1
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Kim BM, Park SU, Schmelzer L, Yang SB, Lee SD, Kim MY, Naue J, Lee HY. DNA methylation-based organ tissue identification: Marker identification, SNaPshot multiplex assay development, and interlaboratory comparison. Forensic Sci Int Genet 2024; 71:103052. [PMID: 38678764 DOI: 10.1016/j.fsigen.2024.103052] [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: 01/17/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024]
Abstract
Identifying body fluids and organ tissues is highly significant as they can offer crucial evidence in criminal investigations and aid the court in making informed decisions, primarily through evaluating the biological source and possibly at the activity level up to death or fatal damage. In this study, organ tissue-specific CpG markers were identified from Illumina's methylation EPIC array data of nine organ tissues, including epidermis, dermis, heart, skeletal muscle, blood, kidney, brain, lung, and liver, from autopsies of 10 Koreans. Through the validation test using 43 samples, 18 hypomethylation markers, with two markers for each organ tissue type, were selected to construct a SNaPshot assay. Two multiplex assays involving forward and reverse SBE primers were designed to help investigators accurately determine the organ origin of the analyzed tissue samples through repeated analysis of the same PCR products for markers. The developed multiplex demonstrated high accuracy, achieving 100.0 % correct detection of the presence of nine organ tissue types in 88 samples from autopsies of 10 Asians. However, two lung samples showed additional positive indications of the presence of blood. An interlaboratory comparison using 80 autopsy samples (heart, skeletal muscle, blood, kidney cortex, kidney medulla, brain, lung, and liver) from 10 individuals in Germany revealed overall comparable results with correct detection of the presence of eight organ tissue types in 92.5 % samples (74 of 80 samples). In the case of six samples, it was impossible to determine the correct tissue successfully due to drop-outs of unmethylation signals at target tissue marker loci. One of these lung samples revealed only non-intended off-target signals for blood. The observed differences might be due to differences in sample collection during routine autopsy, technical differences due to the PCR cycler, and the threshold used for signal calling. Indicating the presence of additional tissue type and off-target unmethylation signals seems alleviated by applying more stringent hypomethylation thresholds. Therefore, the developed SNaPshot multiplex assays will be valuable for forensic investigators dealing with organ tissue identification, as well as for prosecutors and defense aiming to establish the circumstances that occurred at the crime scene.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Laura Schmelzer
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Young Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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2
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Oura P, Hakkarainen A, Sajantila A. Forensic neuropathology in the past decade: a scoping literature review. Forensic Sci Med Pathol 2024; 20:724-735. [PMID: 37439948 PMCID: PMC11297074 DOI: 10.1007/s12024-023-00672-9] [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] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
While there has been notable research activity in the field of clinical neuropathology over the recent years, forensic approaches have been less frequent. This scoping literature review explored original research on forensic neuropathology over the past decade (January 1, 2010, until February 12, 2022) using the MEDLINE database. The aims were to (1) analyze the volume of research on the topic, (2) describe meta-level attributes and sample characteristics, and (3) summarize key research themes and methods. Of 5053 initial hits, 2864 fell within the target timeframe, and 122 were included in the review. Only 3-17 articles were published per year globally. Most articles originated from the Europe (39.3%) and Asia (36.1%) and were published in forensic journals (57.4%). A median sample included 57 subjects aged between 16 and 80 years. The most common research theme was traumatic intracranial injury (24.6%), followed by anatomy (12.3%) and substance abuse (11.5%). Key methods included immunotechniques (31.1%) and macroscopic observation (21.3%). Although a number of novel findings were reported, most were of preliminary nature and will require further validation. In order to reach breakthroughs and validate novel tools for routine use, more research input is urged from researchers across the world. It would be necessary to ensure appropriate sample sizes and make use of control groups.
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Affiliation(s)
- Petteri Oura
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, P.O. Box 21, Helsinki, FI-00014, Finland.
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland.
| | - Antti Hakkarainen
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, P.O. Box 21, Helsinki, FI-00014, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, P.O. Box 21, Helsinki, FI-00014, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
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3
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Euteneuer J, Moitinho-Silva L, Courts C. Forensically relevant anatomical brain regions cannot be sub-differentiated by RNA expression analysis. Forensic Sci Med Pathol 2024:10.1007/s12024-024-00787-7. [PMID: 38294632 DOI: 10.1007/s12024-024-00787-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
The contextualization of biological traces generated by severe head injuries can be beneficial for criminal investigations. Here we aimed to identify and validate mRNA candidates for a robust sub-differentiation of forensically and traumatologically relevant brain regions. To this purpose, massively parallel sequencing of whole transcriptomes in sample material taken from four different areas of the cerebral cortex (frontal, temporal, parietal, occipital lobe) was performed, followed by bioinformatical data analysis, classification, and biostatistical candidate selection. Candidates were evaluated by Multiplex-RT-PCR and capillary electrophoresis. Only a weak relative upregulation and solely for candidates expressed in the parietal lobe was observed. Two candidates with upregulation in the cerebellar region (PVALB and CDR2L) were chosen for further investigation; however, PVALB could not reliably and repeatedly be detected in any lobe whereas CDR2L was detectable in all lobes. Consequently, we suggest that differences in mRNA expression between four regions of the cerebral cortex are too small and less pronounced to be useful for and applicable in forensic RNA analysis. We conclude that sub-differentiation of these brain regions via RNA expression analysis is generally not feasible within a forensic scope.
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Affiliation(s)
- Jan Euteneuer
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Arnold-Heller-Strasse 12, 24105, Kiel, Germany
| | | | - Cornelius Courts
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Arnold-Heller-Strasse 12, 24105, Kiel, Germany.
- Institute of Legal Medicine, University Hospital of Köln, Melatengürtel 60/62, 50823, Cologne, Germany.
