-Lin Ren
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Jia-Rong Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Xiao-Meng Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Xu Liu
- Beijing Center for Physical and Chemical Analysis, Beijing, 100089, People's Republic of China
| | - Yan-Feng Lin
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Hua Bai
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Meng-Chun Wang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Jin-Ding Liu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Peng Li
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Lei Kong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Xiao-Chen Bo
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Sheng-Qi Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Jiang-Wei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China.
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4
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Schayek H, Waiskopf O, Rashkovski K, Amiel M, Wolf E, Avlas O. Concordance testing between Powerplex ESI 16 Fast System and VeriFiler Express. J Forensic Sci 2020; 66:1013-1016. [PMID: 33315267 DOI: 10.1111/1556-4029.14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
DNA profiles generated by different STR kits may show different alleles for identical amplified loci. This well-known phenomenon affects the smooth transition of data generated by new STR kits to a database or casework laboratory or cross-laboratory comparison of STR profiles. As in other DNA databases throughout the world, it has become clear that the number of the analyzed loci should be expanded for a variety of reasons, such as partial profiles resulting from low copy-number DNA template or degraded samples, working with mixtures or when prevalence of familial inbreeding. In the course of introducing a new STR kit, VeriFiler™ Express (Applied Biosystems, Foster City, CA, USA), we compared genotyping data of 1568 samples amplified by the VeriFiler™ Express with the data generated on the same samples by the Powerplex™ ESI FAST (Promega, Madison WI, USA) kit. Discordance was noted in 20 samples (1.27%), 14 (0.89%) of them showing allele dropout mismatch and six (0.38%) showing an additional fixed-size third allele. These rates are well above the reported rates of 0.4% for this kit. Since correct genotyping and accurate consistent allele assignment is of paramount importance, it seems timely to recommend for DNA laboratories and genetic-match search systems to take these possible inconsistencies into account.
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Affiliation(s)
- Hagit Schayek
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Ortal Waiskopf
- DNA and Biology Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Ksenia Rashkovski
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Merav Amiel
- DNA and Biology Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Ehud Wolf
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
| | - Orna Avlas
- DNA Database Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, Jerusalem, Israel
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5
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Li M, Tao R, Zhou W, Li Y, Meng M, Zhang Y, Yu L, Chen L, Bian Y, Li C. Validation studies of the ParaDNA ® Intelligence System with artificial evidence items. Forensic Sci Res 2019; 6:84-91. [PMID: 34007520 PMCID: PMC8110186 DOI: 10.1080/20961790.2019.1665159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Short tandem repeat (STR) profiling is one of the mostly used systems for forensic applications. In certain circumstances, STR profiling is time-consuming and costly, which potentially leads to delays in criminal investigations. LGC (Laboratory of the Government Chemist, UK) Forensics has developed a robust STR profiling platform called the ParaDNA® Intelligence Test System which can provide early tactical intelligence and aid investigators in making informed decisions on sample prioritization for detection. Here, we validated the ParaDNA intelligence test for its application in forensic cases using a range of mock evidence items following guidelines set by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Specifically, we tested the sensitivity and accuracy of the ParaDNA intelligence test, as well as the success rates for detecting mock samples and for use in case scenarios. Our findings demonstrate that the ParaDNA intelligence test generates useful DNA profiles, especially for samples such as blood, saliva, and semen that contain ample DNA, indicating the benefits of including ParaDNA as a prior step in forensic STR profiling pipelines.
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Affiliation(s)
- Min Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China
| | - Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China
| | - Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yanan Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,Department of Forensic Medical, School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, China
| | - Meng Meng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,Department of Histology and Embryology, Harbin Medical University, Harbin, China
| | - Yilun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,School of Basic Medicine, Baotou Medical College, Baotou, China
| | - Linsheng Yu
- Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, China
| | - Liqin Chen
- School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China.,Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, China
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6
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Cornelis S, Tytgat O, Fauvart M, Gansemans Y, Vander Plaetsen AS, Wiederkehr RS, Deforce D, Van Nieuwerburgh F, Stakenborg T. Silicon µPCR Chip for Forensic STR Profiling with Hybeacon Probe Melting Curves. Sci Rep 2019; 9:7341. [PMID: 31089203 PMCID: PMC6517373 DOI: 10.1038/s41598-019-43946-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 11/09/2022] Open
Abstract
The demand to perform forensic DNA profiling outside of centralized laboratories and on the crime scene is increasing. Several criminal investigations would benefit tremendously from having DNA based information available in the first hours rather than days or weeks. However, due to the complexity and time-consuming nature of standard DNA fingerprinting methods, rapid and automated analyses are hard to achieve. We here demonstrate the implementation of an alternative DNA fingerprinting method in a single microchip. By combining PCR amplification and HyBeacon melting assays in a silicon Lab-on-a-chip (LoC), a significant step towards rapid on-site DNA fingerprinting is taken. The small form factor of a LoC reduces reagent consumption and increases portability. Additional miniaturization is achieved through an integrated heating element covering 24 parallel micro-reactors with a reaction volume of 0.14 µl each. The high level of parallelization allows the simultaneous analysis of 4 short tandem repeat (STR) loci and the amelogenin gender marker commonly included in forensic DNA analysis. A reference and crime scene sample can be analyzed simultaneously for direct comparison. Importantly, by using industry-standard semiconductor manufacturing processes, mass manufacturability can be guaranteed. Following assay design and optimization, complete 5-loci profiles could be robustly generated on-chip that are on par with those obtained using conventional benchtop real-time PCR thermal cyclers. Together, our results are an important step towards the development of commercial, mass-produced, portable devices for on-site testing in forensic DNA analysis.
