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Courts C, Gosch A, Rothschild M. RNA Analysis in Forensic Molecular Biology. DEUTSCHES ARZTEBLATT INTERNATIONAL 2024; 121:363-369. [PMID: 38573184 DOI: 10.3238/arztebl.m2024.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND Different types of RNA take on multiple crucial functions in living cells and tissues. Messenger RNA (mRNA) is a temporary molecular carrier of genetic information. Analysis of the composition of all mRNA contained in a cell at a given moment, the so-called transcriptome, enables the determination of the type of cell and its condition, e.g., in pathologically altered states. METHODS This review is based on pertinent publications retrieved by a selective literature search. RESULTS The analysis of differential gene expression has already been used in forensic molecular biology to determine the type of tissue contained in biological specimens. It is also being used in criminal investigations to determine the composition of mixed traces of various bodily fluids and/or organ tissues. The method is limited by degradation of the mRNA molecules through environmental influences. The use of newly developed molecular biological methods such as massive parallel sequencing can expand the information obtainable by this investigative method. Current research also addresses the forensic potential of deriving relevant information about the crime-e.g., its timing, or the condition of the involved persons-from the totality of mRNA species present in the specimens. CONCLUSION Forensic RNA analysis can yield a great deal of relevant information. It is likely to be applicable in a much wider variety of forensic situations in the near future.
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Affiliation(s)
- Cornelius Courts
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Forensic Medicine, Cologne
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2
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Lynch C, Fleming R. Partial validation of multiplexed real-time quantitative PCR assays for forensic body fluid identification. Sci Justice 2023; 63:724-735. [PMID: 38030341 DOI: 10.1016/j.scijus.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 09/04/2023] [Accepted: 10/15/2023] [Indexed: 12/01/2023]
Abstract
Confirmatory body fluid identification using messenger RNA (mRNA) is a well-established technique to address issues encountered with conventional testing - such as poor sensitivity, specificity, and a lack of available tests for all body fluids of interest. For over a decade, endpoint reverse-transcription polymerase chain reaction (RT-PCR) assays have been used in forensic casework for such purposes. However, in comparison with real-time quantitative RT-PCR (RT-qPCR), endpoint RT-PCR has lower sensitivity, precision, and linear dynamic range. This research details the multiplexing and partial validation of confirmatory RT-qPCR assays. We have previously described novel assays for a range of body fluid targets and identified an optimal commercial kit for their amplification. Here, multiplexing was undertaken to form three assays: circulatory blood (SLC4A1) and menstrual fluid (STC1), saliva (HTN3) and vaginal material (CYP2B7P), and spermatozoa (PRM1) and seminal fluid (KLK2), all including a synthetic internal control RNA. Partial validation of the multiplexed assays incorporated the MIQE guidelines, ISO requirements, and SWGDAM guidelines. Using receiver operating characteristic (ROC) curves, each marker was significantly different from an uninformative assay and optimal cut-offs were all above 35 cycles. All assays showed a wide LDR (ranging from 3 to 5 logs with most R2 > 0.99), and high precision (most mean CV < 1 %). STC1 showed some instances of sporadic expression in blood, semen, and vaginal material at high CT values. CYP2B7P showed off-target expression in semen and blood. The sensitivities were approximated as; saliva: 1 in 1,000 dilution of a whole buccal swab, circulatory blood: 0.01-0.1 µL blood, menstrual fluid: 1 in 10,000 dilution of a whole menstrual swab, spermatozoa: 0.001 µL semen, seminal fluid: 0.01 µL semen, and vaginal material: 1 in 1,000 dilution of a whole vaginal swab. A total of 16 mock body fluid extract mixtures and 18 swab mixtures were tested and had 100% and 99% detection of target markers below each specific cut-off, respectively. Some mixtures containing high volumes of blood and semen showed off-target CYP2B7P expression. The successful application of a probabilistic model to the RT-qPCR data was also demonstrated. Further work will involve full developmental validation.
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Affiliation(s)
- Courtney Lynch
- Forensic Science Programme, School of Chemical Sciences, The University of Auckland, Auckland, New Zealand; Forensic Research and Development Team, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd, Auckland, New Zealand.