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4
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Euteneuer J, Moitinho-Silva L, Courts C. Towards localizing head shots – Forensic sub-differentiation of anatomical brain regions by differential RNA expression. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Addition of an adipose marker to the organ tissue identification mRNA assay. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Sijen T, Harbison S. On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime. Genes (Basel) 2021; 12:1728. [PMID: 34828334 PMCID: PMC8617621 DOI: 10.3390/genes12111728] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.
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Affiliation(s)
- Titia Sijen
- Division Human Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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7
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Wang S, Shanthan G, Bouzga MM, Thi Dinh HM, Haas C, Fonneløp AE. Evaluating the performance of five up-to-date DNA/RNA co-extraction methods for forensic application. Forensic Sci Int 2021; 328:110996. [PMID: 34592582 DOI: 10.1016/j.forsciint.2021.110996] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/31/2021] [Accepted: 09/06/2021] [Indexed: 12/21/2022]
Abstract
The importance of RNA evidence is growing with new developments in RNA profiling methods and purposes. As forensic samples often can be of small quantity, extraction methods with high yields of both DNA and RNA are desirable. In order to identify the optimal DNA/RNA co-extraction workflow for forensic samples, we evaluated the performance of three frequently-used methods, two new approaches for DNA/RNA co-extraction and a manual phenol/chloroform RNA-only extraction method on blood and saliva samples. Based on a comprehensive analysis of the RNA and DNA quantities, as well as the STR genotyping and mRNA profiling results, we conclude that the two frequently-used co-extraction methods, combining commercially available DNA and RNA extraction kits, achieved the best performance. However, not any combination of commercially available DNA and RNA extraction kits works well and extensive optimization is necessary, as seen in the poor results of the two new approaches.
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Affiliation(s)
- Shouyu Wang
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland; Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | | | | | | | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
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8
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Antiga LG, Sibbens L, Abakkouy Y, Decorte R, Van Den Bogaert W, Van de Voorde W, Bekaert B. Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death. Sci Rep 2021; 11:16585. [PMID: 34400689 PMCID: PMC8368024 DOI: 10.1038/s41598-021-96095-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/30/2021] [Indexed: 11/09/2022] Open
Abstract
RNA analysis of post-mortem tissues, or thanatotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual. For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death. The results reveal that, after death, two clearly differentiated groups of up- and down-regulated genes can be detected. Pathway analysis suggests active processes that promote cell survival and DNA damage repair, rather than passive degradation, are the source of early post-mortem changes of gene expression in blood. In addition, a generalized linear model with an elastic net restriction predicted post-mortem interval with a root mean square error of 4.75 h. In conclusion, we demonstrate that post-mortem gene expression data can be used as biomarkers to estimate the post-mortem interval though further validation using independent sample sets is required before use in forensic casework.
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Affiliation(s)
- Laura G Antiga
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Department of Experimental and Health Sciences (CEXS), University Pompeu Fabra (UPF), Barcelona, Spain
| | - Lode Sibbens
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
| | - Yasmina Abakkouy
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Wouter Van Den Bogaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Wim Van de Voorde
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium
| | - Bram Bekaert
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Box 7003 71, 3000, Leuven, Belgium.
- Laboratory of Forensic Genetics, UZ Leuven, 3000, Leuven, Belgium.
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9
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Salzmann AP, Russo G, Kreutzer S, Haas C. Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces. Forensic Sci Int Genet 2021; 53:102524. [PMID: 34015741 DOI: 10.1016/j.fsigen.2021.102524] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation.
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Affiliation(s)
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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10
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Nothing but hot air?-On the molecular ballistic analysis of backspatter generated by and the hazard potential of blank guns. Int J Legal Med 2021; 135:2061-2071. [PMID: 33686487 PMCID: PMC8354942 DOI: 10.1007/s00414-021-02541-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/10/2021] [Indexed: 01/26/2023]
Abstract
Blank cartridge guns are prevalent especially in countries with laws restricting access to conventional firearms, and it is a common misconception that these weapons are harmless and only used as toys or for intimidation. However, although their harming potential is well-documented by numerous reports of accidents, suicides, and homicides, a systematic molecular biological investigation of traces generated by shots from blank cartridges at biological targets has not been done so far. Herein, we investigate the occurrence and analyzability of backspatter generated by shots of different types of blank cartridge guns firing different types of blank ammunition at ballistic gelatin model cubes doped with human blood and radiological contrast agent soaked into a spongious matrix and covered with three different variants of skin simulants. All skin simulants were penetrated, and backspatter was created in 100% of the shots in amounts sufficient for forensic short tandem repeat (STR) typing that resulted in the correct identification of the respective blood donor. Visible backspatter was documented on the muzzle and/or inside the barrel in all cases, and in 75% of cases also on the outer surfaces and on the shooter’s hand(s). Wound cavities were measured and ranged between 1 and 4.5 cm in depth. Discussing our findings, we provide recommendations for finding, recovering, and analyzing trace material from blank guns, and we demonstrate the considerable hazard potential of these devices, which is further emphasized by the presentation of a comprehensive overview of the pertinent literature on injuries inflicted by blank guns.
