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McDonald C, Taylor D, Brinkworth RSA, Linacre A. Developing a Machine Learning 'Smart' Polymerase Chain Reaction Thermocycler Part 2: Putting the Theoretical Framework into Practice. Genes (Basel) 2024; 15:1199. [PMID: 39336790 PMCID: PMC11431514 DOI: 10.3390/genes15091199] [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: 08/13/2024] [Revised: 09/04/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
The introduction of PCR into forensic science and the rapid increases in the sensitivity, specificity and discrimination power of DNA profiling that followed have been fundamental in shaping the field of forensic biology. Despite these developments, the challenges associated with the DNA profiling of trace, inhibited and degraded samples remain. Thus, any improvement to the performance of sub-optimal samples in DNA profiling would be of great value to the forensic community. The potential exists to optimise the PCR performance of samples by altering the cycling conditions used. If the effects of changing cycling conditions upon the quality of a DNA profile can be well understood, then the PCR process can be manipulated to achieve a specific goal. This work is a proof-of-concept study for the development of a smart PCR system, the theoretical foundations of which are outlined in part 1 of this publication. The first steps needed to demonstrate the performance of our smart PCR goal involved the manual alteration of cycling conditions and assessment of the DNA profiles produced. In this study, the timing and temperature of the denaturation and annealing stages of the PCR were manually altered to achieve the goal of reducing PCR runtime while maintaining an acceptable quality and quantity of DNA product. A real-time feedback system was also trialled using an STR PCR and qPCR reaction mix, and the DNA profiles generated were compared to profiles produced using the standard STR PCR kits. The aim of this work was to leverage machine learning to enable real-time adjustments during a PCR, allowing optimisation of cycling conditions towards predefined user goals. A set of parameters was found that yielded similar results to the standard endpoint PCR methodology but was completed 30 min faster. The development of an intelligent system would have significant implications for the various biological disciplines that are reliant on PCR technology.
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Affiliation(s)
- Caitlin McDonald
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Duncan Taylor
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Russell S A Brinkworth
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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2
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Eaton M, Woolf MS, Pemmasani S, Turner T, Deeb JG, Dawson Green T. Two simplified tooth sample preparation methods for conventional laboratory and RapidHIT™ ID workflows. J Forensic Sci 2024. [PMID: 39233363 DOI: 10.1111/1556-4029.15624] [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: 05/03/2024] [Revised: 07/26/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
Disaster victim identification (DVI) refers to the forensic identification of unknown individuals following a mass disaster event. Human dental structures can contain viable DNA sources when other soft tissues are compromised. However, labor-intensive sample preparation performed by extensively trained personnel is needed to expose the nuclear material for traditional forensic DNA workflows. With this in mind, we evaluated two simplified sample preparation protocols for processing tooth samples using either a conventional forensic DNA workflow or the Applied Biosystems® RapidHIT™ ID instrument. Briefly, sample sets for both protocols included 10 deciduous teeth that were cleaned prior to either fragmentation with a claw hammer (for RapidHIT™ ID processing) or fine-powder pulverization with a consumer-grade coffee grinder (for traditional workflows). The average percentage of expected STR alleles that were detected above analytical threshold for these tooth samples were comparable between methods: RapidHIT™ ID = 99.0% and GlobalFiler™ = 99.8%. Average intralocus heterozygote peak height ratios (PHRs) were comparable: RapidHIT™ ID = 0.80 and GlobalFiler™ = 0.86. Importantly, 9 of 10 samples analyzed via the RapidHIT™ ID required analyst review for flagged artifact peaks and quality issues. Across all profiles, 91% of alleles passed quality metrics for the RapidHIT™ workflow versus 100% for conventional GlobalFiler™ analysis. Collectively, these results suggest that quick, low-tech tooth sample fragmentation followed by analysis with the RapidHIT™ ID instrument can produce complete STR profiles from aged tooth samples. Future studies should include larger samples sets, more challenging tooth samples, and further simplification of sample preparation to enable field-forward, on-scene DVI.
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Affiliation(s)
- Morgan Eaton
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - M Shane Woolf
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Samyuktha Pemmasani
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Triniti Turner
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Janina Golob Deeb
- Department of Periodontology, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Tracey Dawson Green
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
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McDonald C, Taylor D, Linacre A. PCR in Forensic Science: A Critical Review. Genes (Basel) 2024; 15:438. [PMID: 38674373 PMCID: PMC11049589 DOI: 10.3390/genes15040438] [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: 03/07/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
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Affiliation(s)
- Caitlin McDonald
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
- Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; (C.M.); (A.L.)