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3
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Chierto E, Alessandrini F, Bini C, Carnevali E, Fabbri M, Fattorini P, Grignani P, Scarnicci F, Tozzo P, Verzeletti A, Pelotti S, Buscemi L, Robino C. An mRNA Profiling Study of Vaginal Swabs from Pre- and Postmenopausal Women. Curr Issues Mol Biol 2023; 45:6526-6537. [PMID: 37623230 PMCID: PMC10453267 DOI: 10.3390/cimb45080411] [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] [Received: 07/14/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Body fluid identification by means of mRNA profiling provides valuable supplementary information in forensic investigations. In particular, the detection of vaginal mucosa mRNA markers is highly relevant in sexual assault cases. Although the vagina undergoes characteristic age-related physiological changes over a lifetime, few studies have evaluated the efficacy of vaginal mRNA markers in women of different ages. In this multicentric study, a 19-plex mRNA profiling assay including vaginal-specific markers (CYP2B7P1, MUC4, MYOZ1) was tested in a collection of 6-20-month-old vaginal swabs obtained from pre- (n = 84) and postmenopausal (n = 55) female volunteer donors. Overall, participating laboratories were able to correctly identify ~85% of samples as vaginal mucosa by mRNA profiling. The assay's success rate did not differ between the two age groups and was not affected by the time interval between swab collection and RNA analysis. MYOZ1 resulted a less sensitive vaginal marker compared to MUC4 and CYP2B7P1. A significant relative increase in the contribution to the total amplification signal was observed for MUC4, compared to CYP2B7P1 and MYOZ1, in postmenopausal women. Observation of other body fluids and tissues different from vaginal mucosa was also evaluated in connection to information on previous sexual activity and menstrual cycle phase at the time of sampling.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy;
| | - Federica Alessandrini
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Eugenia Carnevali
- Unità Operativa Semplice Laboratory of Forensic Science, Section of Legal Medicine, Department of Medicine and Surgery, S. Maria Hospital, University of Perugia, 05100 Terni, Italy
| | - Matteo Fabbri
- Section of Legal Medicine, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, 34129 Trieste, Italy
| | - Pierangela Grignani
- Section of Legal Medicine and Forensic Sciences, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Francesca Scarnicci
- Section of Legal Medicine, Department of Health Surveillance and Bioethics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Pamela Tozzo
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Forensic Medicine Unit, University of Brescia, 25123 Brescia, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Loredana Buscemi
- AOU Ospedali Riuniti Ancona, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy;
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Meijrink L, van der Scheer M, Kokshoorn B. Bloodstain pattern analysis & Bayes: A case report. Sci Justice 2023; 63:551-561. [PMID: 37453788 DOI: 10.1016/j.scijus.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
The findings from a bloodstain pattern analysis (BPA) may assist in formulating or falsifying scenarios that are considered in the investigative stages of a criminal investigation. When a case proceeds to trial the bloodstain pattern expert may be asked about the relevance of their findings given scenarios that are proposed by the prosecution and defense counsel. Such opinions provided by an expert are highly relevant to police investigation or legal proceedings, but the reasoning behind the opinion or implicit assumptions made by the expert may not be transparent. A proper framework for the evaluation of forensic findings has been developed since the late twentieth century, based on the hierarchy of propositions, Bayesian reasoning and a model for case assessment and interpretation. This framework, when implemented in casework, mitigates some of the risks of cognitive biases, and makes the reasoning and scientific basis for the opinion transparent. This framework is broadly used across forensic science disciplines. In this paper we describe its application to the field of BPA using a case example from the Netherlands Forensic Institute (NFI).
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Affiliation(s)
- Leon Meijrink
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands.