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11
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Evaluation of one-step RT-PCR multiplex assay for body fluid identification. Int J Legal Med 2021; 135:1727-1735. [PMID: 33666691 DOI: 10.1007/s00414-021-02535-w] [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: 12/20/2020] [Accepted: 02/10/2021] [Indexed: 01/27/2023]
Abstract
The discrimination of body fluid stains provides crucial evidence during the investigation of criminal cases. Previous studies have demonstrated the practical value of mRNA profiling in body fluid identification. Conventional strategy of mRNA profiling entails reverse transcription and PCR amplification in two separate procedures with different buffer systems. In this study, we subjected the one-step multiplex reverse transcription PCR strategy to mRNA profiling with the inclusion of the same 18 tissue-specific biomarkers in the F18plex system targeting peripheral blood, menstrual blood, vaginal secretion, saliva, semen, and urine. The Qiagen OneStep RT-PCR kit and Titanium One-Step RT-PCR kit were applied to multiplex construction, while reproducible profiling results were obtained with both kits. Compared to the F18plex system, similar expression profiles of biomarkers were obtained in targeted tissues, while expected cross-reaction was observed in non-targeted body fluids. However, CYP2B7P1 and SPINK5 were detected in menstrual blood samples, which was not observed using the F18plex system. Full-profiling results were obtained in all samples using 0.1 ng peripheral blood and semen RNA, and 1 ng menstrual blood, vaginal secretion, saliva, and urine RNA. In conclusion, the application of one-step mRNA profiling strategy could be a reliable and economical method for the simplified, specific, and simultaneous analysis of tissue-specific biomarkers for the discrimination of body fluid origin.
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12
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Ten years of molecular ballistics-a review and a field guide. Int J Legal Med 2021; 135:1121-1136. [PMID: 33594457 PMCID: PMC8205864 DOI: 10.1007/s00414-021-02523-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/27/2021] [Indexed: 01/23/2023]
Abstract
Molecular ballistics combines molecular biological, forensic ballistic, and wound ballistic insights and approaches in the description, collection, objective investigation, and contextualization of the complex patterns of biological evidence that are generated by gunshots at biological targets. Setting out in 2010 with two seminal publications proving the principle that DNA from backspatter collected from inside surfaces of firearms can be retreived and successfully be analyzed, molecular ballistics covered a lot of ground until today. In this review, 10 years later, we begin with a comprehensive description and brief history of the field and lay out its intersections with other forensic disciplines like wound ballistics, forensic molecular biology, blood pattern analysis, and crime scene investigation. In an application guide section, we aim to raise consciousness to backspatter traces and the inside surfaces of firearms as sources of forensic evidence. Covering crime scene practical as well as forensic genetic aspects, we introduce operational requirements and lay out possible procedures, including forensic RNA analysis, when searching for, collecting, analyzing, and contextualizing such trace material. We discuss the intricacies and rationales of ballistic model building, employing different tissue, skin, and bone simulants and the advantages of the “triple-contrast” method in molecular ballistics and give advice on how to stage experimental shootings in molecular ballistic research. Finally, we take a look at future applications and prospects of molecular ballistics.
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13
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Haas C, Neubauer J, Salzmann AP, Hanson E, Ballantyne J. Forensic transcriptome analysis using massively parallel sequencing. Forensic Sci Int Genet 2021; 52:102486. [PMID: 33657509 DOI: 10.1016/j.fsigen.2021.102486] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
The application of transcriptome analyses in forensic genetics has experienced tremendous growth and development in the past decade. The earliest studies and main applications were body fluid and tissue identification, using targeted RNA transcripts and a reverse transcription endpoint PCR method. A number of markers have been identified for the forensically most relevant body fluids and tissues and the method has been successfully used in casework. The introduction of Massively Parallel Sequencing (MPS) opened up new perspectives and opportunities to advance the field. Contrary to genomic DNA where two copies of an autosomal DNA segment are present in a cell, abundant RNA species are expressed in high copy numbers. Even whole transcriptome sequencing (RNA-Seq) of forensically relevant body fluids and of postmortem material was shown to be possible. This review gives an overview on forensic transcriptome analyses and applications. The methods cover whole transcriptome as well as targeted MPS approaches. High resolution forensic transcriptome analyses using MPS are being applied to body fluid/ tissue identification, determination of the age of stains and the age of the donor, the estimation of the post-mortem interval and to post mortem death investigations.
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Affiliation(s)
- Cordula Haas
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland.
| | - Jacqueline Neubauer
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland
| | - Andrea Patrizia Salzmann
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland
| | - Erin Hanson
- National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA; Department of Chemistry, National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA
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14
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Ypma RJF, Maaskant-van Wijk PA, Gill R, Sjerps M, van den Berge M. Calculating LRs for presence of body fluids from mRNA assay data in mixtures. Forensic Sci Int Genet 2021; 52:102455. [PMID: 33461104 DOI: 10.1016/j.fsigen.2020.102455] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/20/2020] [Accepted: 12/12/2020] [Indexed: 12/12/2022]
Abstract
Messenger RNA (mRNA) profiling can identify body fluids present in a stain, yielding information on what activities could have taken place at a crime scene. To account for uncertainty in such identifications, recent work has focused on devising statistical models to allow for probabilistic statements on the presence of body fluids. A major hurdle for practical adoption is that evidentiary stains are likely to contain more than one body fluid and current models are ill-suited to analyse such mixtures. Here, we construct a likelihood ratio (LR) system that can handle mixtures, considering the hypotheses H1: the sample contains at least one of the body fluids of interest (and possibly other body fluids); H2: the sample contains none of the body fluids of interest (but possibly other body fluids). Thus, the LR-system outputs an LR-value for any combination of mRNA profile and set of body fluids of interest that are given as input. The calculation is based on an augmented dataset obtained by in silico mixing of real single body fluid mRNA profiles. These digital mixtures are used to construct a probabilistic classification method (a 'multi-label classifier'). The probabilities produced are subsequently used to calculate an LR, via calibration. We test a range of different classification methods from the field of machine learning, ways to preprocess the data and multi-label strategies for their performance on in silico mixed test data. Furthermore, we study their robustness to different assumptions on background levels of the body fluids. We find logistic regression works as well as more flexible classifiers, but shows higher robustness and better explainability. We test the system's performance on lab-generated mixture samples, and discuss practical usage in case work.