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Aljumaili T, Haines AM. An evaluation of the RapidHIT™ ID system for hair roots stained with Diamond™ Nucleic Acid Dye. Forensic Sci Int Genet 2024; 69:103003. [PMID: 38154325 DOI: 10.1016/j.fsigen.2023.103003] [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: 09/04/2023] [Revised: 11/09/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
The RapidHIT™ ID (RHID) system was evaluated for its suitability in processing a single hair root to obtain informative DNA profiles. Hair samples were assessed for nuclear DNA prior to DNA analysis using Diamond™ Nucleic Acid Dye (DD) and real-time Extended Depth of Field (EDF) imaging to visualise and count nuclei if present. Hairs were viewed under an Optico N300F LED Fluorescent Microscope and imaged using a MIchrome 5 Pro camera. Hair roots were processed through both the ACE GlobalFiler™ Express sample cartridge and the RapidINTEL™ sample cartridge. A total of 44 hairs including shed hairs (9) and plucked hairs (35) from 8 donors were evaluated in this study. The processing of hairs using the RHID system required the modification of a standard swab that allowed for hairs to be easily collected and placed into the cartridge but also allowed for the re-collection of hair roots post RHID analysis (for potential standard DNA workflow). 90% of plucked hairs with a high nuclei count (>100) resulted in a high partial or full DNA profile, with the remaining 10% resulting in a low partial profile. 44% of shed hairs resulted in a low partial profile, with the remaining hairs resulting in a null profile. This study demonstrated that the RHID system could successfully obtain a DNA profile from a single hair root with nuclei present post-DD staining. According to these results, it is suggested that when dealing with hairs containing fewer than 50 nuclei, using the RapidINTEL™ cartridge can enhance allele recovery.
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Affiliation(s)
| | - Alicia M Haines
- School of Science, Western Sydney University, Penrith, Australia.
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Laurin N, Boulianne H, Frégeau C. Comparative analysis of two Rapid DNA technologies for the processing of blood and saliva-based samples. Forensic Sci Int Genet 2023; 67:102928. [PMID: 37573630 DOI: 10.1016/j.fsigen.2023.102928] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Rapid DNA technologies recently gained significant momentum as a means to generate DNA profiles faster than with standard laboratory workflows. Initially developed for the analysis of buccal reference samples, applications are being considered for other types of forensic samples. In this study, an identical set of 150 blood and saliva-based samples was processed using two different Rapid DNA technologies, the Applied BioSystems™ RapidHIT™ ID System using the RapidINTEL™ sample cartridge and the ANDE™ 6C Rapid DNA Analysis™ System using the I-Chip. A subset of samples were subjected to alternative collection methods or sample pre-treatments to determine the optimal strategy for each instrument. An equivalent sample set was also processed using a conventional DNA analysis workflow. The sensitivity range of the two Rapid DNA technologies was comparable based on blood and saliva dilution series, with both technologies able to generate full profiles from samples typically yielding 5-10 ng of DNA when processed using conventional DNA analysis. The brand of cotton swabs used for Rapid DNA analysis had an impact on the results for both systems. Differences were observed in success rate between the two systems when processing blood (on fabrics, FTA paper or hard surfaces) and saliva-based samples (drink containers, FTA paper, chewing gum, cigarette butt filter paper) and depended on the sample type. Importantly, deviating from the manufacturer's instructions for sample collection and pre-treatment was more detrimental to the ANDE 6C results. The quality of DNA profiles, as assessed using heterozygote peak height ratios, interloci balance and artifact presence, confirmed the results to be reliable and acceptable for single source samples. Profiling results were obtained when samples were reprocessed using the same Rapid DNA technology or conventional DNA analysis. Secondary analysis using a substitute software (GeneMapper ID-X v1.5) to recover additional genetic information was shown to be feasible. Finally, a comparison between the Applied Biosystems™ RapidHIT™ ID System Software v1.3.1 and v1.3.2 was also performed. Findings of this study could assist those interested in using Rapid DNA technology for blood or saliva-based samples, in various settings and for different applications.
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Affiliation(s)
- Nancy Laurin
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Science and Strategic Policy, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
| | - Hélène Boulianne
- Royal Canadian Mounted Police, Forensic Science & Identification Services, National Forensic Laboratory Services, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada
| | - Chantal Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, National Forensic Laboratory Services, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada
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de Roo R, Mapes A, van Cooten M, van Hooff B, Kneppers S, Kokshoorn B, Valkenburg T, de Poot C. Introducing a Rapid DNA Analysis Procedure for Crime Scene Samples Outside of the Laboratory-A Field Experiment. SENSORS (BASEL, SWITZERLAND) 2023; 23:4153. [PMID: 37112494 PMCID: PMC10145755 DOI: 10.3390/s23084153] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
Technological innovations enable rapid DNA analysis implementation possibilities. Concordantly, rapid DNA devices are being used in practice. However, the effects of implementing rapid DNA technologies in the crime scene investigation procedure have only been evaluated to a limited extent. In this study a field experiment was set up comparing 47 real crime scene cases following a rapid DNA analysis procedure outside of the laboratory (decentral), with 50 cases following the regular DNA analysis procedure at the forensic laboratory. The impact on duration of the investigative process, and on the quality of the analyzed trace results (97 blood and 38 saliva traces) was measured. The results of the study show that the duration of the investigation process has been significantly reduced in cases where the decentral rapid DNA procedure was deployed, compared to cases where the regular procedure was used. Most of the delay in the regular process lies in the procedural steps during the police investigation, not in the DNA analysis, which highlights the importance of an effective work process and having sufficient capacity available. This study also shows that rapid DNA techniques are less sensitive than regular DNA analysis equipment. The device used in this study was only to a limited extent suitable for the analysis of saliva traces secured at the crime scene and can mainly be used for the analysis of visible blood traces with an expected high DNA quantity of a single donor.