| | - Mikle van der Scheer
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - Bas Kokshoorn
- Netherlands Forensic Institute, Division of Biological Traces, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands; Amsterdam University of Applied Sciences, Faculty of Technology, Amsterdam, The Netherlands
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5
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Raza Q, Wang X, Qureshi MZA, Eldin SM, Mousa AAA, Ali B, Siddique I. Mathematical modeling of nanolayer on biological fluids flow through porous surfaces in the presence of CNT. CASE STUDIES IN THERMAL ENGINEERING 2023; 45:102958. [DOI: 10.1016/j.csite.2023.102958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Johannessen H, Hanson E, Gill P, Haas C, Bergseth EF, Ballantyne J, Fonneløp AE. Body Fluid Identification in Samples Collected after Intimate and Social Contact: A Comparison of Two mRNA Profiling Methods and the Additional Information Gained by cSNP Genotypes. Genes (Basel) 2023; 14:genes14030636. [PMID: 36980908 PMCID: PMC10048544 DOI: 10.3390/genes14030636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The ability to associate a contributor with a specific body fluid in a crime stain can aid casework investigation. The detection of body fluids combined with DNA analyses may supply essential information, but as the two tests are independent, they may not be associated. Recently, the analysis of coding region SNPs (cSNPs) within the RNA transcript has been proven to be a promising method to face this challenge. In this study, we performed targeted RNA sequencing of 158 samples (boxershorts, fingernail swabs and penile swabs) collected from 12 couples at different time points post-intimate contact and after non-intimate contact, using the Ion S5™ System and BFID-cSNP-6F assay. The aim of the study was to compare the performance of the MPS and CE methods in the detection of mRNA markers, and to associate body fluids with contributors by their cSNP genotypes. The results of the study show a lower success rate in the detection of vaginal mucosa by the MPS compared to the CE method. However, the additional information obtained with the cSNP genotypes could successfully associate body fluids with contributors in most cases.
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Affiliation(s)
- Helen Johannessen
- Department of Forensic Medicine, University of Oslo, 0315 Oslo, Norway
- Correspondence: or
| | - Erin Hanson
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32826, USA
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA
| | - Peter Gill
- Department of Forensic Medicine, University of Oslo, 0315 Oslo, Norway
- Department of Forensic Sciences, Oslo University Hospital, 0372 Oslo, Norway
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland
| | | | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32826, USA
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA
| | - Ane Elida Fonneløp
- Department of Forensic Sciences, Oslo University Hospital, 0372 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0371 Oslo, Norway
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7
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Hanson E, Dørum G, Zamborlin M, Wang S, Gysi M, Ingold S, Lagace R, Roth C, Haas C, Ballantyne J. Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures. Int J Legal Med 2023; 137:13-32. [PMID: 36333511 DOI: 10.1007/s00414-022-02908-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
The evidentiary value of DNA profiles varies depending upon the context in which the DNA was found. Linking a DNA profile to a particular cellular phenotype in mixtures may aid in assessing its evidentiary relevance and value. We report the development of two dual-function high-resolution messenger RNA (mRNA) sequencing assays that can each identify the presence of 6 body fluids/tissues (blood, semen, saliva, vaginal secretions, menstrual blood, skin) and, via coding region SNPs (cSNPs) present in the body fluid-specific mRNA transcripts, directly associate particular body fluids with their specific DNA donors in mixtures. The original blood, semen, and saliva (BSS) assay contains 23 cSNPs for blood, semen, and saliva, while the expanded 6F (all 6 fluids/tissues) assay encompasses the BSS assay and also contains 23 additional cSNPs for vaginal secretions, menstrual blood, and skin. Software tools were developed to infer the identity of the body fluids present as well as providing the corresponding cSNP genotypes. Concomitant genomic DNA assays (BSS-d and 6F-d), required to genotype the same cSNPs from persons of interest/inferred contributors to the body fluid mixture, were also developed. Body fluid specificity was demonstrated by the ability to identify the body fluid origin of single-source and two-fluid admixtures. The discriminatory power (European Caucasians) for all body fluids is 0.957-0.997, with linkage disequilibrium considered. Reciprocal body fluid admixtures (mixture pairs with the same two donors but reversed body fluid types) were used to demonstrate the ability to identify the body fluid source of origin as well as associate the donor of each of the two fluids.
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Affiliation(s)
- Erin Hanson
- Department of Chemistry, University of Central Florida, P.O. Box 162367, Orlando, FL, 32816-2367, USA.,National Center for Forensic Science, Orlando, FL, USA
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Manuel Zamborlin
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Shouyu Wang
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Sabrina Ingold
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Robert Lagace
- Life Sciences/HID, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Life Sciences/HID, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jack Ballantyne
- Department of Chemistry, University of Central Florida, P.O. Box 162367, Orlando, FL, 32816-2367, USA. .,National Center for Forensic Science, Orlando, FL, USA.