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Affiliation(s)
- R J F Ypma
- Division of digital and biometric traces, Netherlands Forensic Institute, the Netherlands.
| | - P A Maaskant-van Wijk
- Division of human biological traces, Netherlands Forensic Institute, the Netherlands
| | - R Gill
- Mathematical institute, Faculty of Science, Leiden University, the Netherlands
| | - M Sjerps
- Division of digital and biometric traces, Netherlands Forensic Institute, the Netherlands; Korteweg-de Vries Institute for Mathematics, University of Amsterdam, the Netherlands
| | - M van den Berge
- Division of human biological traces, Netherlands Forensic Institute, the Netherlands
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15
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Salzmann AP, Bamberg M, Courts C, Dørum G, Gosch A, Hadrys T, Hadzic G, Neis M, Schneider PM, Sijen T, den Berge MV, Wiegand P, Haas C. mRNA profiling of mock casework samples: Results of a FoRNAP collaborative exercise. Forensic Sci Int Genet 2020; 50:102409. [PMID: 33220528 DOI: 10.1016/j.fsigen.2020.102409] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 01/23/2023]
Abstract
In recent years, forensic mRNA profiling has increasingly been used to identify the origin of human body fluids. By now, several laboratories have implemented mRNA profiling and also use it in criminal casework. In 2018 the FoRNAP (Forensic RNA Profiling) group was established among a number of these laboratories with the aim of sharing experiences, discussing optimization potential, identifying challenges and suggesting solutions with regards to mRNA profiling and casework. To compare mRNA profiling methods and results a collaborative exercise was organized within the FoRNAP group. Seven laboratories from four countries received 16 stains, comprising six pure body fluid / tissue stains and ten mock casework samples. The laboratories were asked to analyze the provided stains with their in-house method (PCR/CE or MPS) and markers of choice. Five laboratories used a DNA/RNA co-extraction strategy. Overall, up to 11 mRNA markers per body fluid were analyzed. We found that mRNA profiling using different extraction and analysis methods as well as different multiplexes can be applied to casework-like samples. In general, high input samples were typed with high accuracy by all laboratories, regardless of the method used. Irrespective of the analysis strategy, samples of low input or mixed stains were more challenging to analyze and interpret since, alike to DNA profiling, a higher number of markers dropped out and/or additional unexpected markers not consistent with the cell type in question were detected. It could be shown that a plethora of different but valid analysis and interpretation strategies exist and are successfully applied in the Forensic Genetics community. Nevertheless, efforts aiming at optimizing and harmonizing interpretation approaches in order to achieve a higher consistency between laboratories might be desirable in the future. The simultaneous extraction of DNA alongside RNA showed to be an effective approach to identify not only the body fluid present but also to identify the donor(s) of the stain. This allows investigators to gain valuable information about the origin of crime scene samples and the course of events in a crime case.
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Affiliation(s)
| | - Malte Bamberg
- Institute of Legal Medicine, University Hospital, University of Ulm, Germany
| | - Cornelius Courts
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Annica Gosch
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, Munich, Germany
| | | | - Maximilian Neis
- Institute of Legal Medicine, Faculty of Medicine, University Hospital, University of Cologne, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University Hospital, University of Cologne, Germany
| | - Titia Sijen
- Netherlands Forensic Institute, The Hague, the Netherlands
| | | | - Peter Wiegand
- Institute of Legal Medicine, University Hospital, University of Ulm, Germany
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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16
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Liu B, Yang Q, Meng H, Shao C, Jiang J, Xu H, Sun K, Zhou Y, Yao Y, Zhou Z, Li H, Shen Y, Zhao Z, Tang Q, Xie J. Development of a multiplex system for the identification of forensically relevant body fluids. Forensic Sci Int Genet 2020; 47:102312. [PMID: 32480323 DOI: 10.1016/j.fsigen.2020.102312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Currently, mRNA profiling is widely investigated for forensic body fluid identification, while it is still required to advance the approach for those casework samples of limited quantity or low quality. The inclusion of circular RNAs (circRNAs) can facilitate the detection of mRNA markers in forensic body fluid identification. In this study, a multiplex assay for forensic body fluid identification (F18plex assay) was developed by incorporating 14 tissue-specific mRNA markers with circRNAs expression, 2 mRNA markers with high abundance and 2 housekeeping markers for the discrimination of the most common forensic body fluids, including blood, menstrual blood, saliva, vaginal secretion, semen and urine. The markers employed in the F18plex assay show similar specificity to previous reports. Additionally, even if all linear transcripts were completely erased, the expected markers in target biofluids could still be identified, which should help the discrimination of those aged biological stains. Results from sensitivity testing and the detection of mixtures demonstrate good sensitivity of the multiplex assay. Generally, full biomarker profiles could be obtained with ≥1 μl of blood, saliva, or semen, and ≥1 ng of total RNAs from menstrual blood, vaginal secretion, or urine samples, respectively, using this multiplex assay under the established conditions. Collectively, the newly established multiplex assay can assist in determining the biological origin of forensic stains.
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Affiliation(s)
- Baonian Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jieqing Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Kuan Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxiang Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Yiwen Shen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ziqin Zhao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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17
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van den Berge M, Wagner S, Meijers E, Kokshoorn B, Kloosterman A, van der Scheer M, Sijen T. Minimizing hand-to-glove DNA contamination. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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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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19
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Kulstein G, Schacker U, Wiegand P. Old meets new: Comparative examination of conventional and innovative RNA-based methods for body fluid identification of laundered seminal fluid stains after modular extraction of DNA and RNA. Forensic Sci Int Genet 2018; 36:130-140. [DOI: 10.1016/j.fsigen.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/05/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
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20
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Hanson E, Ballantyne J. Human Organ Tissue Identification by Targeted RNA Deep Sequencing to Aid the Investigation of Traumatic Injury. Genes (Basel) 2017; 8:genes8110319. [PMID: 29125589 PMCID: PMC5704232 DOI: 10.3390/genes8110319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 11/16/2022] Open
Abstract
Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers. The identifiable organs and tissues include brain, lung, liver, heart, kidney, intestine, stomach, skeletal muscle, adipose, and trachea. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific, with little cross-reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues. We also demonstrate the ability of the assay to successful identify the tissue source of origin using a single blind study.
