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Luo Y, Zhang J, Ni M, Mei Z, Ye Q, Guo B, Fang L, Feng D, Wang L, Yan J, Wang G. Pilot validation of on-field STR typing and human identity testing by MinION nanopore sequencing. Electrophoresis 2024; 45:885-896. [PMID: 38356010 DOI: 10.1002/elps.202300234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024]
Abstract
Nanopore sequencing technology has broad application prospects in forensic medicine due to its small size, portability, fast speed, real-time result analysis capabilities, single-molecule sequencing abilities, and simple operation. Here, we demonstrate for the first time that nanopore sequencing platforms can be used to identify individuals in the field. Through scientific and reasonable design, a nanopore MinION MK1B device and other auxiliary devices are integrated into a portable detection box conducive to individual identification at the accident site. Individual identification of 12 samples could be completed within approximately 24 h by jointly detecting 23 short tandem repeat (STR) loci. Through double-blinded experiments, the genotypes of 49 samples were successfully determined, and the accuracy of the STR genotyping was verified by the gold standard. Specifically, the typing success rate for 1150 genotypes was 95.3%, and the accuracy rate was 86.87%. Although this study focused primarily on demonstrating the feasibility of full-process testing, it can be optimistically predicted that further improvements in bioinformatics workflows and nanopore sequencing technology will help enhance the feasibility of Oxford Nanopore Technologies equipment for real-time individual identification at accident sites.
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Affiliation(s)
- Yuan Luo
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Jiarong Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing, P. R. China
| | - Zhusong Mei
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Qiao Ye
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Bingqian Guo
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Longmei Fang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Dongyun Feng
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Lu Wang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, P. R. China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, P. R. China
| | - Guangyun Wang
- Laboratory of Clinical Medicine, Air Force Medical Center, Air Force Medical University, PLA, Beijing, P. R. China
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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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Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
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Rapid DNA from a Disaster Victim Identification Perspective: is it a game changer? Forensic Sci Int Genet 2022; 58:102684. [DOI: 10.1016/j.fsigen.2022.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/03/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
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An in-field evaluation of rapid DNA instruments for disaster victim identification. Int J Legal Med 2021; 136:493-499. [PMID: 34816308 DOI: 10.1007/s00414-021-02748-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
In 2019 and 2020, disaster victim identification (DVI) simulations were conducted at the Australian Facility for Taphonomic Experimental Research. Whole and fragmented cadavers were positioned to replicate a building collapse scenario and left to decompose for up to 4 weeks. This study evaluated the utility of the ANDE™ 6C Rapid DNA System and the RapidHITTM ID System for DVI in the field and mortuary. Applying post-mortem nail and tissue biopsy samples showed promise, with the added benefit of minimally invasive collection procedures and limited preparation requirements. The preferred platform will depend on a number of factors, including its intended use and operating environment.
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Hinton N, Springstead T, Wright K, McNamara KP. Evaluation of rapid DNA using ANDE™ in a technical exploitation Level 2 laboratory workflow. J Forensic Sci 2021; 66:1879-1888. [PMID: 33885155 DOI: 10.1111/1556-4029.14728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 01/12/2023]
Abstract
A trial of rapid DNA (rDNA), a fully automated DNA profiling system, within a technical exploitation (TE) workflow is an important endeavor. In the 2019 Ardent Defender (AD) exercise, the Deployable Technical Analysis Laboratory (DTAL), of the Canadian Department of National Defence (DND), evaluated the use of rDNA using ANDE™. Sixteen samples were processed during a pre-exercise "controlled" setting, 44 samples were from an "uncontrolled" environment during the exercise, and 22 samples were buccal swabs. The proportion of profiles suitable for upload to ANDE™ was 95.5% of buccal samples (21/22), 66.7% controlled samples, and 15.9% for uncontrolled samples. A considerable difference was observed in the proportions of complete DNA profiles obtained from all exploited items between the controlled (58.3%) and uncontrolled (15.9%) trials and in the proportions of samples where no DNA was detected (16.7% controlled trial vs. 56.8% uncontrolled trial). Overall, the trials highlighted the potential to gain identity intelligence using rDNA within a TE workflow and revealed the impact of operational constraints and the need to improve certain TE practices to gain the most benefit from rDNA. It also demonstrated the benefit of including an uncontrolled component for a more realistic indication of rDNA effectiveness in operational settings and highlighted operational practices impacting rDNA success. Mixture deconvolution was difficult as current guidelines do not consider some of the stochastic effects produced by the rDNA analysis; however, overall, the study demonstrated that rDNA using the ANDE™ instrument could be successfully incorporated into a TE workflow within a deployable laboratory.
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Affiliation(s)
- Nicole Hinton
- Deployable Technical Analysis Laboratory, Department of National Defence, Ottawa, ON, Canada
| | - Tyson Springstead
- Deployable Technical Analysis Laboratory, Department of National Defence, Ottawa, ON, Canada
| | - Kirsty Wright
- Australia Defence Force, Canberra, ACT, Australia.,Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Qld, Australia
| | - Kevin P McNamara
- Deployable Technical Analysis Laboratory, Department of National Defence, Ottawa, ON, Canada
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Ragazzo M, Melchiorri S, Manzo L, Errichiello V, Puleri G, Nicastro F, Giardina E. Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods. Genes (Basel) 2020; 11:E582. [PMID: 32456006 PMCID: PMC7288309 DOI: 10.3390/genes11050582] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/10/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This "swab in-profile out" method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality.
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Affiliation(s)
- Michele Ragazzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Stefano Melchiorri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Laura Manzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Giulio Puleri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | | | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
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Butler JM, Willis S. Interpol review of forensic biology and forensic DNA typing 2016-2019. Forensic Sci Int Synerg 2020; 2:352-367. [PMID: 33385135 PMCID: PMC7770417 DOI: 10.1016/j.fsisyn.2019.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 12/23/2022]
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium. The review papers are also available at the Interpol website at: https://www.interpol.int/content/download/14458/file/Interpol%20Review%20Papers%202019.pdf.
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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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