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8
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van den Berge M, Maaskant-van Wijk P, Sijen T, van Soest S, Ypma R. Weight of evidence from mRNA data: Implementation of an LR-system for forensic body fluid identification in casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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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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10
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Johannessen H, Gill P, Shanthan G, Fonneløp AE. Transfer, persistence and recovery of DNA and mRNA vaginal mucosa markers after intimate and social contact with Bayesian network analysis for activity level reporting. Forensic Sci Int Genet 2022; 60:102750. [PMID: 35914368 DOI: 10.1016/j.fsigen.2022.102750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/25/2023]
Abstract
In sexual assault cases, it can be challenging to identify the type of body fluids/ cell types present in a crime scene sample, especially the origin of epithelial cells. Therefore, more labs are applying mRNA body fluid analysis for saliva, skin and vaginal mucosa markers. To address activity level propositions, it is necessary to assign probabilities of transfer, persistence, prevalence and recovery of DNA and mRNA markers. In this study we analysed 158 samples (fingernail swabs, penile swabs and boxershorts) from 12 couples collected at different time points post intimate contact and after non-intimate contact in order to detect DNA from the person of interest (POI) and mRNA vaginal mucosa markers. Samples were DNA and RNA co-extracted and analysed with PowerPlex®Fusion 6C System and 19-plex mRNA primer mix respectively, using Endpoint PCR and the CE platform. Vaginal mucosa was detected up to 36 h post intimate contact, but also detected in one non-intimate contact sample. In 94% of intimate contact and 50 % of non-intimate contact samples the DNA results support the proposition that POI is the donor (LR ≥ 10,000). There was a strong association between the detection of vaginal mucosa and the average RFU value of the POI. The data were used to instantiate a comprehensive Bayesian network to evaluate the evidence at activity level, given alternate propositions conditioned upon indirect or direct transfer events. It is shown that the value of the evidence is mainly affected by the high DNA quantity (measured as mean RFU) that is recovered from the POI. The detection of vaginal mucosa had low impact upon the resultant likelihood ratio.
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Affiliation(s)
| | - Peter Gill
- Department of Forensic Medicine, University of Oslo, Norway; Department of Forensic Sciences, Oslo University Hospital, Norway
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11
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Evaluation of the Effects of Different Sample Collection Strategies on DNA/RNA Co-Analysis of Forensic Stains. Genes (Basel) 2022; 13:genes13060983. [PMID: 35741745 PMCID: PMC9222428 DOI: 10.3390/genes13060983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). Analyses were conducted on whole blood, luminol-treated diluted blood, saliva, semen, and mock skin stains. The effects of swab storage temperature and the time interval between sample collection and DNA/RNA extraction were also investigated. Water provided significantly higher DNA yields than ethanol in whole blood and semen samples, while ethanol and RNAlater® significantly outperformed water in skin samples, with full STR profiles obtained from over 98% of the skin samples collected with either ethanol or RNAlater®, compared to 71% of those collected with water. A significant difference in mRNA profiling success rates was observed in whole blood samples between swabs treated with either ethanol or RNAlater® (100%) and water (37.5%). Longer swab storage times before processing significantly affected mRNA profiling in saliva stains, with the success rate decreasing from 91.7% after 1 day of storage to 25% after 7 days. These results may contribute to the future development of optimal procedures for the collection of different types of biological traces.
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12
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Precise and comprehensive determination of multiple body fluids by applying statistical cutoff values to a multiplex reverse transcription-PCR and capillary electrophoresis procedure for forensic purposes. Leg Med (Tokyo) 2022; 58:102087. [DOI: 10.1016/j.legalmed.2022.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022]
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13
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Bamberg M, Bruder M, Dierig L, Kunz SN, Schmidt M, Wiegand P. Best of both: a simultaneous analysis of mRNA and miRNA markers for body fluid identification. Forensic Sci Int Genet 2022; 59:102707. [DOI: 10.1016/j.fsigen.2022.102707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/19/2022]
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14
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Dørum G, Bleka Ø, Gill P, Haas C. Source level interpretation of mixed biological stains using coding region SNPs. Forensic Sci Int Genet 2022; 59:102685. [DOI: 10.1016/j.fsigen.2022.102685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
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15
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Development of a combined differential DNA/RNA co-extraction protocol and its application in forensic casework. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Neis M, Siegel S, Banaschak S, Schneider PM. Schwere sexualisierte Gewalt – Aufklärung eines Falls durch Kombination aus DNA- und mRNA-Analyse. Rechtsmedizin (Berl) 2021. [DOI: 10.1007/s00194-021-00544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ZusammenfassungMithilfe der Analyse von mRNA-Expressionsmustern durch Einsatz der PCR-Amplifikation von zellspezifischen cDNA-Transkripten und Nachweis der Amplifikate mittels Kapillarelektrophorese (CE) lässt sich die Frage klären, aus welchen Zelltypen (Blut, Speichel, Sperma, Vaginalschleimhaut, Menstrual- und Nasensekret) sich eine biologische Spur zusammensetzt. Durch Verwendung der DNA-RNA-Koextraktion kann dieses Verfahren unabhängig von der STR-Typisierung durchgeführt werden. Am Beispiel des hier dargestellten Falles, bei dem Vaginalsekret der verletzten Frau am Mittelfinger des Beschuldigten nachgewiesen wurde, wird gezeigt, dass der Einsatz dieser Methode besonders bei Fällen von sexualisierter Gewalt sinnvoll ist.