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Affiliation(s)
- Erin Hanson
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, USA.
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, USA.
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
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21
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Langstraat K, Knijnenberg A, Edelman G, van de Merwe L, van Loon A, Dik J, van Asten A. Large area imaging of forensic evidence with MA-XRF. Sci Rep 2017; 7:15056. [PMID: 29118445 PMCID: PMC5678136 DOI: 10.1038/s41598-017-15468-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 11/10/2022] Open
Abstract
This study introduces the use of macroscopic X-ray fluorescence (MA-XRF) for the detection, classification and imaging of forensic traces over large object areas such as entire pieces of clothing and wall paneling. MA-XRF was sufficiently sensitive and selective to detect human biological traces like blood, semen, saliva, sweat and urine on fabric on the basis of Fe, Zn, K, Cl and Ca elemental signatures. With MA-XRF a new chemical contrast is introduced for human stain detection and this can provide a valuable alternative when the evidence item is challenging for conventional techniques. MA-XRF was also successfully employed for the chemical imaging and classification of gunshot residues (GSR). The full and non-invasive elemental mapping (Pb, Ba, Sr, K and Cl) of intact pieces of clothing allows for a detailed shooting incident reconstruction linking firearms and ammunition to point of impact and providing information on the shooting angle. In high resolution mode MA-XRF can even be used to provide information on the shooting order of different ammunition types. Finally, by using the surface penetration of X-rays we demonstrate that the lead signature of a bullet impact can be easily detected even if covered by multiple layers of wall paint or human blood.
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Affiliation(s)
- Kirsten Langstraat
- Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands
| | - Alwin Knijnenberg
- Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands
| | - Gerda Edelman
- Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands
| | - Linda van de Merwe
- Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands
| | | | - Joris Dik
- Delft University of Technology, Materials Science and Engineering, P.O. Box 5, 2600 AA, Delft, The Netherlands
| | - Arian van Asten
- Netherlands Forensic Institute, P.O. Box 24044, 2490 AA, The Hague, The Netherlands. .,University of Amsterdam, Faculty of Science, Van't Hoff Institute for Molecular Sciences, P.O. Box 94157, 1090 GD, Amsterdam, The Netherlands. .,CLHC, Amsterdam Center for Forensic Science and Medicine, P.O. Box 94157, 1090 GD, Amsterdam, The Netherlands.
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22
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RNA/DNA co-analysis from bloodstains on aged polyvinyl-alcohol gloves prepared for securing evidence from the hands of victims of fatal gunshot injuries. Int J Legal Med 2017; 132:53-66. [PMID: 28956148 DOI: 10.1007/s00414-017-1687-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/30/2017] [Indexed: 12/22/2022]
Abstract
In contrast to cumulative techniques (e.g., tape-lift) for qualitative gunshot residues (GSR) analysis, topographic methods are commonly applied to preserve the integrity of evidence from a shooter's or victim's hand in cases of gun-related crimes. Topographic sampling techniques employing adhesive foils, latex, or the polyvinyl alcohol (PVAL) method enable unambiguous sampling of biological and non-biological trace material while preserving its spatial distribution and relation to each other. The PVAL method in particular allows for a topographically veridic and quantitative conservation of traces of GSR and biological stains that are embedded in the PVAL glove, because it completely removes these traces from the hand. The present study investigated the success rates of STR profiling and the detection of blood and brain-specific gene expression from minimal traces of blood splatter as well as parallel to the positive detection of gunshot residues embedded in 17 PVAL gloves taken from the hands of deceased persons in the context of homicide cases in the period between 1996 and 2003. The water-soluble PVAL matrix is shown to be fully compatible with successful STR profiling and the detection of blood- and brain-specific miRNA expression, even after up to 20 years of storage, demonstrating that this sampling technique offers advantages compared to other more simplistic sampling methods like taping.
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23
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Evaluation of the inclusion of circular RNAs in mRNA profiling in forensic body fluid identification. Int J Legal Med 2017; 132:43-52. [PMID: 28948359 DOI: 10.1007/s00414-017-1690-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023]
Abstract
The use of messenger RNA (mRNA) profiling is considered a promising method in the identification of forensically relevant body fluids which can provide crucial information for reconstructing a potential crime. However, casework samples are usually of limited quantity or have been subjected to degradation, which requires improvement of body fluid identification. Circular RNAs (circRNAs), a class of products from the backsplicing of pre-mRNAs, are shown to have high abundance, remarkable stability, and cell type-specific expression in human cells. In this study, we investigated whether the inclusion of circRNAs in mRNA profiling improve the detection of biomarkers including δ-aminolevulinate synthase 2 (ALAS2) and matrix metallopeptidase 7 (MMP7) in body fluid identification. The major circRNAs of ALAS2 and MMP7 were first identified and primer sets for the simultaneous detection of linear and circular transcripts were developed. The inclusion of circRNAs in mRNA profiling showed improved detection sensitivity and stability of biomarkers revealed by using serial dilutions, mixed samples, and menstrual bloodstains as well as degraded and aged samples. Therefore, the inclusion of circRNAs in mRNA profiling should facilitate the detection of mRNA markers in forensic body fluid identification.