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Affiliation(s)
- Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Maarten Fauvart
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium
| | | | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Gent, Belgium.
| | | | - Tim Stakenborg
- Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
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7
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Lynch C, Fleming R. A review of direct polymerase chain reaction of DNA and RNA for forensic purposes. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Courtney Lynch
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
- School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
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8
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Morrison J, Watts G, Hobbs G, Dawnay N. Field-based detection of biological samples for forensic analysis: Established techniques, novel tools, and future innovations. Forensic Sci Int 2018. [DOI: 10.1016/j.forsciint.2018.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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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.
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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
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10
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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.
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11
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Dawnay N, Hughes R, Court DS, Duxbury N. Species detection using HyBeacon(®) probe technology: Working towards rapid onsite testing in non-human forensic and food authentication applications. Forensic Sci Int Genet 2015; 20:103-111. [PMID: 26561743 DOI: 10.1016/j.fsigen.2015.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 10/05/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Identifying individual species or determining species' composition in an unknown sample is important for a variety of forensic applications. Food authentication, monitoring illegal trade in endangered species, forensic entomology, sexual assault case work and counter terrorism are just some of the fields that can require the detection of the biological species present. Traditional laboratory based approaches employ a wide variety of tools and technologies and exploit a number of different species specific traits including morphology, molecular differences and immuno-chemical analyses. A large number of these approaches require laboratory based apparatus and results can take a number of days to be returned to investigating authorities. Having a presumptive test for rapid identification could lead to savings in terms of cost and time and allow sample prioritisation if confirmatory testing in a laboratory is required later. This model study describes the development of an assay using a single HyBeacon(®) probe and melt curve analyses allowing rapid screening and authentication of food products labelled as Atlantic cod (Gadus morhua). Exploiting melt curve detection of species specific SNP sites on the COI gene the test allows detection of a target species (Atlantic cod) and closely related species which may be used as substitutes. The assay has been designed for use with the Field Portable ParaDNA system, a molecular detection platform for non-expert users. The entire process from sampling to result takes approximately 75min. Validation studies were performed on both single source genomic DNA, mixed genomic DNA and commercial samples. Data suggests the assay has a lower limit of detection of 31 pg DNA. The specificity of the assay to Atlantic cod was measured by testing highly processed food samples including frozen, defrosted and cooked fish fillets as well as fish fingers, battered fish fillet and fish pie. Ninety-six (92.7%) of all Atlantic cod food products, tested, provided a correct single species result with the remaining samples erroneously identified as containing non-target species. The data shows that the assay was quick to design and characterise and is also capable of yielding results that would be beneficial in a variety of fields, not least the authentication of food.
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Affiliation(s)
- Nick Dawnay
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK.
| | - Rebecca Hughes
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Nicola Duxbury
- Product Development Group, LGC Forensics, Culham Science Centre, Abingdon OX14 3ED, UK
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12
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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]
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13
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Blackman S, Dawnay N, Ball G, Stafford-Allen B, Tribble N, Rendell P, Neary K, Hanson EK, Ballantyne J, Kallifatidis B, Mendel J, Mills DK, Wells S. Developmental validation of the ParaDNA ® Intelligence System—A novel approach to DNA profiling. Forensic Sci Int Genet 2015; 17:137-148. [DOI: 10.1016/j.fsigen.2015.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/01/2015] [Accepted: 04/24/2015] [Indexed: 11/25/2022]
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14
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Donachie GE, Dawnay N, Ahmed R, Naif S, Duxbury NJ, Tribble ND. Assessing the impact of common forensic presumptive tests on the ability to obtain results using a novel rapid DNA platform. Forensic Sci Int Genet 2015; 17:87-90. [PMID: 25864157 DOI: 10.1016/j.fsigen.2015.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/25/2015] [Accepted: 04/03/2015] [Indexed: 11/16/2022]
Abstract
The rise of DNA evidence to the forefront of forensic science has led to high sample numbers being submitted for profiling by investigators to casework laboratories: bottleneck effects are often seen resulting in slow turnaround times and sample backlog. The ParaDNA(®) Screening and Intelligence Tests have been designed to guide investigators on the viability of potential sources of DNA allowing them to determine which samples should be sent for full DNA analysis. Both tests are designed to augment the arsenal of available forensic tests for end users and be used concurrently to those commonly available. Therefore, assessing the impact that common forensic tests have on such novel technology is important to measure. The systems were tested against various potential inhibitors to which samples may be exposed as part of the investigative process. Presumptive test agents for biological materials (blood, semen and saliva) and those used as fingerprint enhancement agents were both used. The Screening Test showed a drop in performance following application of aluminium powder and cyanoacrylate (CNA) on fingerprints samples; however this drop in performance was not replicated with high template DNA. No significant effect was observed for any agent using the Intelligence Test. Therefore, both tests stand up well to the chemical agents applied and can be used by investigators with confidence that system performance will be maintained.
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Affiliation(s)
- Gillian E Donachie
- Centre for Forensic Science, University of Strathclyde, Department of Pure and Applied Chemistry, Royal College Building, Glasgow G1 1XW, UK
| | - Nick Dawnay
- LGC, F5Culham Science Centre, Abingdon OX14 3ED, UK.
| | - Romana Ahmed
- LGC, F5Culham Science Centre, Abingdon OX14 3ED, UK
| | - Sarah Naif
- LGC, F5Culham Science Centre, Abingdon OX14 3ED, UK
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