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Hussein RF, El Mahdy SM, Saged NM, Rashed L, Ghaleb SS. Identification of body fluids—menstrual blood, saliva, and nasal secretions—over different periods of time, using mRNA. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2021. [DOI: 10.1186/s41935-021-00256-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Forensic examination of biological samples started at the beginning of the twentieth century by applying the ABO blood group system in evidence related to crimes or human identification. In the present study, real-time PCR multiplex was used to identify dried and stored swabs (saliva, nasal secretions, and menstrual blood) through the target genes of saliva (histatin 3 and statherin), nasal secretions (statherin and BPIFA1), and menstrual blood (metalloproteinases 10 and 7).
Results
The expressions of histatin 3 and statherin in the dried saliva decreased over days of storage with a significant p value of <0.001. BPIFA1 was highly expressed in nasal secretions, and the expression level significantly decreased throughout the study with a significant p value of <0.001. The MMP7 and MMP10 genes were highly expressed in the menstrual blood, and the expression level decreased over days of storage with a significant p value of p<0.001.
Conclusions
Dried swabs of the saliva, Nasal secretions, Menstrual blood can be identified over the storage duration of the study using mRNA profiling of specific markers.
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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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19
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Huang H, Liu X, Cheng J, Xu L, He X, Xiao C, Huang D, Yi S. A novel multiplex assay system based on 10 methylation markers for forensic identification of body fluids. J Forensic Sci 2021; 67:136-148. [PMID: 34431515 DOI: 10.1111/1556-4029.14872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/12/2021] [Accepted: 08/10/2021] [Indexed: 12/23/2022]
Abstract
Identifying the source of body fluids found at a crime scene is an essential forensic step. Some methods based on DNA methylation played significant role in body fluids identification. Since DNA methylation is related to multiple factors, such as race, age, and diseases, it is necessary to know the methylation profile of a given population. In this study, we tested 19 body fluid-specific methylation markers in a Chinese Han population. A novel multiplex assay system based on the selected markers with smaller variation in methylation and stronger tissue-specific methylation were developed for the identification of body fluids. The multiplex assay were tested in 265 body fluid samples. A random forest model was established to predict the tissue source based on the methylation data of the 10 markers. The multiplex assay was evaluated by testing the sensitivity, the mixtures, and old samples. For the result, the novel multiplex assay based on 10 selected methylation markers presented good methylation profiles in all tested samples. The random forest model worked extremely well in predicting the source of body fluids, with an accuracy of 100% and 97.5% in training data and test data, respectively. The multiplex assay could accurately predict the tissue source from 0.5 ng genomic DNA, six-months-old samples and distinguish the minor component from a mixture of two components. Our results indicated that the methylation multiplex assay and the random forest model could provide a convenient tool for forensic practitioners in body fluid identification.