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24
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van den Berge M, Sijen T. Extended specificity studies of mRNA assays used to infer human organ tissues and body fluids. Electrophoresis 2017; 38:3155-3160. [DOI: 10.1002/elps.201700241] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Margreet van den Berge
- Department of Biological Traces; Netherlands Forensic Institute; The Hague The Netherlands
| | - Titia Sijen
- Department of Biological Traces; Netherlands Forensic Institute; The Hague The Netherlands
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25
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Identification of organ tissue types and skin from forensic samples by microRNA expression analysis. Forensic Sci Int Genet 2017; 28:99-110. [DOI: 10.1016/j.fsigen.2017.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/26/2017] [Accepted: 02/03/2017] [Indexed: 01/19/2023]
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26
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Zhao H, Wang C, Yao L, Lin Q, Xu X, Hu L, Li W. Identification of aged bloodstains through mRNA profiling: Experiments results on selected markers of 30- and 50-year-old samples. Forensic Sci Int 2017; 272:e1-e6. [DOI: 10.1016/j.forsciint.2017.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 12/28/2016] [Accepted: 01/06/2017] [Indexed: 02/05/2023]
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27
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van den Berge M, Sijen T. A male and female RNA marker to infer sex in forensic analysis. Forensic Sci Int Genet 2016; 26:70-76. [PMID: 27816848 DOI: 10.1016/j.fsigen.2016.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 01/18/2023]
Abstract
In forensics, DNA profiling is used for the identification of the donor of a trace, while messenger RNA (mRNA) profiling can be applied to identify the cellular origin such as body fluids or organ tissues. The presence of male cell material can be readily assessed by the incorporation of Y-chromosomal markers in quantitation or STR profiling systems. However, no forensic marker exists to positively identify female cell material; merely the presence of female DNA is deduced from the absence of a Y peak, or unbalanced X-Y signals at the Amelogenin locus or unbalanced response of the total and Y-specific quantifier. The presence of two X-chromosomes in female cells invokes dosage compensation, which is achieved through inactivation of one of the X-chromosomes in females. Since this process involves specific RNA molecules, identification of female cellular material may be possible through RNA profiling. Additionally, male material may be identified through RNAs expressed from the Y-chromosome. RNAs preferentially expressed in either sex were assessed for their potential to act as sex markers in forensic RNA assays. To confirm sex-specificity, body fluids and organ tissues of multiple donors of either sex were tested. Additionally, sensitivity of the markers and the suitability of positively identifying male-female mixtures were assessed and degraded samples were used to assess performance of the markers in forensic settings. The addition of sex-specific markers is of added informative value in any RNA profiling system and both markers were incorporated into existing RNA assays that either target body fluids or organs. These are the first forensic assays that enable positive identification of female cellular material.
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Affiliation(s)
- M van den Berge
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
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28
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DNA and RNA profiling of excavated human remains with varying postmortem intervals. Int J Legal Med 2016; 130:1471-1480. [PMID: 27627902 DOI: 10.1007/s00414-016-1438-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/09/2016] [Indexed: 01/03/2023]
Abstract
When postmortem intervals (PMIs) increase such as with longer burial times, human remains suffer increasingly from the taphonomic effects of decomposition processes such as autolysis and putrefaction. In this study, various DNA analysis techniques and a messenger RNA (mRNA) profiling method were applied to examine for trends in nucleic acid degradation and the postmortem interval. The DNA analysis techniques include highly sensitive DNA quantitation (with and without degradation index), standard and low template STR profiling, insertion and null alleles (INNUL) of retrotransposable elements typing and mitochondrial DNA profiling. The used mRNA profiling system targets genes with tissue specific expression for seven human organs as reported by Lindenbergh et al. (Int J Legal Med 127:891-900, 27) and has been applied to forensic evidentiary traces but not to excavated tissues. The techniques were applied to a total of 81 brain, lung, liver, skeletal muscle, heart, kidney and skin samples obtained from 19 excavated graves with burial times ranging from 4 to 42 years. Results show that brain and heart are the organs in which both DNA and RNA remain remarkably stable, notwithstanding long PMIs. The other organ tissues either show poor overall profiling results or vary for DNA and RNA profiling success, with sometimes DNA and other times RNA profiling being more successful. No straightforward relations were observed between nucleic acid profiling results and the PMI. This study shows that not only DNA but also RNA molecules can be remarkably stable and used for profiling of long-buried human remains, which corroborate forensic applications. The insight that the brain and heart tissues tend to provide the best profiling results may change sampling policies in identification cases of degrading cadavers.
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29
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Prevalence of human cell material: DNA and RNA profiling of public and private objects and after activity scenarios. Forensic Sci Int Genet 2016; 21:81-9. [DOI: 10.1016/j.fsigen.2015.12.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/11/2015] [Accepted: 12/19/2015] [Indexed: 11/22/2022]
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30
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Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method. Sci Justice 2016; 56:96-103. [DOI: 10.1016/j.scijus.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/09/2015] [Accepted: 11/09/2015] [Indexed: 11/19/2022]
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31
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On the effect of shooting distance, ballistic model construction, doping and weapon type on the simultaneous analysis of DNA and RNA from backspatter recovered from inside surfaces of firearms. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Grabmüller M, Cachée P, Madea B, Courts C. How far does it get?--The effect of shooting distance and type of firearm on the simultaneous analysis of DNA and RNA from backspatter recovered from inside and outside surfaces of firearms. Forensic Sci Int 2015; 258:11-8. [PMID: 26625183 DOI: 10.1016/j.forsciint.2015.10.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/24/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Abstract
When a firearm projectile hits a biological target a spray of biological material (e.g. blood and tissue) is ejected from the entrance wound and propelled back into the direction of the firearm. This phenomenon has been termed 'backspatter' and if backspattered biological material reaches the firearm on its backward trajectory it may persist on and be recovered from the firearm's inside surfaces. Molecular genetic analysis of backspatter generated by contact shots and shots from very short distances has already been demonstrated to critically contribute to victim identification and the reconstruction of firearm-related crimes. It is not known, however, up to what shooting distance can backspatter be found on firearms' inside surfaces and what influence the weapon's type and caliber has on backspatter attributes (e.g. reach, amount and distribution). Therefore, the present pilot study investigated the effect of serval combinations of shooting distances and types of firearms and ammunitions on the analyzability of co-extracted DNA and micro-RNA in samples of backspatter collected from interior and exterior surfaces of the firearms after experimental shootings employing standardized ballistic models. We demonstrate the limiting effect of shooting distance and the type of firearm on the yield of nucleic acids recovered from backspatter and the success rates of forensic DNA profiling and RNA based body-fluid and organ tissue identification in experimental shootings.