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Affiliation(s)
- Rosanne de Roo
- Forensic Science Department, Amsterdam University of Applied Sciences, Tafelbergweg 51, 1105 BD Amsterdam, The Netherlands
| | - Anna Mapes
- Midden-Nederland Police Department, Forensic Investigative Division, 1276 KA Huizen, The Netherlands
| | - Merel van Cooten
- Midden-Nederland Police Department, Forensic Investigative Division, 1276 KA Huizen, The Netherlands
| | - Britt van Hooff
- Amsterdam Police Department, Forensic Investigative Division, 1014 BA Amsterdam, The Netherlands
| | - Sander Kneppers
- Division Biological Traces, Netherlands Forensic Institute, 2497 GB The Hague, The Netherlands
| | - Bas Kokshoorn
- Forensic Science Department, Amsterdam University of Applied Sciences, Tafelbergweg 51, 1105 BD Amsterdam, The Netherlands
- Division Biological Traces, Netherlands Forensic Institute, 2497 GB The Hague, The Netherlands
| | - Thalassa Valkenburg
- Amsterdam Police Department, Forensic Investigative Division, 1014 BA Amsterdam, The Netherlands
| | - Christianne de Poot
- Forensic Science Department, Amsterdam University of Applied Sciences, Tafelbergweg 51, 1105 BD Amsterdam, The Netherlands
- Police Academy, 7334 AC Apeldoorn, The Netherlands
- Department of Criminal Law and Criminology, Faculty of Law, VU University, 1081 HV Amsterdam, The Netherlands
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7
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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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Benschop CCG, Slagter M, Nagel JHA, Hovers P, Tuinman S, Duijs FE, Grol LJW, Jegers M, Berghout A, van der Zwan AW, Ypma RJF, de Jong J, Kneppers ALJ. Development and validation of a fast and automated DNA identification line. Forensic Sci Int Genet 2022; 60:102738. [PMID: 35691141 DOI: 10.1016/j.fsigen.2022.102738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
The importance of DNA evidence for gaining investigative leads demands a fast workflow for forensic DNA profiling performed in large volumes. Therefore, we developed software solutions for automated DNA profile analysis, contamination check, major donor inference, DNA database (DDB) comparison and reporting of the conclusions. This represents the Fast DNA IDentification Line (FIDL) and this study describes its development, validation and implementation in criminal casework at the authors' institute. This first implementation regards single donor profiles and major contributors to mixtures. The validation included testing of the software components on their own and examination of the performance of different DDB search strategies. Furthermore, end-to-end testing was performed under three conditions: (1) testing of scenarios that can occur in DNA casework practice, (2) tests using three months of previous casework data, and (3) testing in a casework production environment in parallel to standard casework practices. The same DNA database candidates were retrieved by this automated line as by the manual workflow. The data flow was correct, results were reproducible and robust, results requiring manual analysis were correctly flagged, and reported results were as expected. Overall, we found FIDL valid for use in casework practice in our institute. The results from FIDL are automatically reported within three working days from receiving the trace sample. This includes the time needed for registration of the case, DNA extraction, quantification, polymerase chain reaction and capillary electrophoresis. FIDL itself takes less than two hours from intake of the raw CE data to reporting. Reported conclusions are one of five options: (1) candidate retrieved from DDB, (2) no candidate retrieved from DDB, (3) high evidential value with regards to reference within the case, (4) results require examination of expert, or (5) insufficient amount of DNA obtained to generate a DNA profile. In our current process, the automated report is sent within three working days and a complete report, with confirmation of the FIDL results, and signed by a reporting officer is sent at a later time. The signed report may include additional analyses regarding e.g. minor contributors. The automated report with first case results is quickly available to the police enabling them to act upon the DNA results prior to receiving the full DNA report. This line enables a uniform and efficient manner of handling large numbers of traces and cases and provides high value investigative leads in the early stages of the investigation.
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Affiliation(s)
- Corina C G Benschop
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Martin Slagter
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Jord H A Nagel
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Pauline Hovers
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Sietske Tuinman
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Francisca E Duijs
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Laurens J W Grol
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Mariëlle Jegers
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Abigayle Berghout
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Anne-Wil van der Zwan
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Rolf J F Ypma
- Netherlands Forensic Institute, Division of Digital and Biometric Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Jeroen de Jong
- Netherlands Forensic Institute, Division of Digital and Biometric Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
| | - Alexander L J Kneppers
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497GB The Hague, the Netherlands.
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