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Affiliation(s)
- Melanie Grabmüller
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Philipp Cachée
- Firearms and Ballistic Expert Witness P. Cachée, Birkenweg 6, 14554 Neuseddin, Germany
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany.
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33
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Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling. Forensic Sci Int Genet 2015; 20:119-129. [PMID: 26590860 DOI: 10.1016/j.fsigen.2015.10.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/12/2015] [Accepted: 10/31/2015] [Indexed: 11/23/2022]
Abstract
The forensic identification of human body fluids and tissues by means of messenger RNA (mRNA) profiling is a long studied methodology that is increasingly applied to casework samples. Previously, we have described an mRNA multiplex system that targets blood, saliva, semen, menstrual secretion, vaginal mucosa and skin (Lindenbergh et al. and van den Berge et al.). In this study we consider various topics to improve this mRNA profiling system or its use and adapt the method accordingly. Bodily secretions that may be encountered at a crime scene whilst not targeted by the multiplex-id est nasal mucosa, sweat, tears, faeces and urine-were examined for false positive signals. The results prompted us to identify a nasal mucosa marker that allows the discrimination of nasal mucosa from saliva or vaginal mucosa and nosebleed blood from peripheral blood. An updated version of the multiplex was prepared to which the nasal mucosa marker was added and in which markers for semen, vaginal mucosa and blood were replaced. Lactobacillus markers were regarded unsuitable as replacement for vaginal mucosa mRNA markers because of background signals on penile swabs that appeared devoid of female DNA. Furthermore, we provide approaches to deal with highly unbalanced mixtures. First, a differential extraction protocol was incorporated into a co-extraction protocol to allow DNA and RNA analysis of separated non-sperm and sperm fractions. In a second approach, besides the standard multiplex, a customized multiplex is used which excludes markers for prevailing cell types. This allows the use of lower cDNA inputs for the prevailing cell types and higher inputs for cell types that appear masked. Additionally, we assessed the relation between the percentage of alleles or markers detected in DNA or RNA profiles when decreasing sample amounts are analysed. While blood, saliva, semen and menstrual secretion show the trend that DNA profiling is more sensitive than RNA profiling, the reverse is seen for skin and variable results occur for vaginal and nasal mucosa. Lastly, we show that replicates are useful for interpretation of RNA data, as variations can be found even for true technical replicates. Increased numbers of replicates (over four) do, however, not cancel out the impact of this variation on data interpretation. Overall, the results of this study further forensic RNA profiling.
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34
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Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci Int Genet 2015; 18:21-32. [DOI: 10.1016/j.fsigen.2014.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
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35
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Grabmüller M, Madea B, Courts C. Comparative evaluation of different extraction and quantification methods for forensic RNA analysis. Forensic Sci Int Genet 2015; 16:195-202. [DOI: 10.1016/j.fsigen.2015.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/20/2014] [Accepted: 01/15/2015] [Indexed: 12/31/2022]
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Danaher P, White RL, Hanson EK, Ballantyne J. Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets. Forensic Sci Int Genet 2015; 14:18-30. [DOI: 10.1016/j.fsigen.2014.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/27/2014] [Accepted: 09/07/2014] [Indexed: 11/25/2022]
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Sauer E, Babion I, Madea B, Courts C. An evidence based strategy for normalization of quantitative PCR data from miRNA expression analysis in forensic organ tissue identification. Forensic Sci Int Genet 2014; 13:217-23. [PMID: 25203915 DOI: 10.1016/j.fsigen.2014.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/01/2014] [Accepted: 08/06/2014] [Indexed: 01/09/2023]
Abstract
Messenger-RNA (mRNA)-based analysis of organ tissues and their differentiation in complex crime stains has recently been introduced as a potential and powerful tool to forensic genetics. Given the notoriously low quality of many forensic samples it seems advisable, though, to substitute mRNA with micro-RNA (miRNA) which is much less susceptible to degradation. However, reliable miRNA detection and quantification using quantitative PCR requires a solid and forensically relevant normalization strategy. In our study we evaluated a panel of 15 carefully selected reference genes for their suitability as endogenous controls in miRNA qPCR normalization in forensically relevant settings. We analyzed assay performances and expression variances in 35 individual samples and mixtures thereof integrating highly standardized protocols with contemporary methodologies and included several well-established computational algorithms. Based on these empirical results, we recommend SNORD48, SNORD24, and RNU6-2 as endogenous references since these exhibit the most stable expression levels and the least expected variation among the evaluated candidate reference genes in the given set of forensically relevant organ tissues including skin. To account for the lack of consensus on how best to perform and interpret quantitative PCR experiments, our study's documentation is according to MIQE guidelines, defining the "minimum information for publication of quantitative real-time PCR experiments".
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Affiliation(s)
- Eva Sauer
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Iris Babion
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Cornelius Courts
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany.
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Xu Y, Xie J, Cao Y, Zhou H, Ping Y, Chen L, Gu L, Hu W, Bi G, Ge J, Chen X, Zhao Z. Development of highly sensitive and specific mRNA multiplex system (XCYR1) for forensic human body fluids and tissues identification. PLoS One 2014; 9:e100123. [PMID: 24991806 PMCID: PMC4089028 DOI: 10.1371/journal.pone.0100123] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/21/2014] [Indexed: 12/21/2022] Open
Abstract
The identification of human body fluids or tissues through mRNA-based profiling is very useful for forensic investigations. Previous studies have shown mRNA biomarkers are effective to identify the origin of biological samples. In this study, we selected 16 tissue specific biomarkers to evaluate their specificities and sensitivities for human body fluids and tissues identification, including porphobilinogen deaminase (PBGD), hemoglobin beta (HBB) and Glycophorin A (GLY) for circulatory blood, protamine 2 (PRM2) and transglutaminase 4 (TGM4) for semen, mucin 4 (MUC4) and human beta defensin 1(HBD1) for vaginal secretion, matrix metalloproteinases 7 and 11 (MMP7 and MMP11) for menstrual blood, keratin 4(KRT4) for oral mucosa, loricrin (LOR) and cystatin 6 (CST6) for skin, histatin 3(HTN3) for saliva, statherin (STATH) for nasal secretion, dermcidin (DCD) for sweat and uromodulin (UMOD) for urine. The above mentioned ten common forensic body fluids or tissues were used in the evaluation. Based on the evaluation, a reverse transcription (RT) PCR multiplex assay, XCYR1, which includes 12 biomarkers (i.e., HBB, GLY, HTN3, PRM2, KRT4, MMP11, MUC4, DCD, UMOD, MMP7, TGM4, and STATH) and 2 housekeeping genes [i.e., glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 18SrRNA], was developed. This assay was further validated with real casework samples and mock samples (with both single source and mixture) and it was approved that XCYR1 is effective to identify common body fluids or tissues (i.e., circulatory blood, saliva, semen, vaginal secretion, menstrual blood, oral mucosa, nasal secretion, sweat and urine) in forensic casework samples.
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Affiliation(s)
- Yan Xu
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Cao
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Huaigu Zhou
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Yuan Ping
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Liankang Chen
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Lihua Gu
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Wei Hu
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Gang Bi
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Jianye Ge
- Human Identification Division, Life Technologies, South San Francisco, California, United States of America
| | - Xin Chen
- Shanghai Key Laboratory of Crime Science Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, China
| | - Ziqin Zhao
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai, China
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Lux C, Schyma C, Madea B, Courts C. Identification of gunshots to the head by detection of RNA in backspatter primarily expressed in brain tissue. Forensic Sci Int 2014; 237:62-9. [PMID: 24598119 DOI: 10.1016/j.forsciint.2014.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 11/17/2022]
Abstract
Traces of backspatter recovered from the inside of the barrel of a gun that was used to deliver suicidal or homicidal contact shots may be a source of valuable forensic evidence and first systematic investigations of the persistence of victim DNA from inside firearms have been presented. The aim of the present study was to include victim RNA in such analyses to determine the origin of tissues in addition and parallel to standard DNA profiling for forensic identification purposes. In a first step, suitable mRNA (C1orf61) and micro-RNAs (miR-124a and miR-124*) that are primarily expressed in brain tissue were selected from potential candidates and confirmed using quantitative PCR (qPCR). Secondly, a co-extraction procedure for RNA and DNA was established and brain differentiability of the selected RNAs was demonstrated via qPCR using samples from experimental shots at ballistic models. In a third step, this procedure was successfully applied to analyse samples from real casework comprising eight cases of suicidal contact shots. In this pilot study, we are first to report the possibility of co-extracting mRNA, miRNA and DNA from ballistic trace samples collected from the inside of firearms and we demonstrate that RNA and DNA based analyses can be performed in parallel to produce informative and highly complementary evidence.
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Affiliation(s)
- Constantin Lux
- Institute of Legal Medicine, University of Bonn, Bonn, Germany
| | - Christian Schyma
- Institute of Legal Medicine, University of Bern, Bern, Switzerland
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Bonn, Germany
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A collaborative European exercise on mRNA-based body fluid/skin typing and interpretation of DNA and RNA results. Forensic Sci Int Genet 2014; 10:40-48. [PMID: 24552886 DOI: 10.1016/j.fsigen.2014.01.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/17/2014] [Accepted: 01/19/2014] [Indexed: 11/23/2022]
Abstract
The European Forensic Genetics Network of Excellence (EUROFORGEN-NoE) undertook a collaborative project on mRNA-based body fluid/skin typing and the interpretation of the resulting RNA and DNA data. Although both body fluids and skin are composed of a variety of cell types with different functions and gene expression profiles, we refer to the procedure as 'cell type inference'. Nine laboratories participated in the project and used a 20-marker multiplex to analyse samples that were centrally prepared and thoroughly tested prior to shipment. Specimens of increasing complexity were assessed that ranged from reference PCR products, cDNAs of indicated or unnamed cell type source(s), to challenging mock casework stains. From this specimen set, information on the overall sensitivity and specificity of the various markers was obtained. In addition, the reliability of a scoring system for inference of cell types was assessed. This scoring system builds on replicate RNA analyses and the ratio observed/possible peaks for each cell type [1]. The results of the exercise support the usefulness of this scoring system. When interpreting the data obtained from the analysis of the mock casework stains, the participating laboratories were asked to integrate the DNA and RNA results and associate donor and cell type where possible. A large variation for the integrated interpretations of the DNA and RNA data was obtained including correct interpretations. We infer that with expertise in analysing RNA profiles, clear guidelines for data interpretation and awareness regarding potential pitfalls in associating donors and cell types, mRNA-based cell type inference can be implemented for forensic casework.
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