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Affiliation(s)
- Hongzhi Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of the Forensic Science, Hubei University of Police, Wuhan, Hubei, China
| | - Xiaozhao Liu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juanbo Cheng
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Linxia Xu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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20
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Tian H, Huang S, Bai P, Xiao X, Peng D, Zhao H, Liu Y, Feng Q, Liao M, Li F, Liang W. The effect of infertile semen on the mRNA-based body fluid identification. Electrophoresis 2021; 42:1614-1622. [PMID: 34233021 DOI: 10.1002/elps.202000238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 11/08/2022]
Abstract
In the past decade, mRNA markers have been well demonstrated as promising molecular markers in forensic body fluid identification (BFI), and successfully used in wide applications. Several studies have assessed the performance of semen-specific mRNA markers in distinguishing semen from other common body fluids at the crime scene. Infertility has been reported as a global health problem that is affecting approximately 15% of couples worldwide. Therefore, it is important for forensic researchers to consider the impact of infertility on semen identification. This study aimed to explore the effect of semen from infertile men (hereinafter "infertile semen") on BFI and to identify semen-specific mRNAs that can efficiently and accurately distinguish normal and infertile semen samples from other body fluids. Results showed that the selected five mRNAs (KLK3, TGM4, SEMG1, PRM1, and PRM2) performed a significantly high semen specificity in normal semen. Moreover, KLK3 was slightly influenced by infertile semen samples with over 98% positive results in all semen samples. The accuracy to predict normal semen reached up to 96.6% using the discrimination function Y1 with KLK3 and PRM1. However, when the infertile semen samples were included in discrimination function (function Y2 with KLK3), the accuracy rate of semen identification (including the normal and infertile semen) was down to 89.5%. Besides, the sensitivity of multiplex assay could reach down to 50pg. Our results suggest that it is important to consider the presence of infertile semen when using mRNAs to identify semen samples, which would have a far-reaching impact in forensic identification.
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Affiliation(s)
- Huan Tian
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Sicheng Huang
- Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu, Sichuan, P. R. China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Xiao Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Duo Peng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Huan Zhao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qian Feng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fuping Li
- Human Sperm Bank, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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21
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Bamberg M, Dierig L, Kulstein G, Kunz SN, Schmidt M, Hadrys T, Wiegand P. Development and validation of an mRNA-based multiplex body fluid identification workflow and a rectal mucosa marker pilot study. Forensic Sci Int Genet 2021; 54:102542. [PMID: 34098418 DOI: 10.1016/j.fsigen.2021.102542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 01/26/2023]
Abstract
Molecular identification of body fluids and tissues is crucial in order to understand the circumstances of crimes. For that reason, molecular investigations used to identify body fluids/tissues have increasingly been examined recently. Various studies have proved that messenger RNA (mRNA) profiling is a sensitive and robust method for body fluid/tissue identification. The forensically relevant body fluids/tissues blood, semen, saliva, vaginal secretion, menstrual blood and skin have all been detected successfully by applying suitable mRNA assay. However, rectal mucosa, which can be found as evidence in sexual assault cases, has been neglected in forensic investigations. So far there is no mRNA marker to detect rectal mucosa, although anal penetration occurs in a large number of sexual assaults (23.2% of female victims and 50% of male victims). In this study, specific and sensitive mRNA markers for forensically relevant body fluids were adapted and validated in an mRNA multiplex assay for routine casework. This included the implementation of a DNA/RNA re-extraction method for automated extraction that can be integrated into casework without loss of DNA. This re-extraction method and the mRNA multiplex assay were tested using casework samples. PCR-primers were designed for the identification of rectal mucosa and the more effective marker MUC12 was integrated into an extended multiplex assay. The result of our study is a highly specific and sensitive mRNA multiplex assay plus an automated DNA/RNA re-extraction method, that can be integrated into casework and identify rectal mucosa for the first time.
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Affiliation(s)
- Malte Bamberg
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Lisa Dierig
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | | | - Sebastian N Kunz
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Max Schmidt
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, DNA Department, Maillingerstr. 15, 80636 Munich, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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22
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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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23
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Meakin GE, Kokshoorn B, Oorschot RAH, Szkuta B. Evaluating forensic
DNA
evidence: Connecting the dots. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/wfs2.1404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Georgina E. Meakin
- Centre for Forensic Science University of Technology Sydney Ultimo NSW Australia
- Centre for the Forensic Sciences, Department of Security and Crime Science University College London London UK
| | - Bas Kokshoorn
- Netherlands Forensic Institute The Hague The Netherlands
| | - Roland A. H. Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department Macleod Australia
- School of Molecular Sciences La Trobe University Bundoora Australia
| | - Bianca Szkuta
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department Macleod Australia
- School of Life and Environmental Sciences Deakin University Geelong Australia
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24
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Cortellini V, Brescia G, Cerri N, Verzeletti A. Simultaneous DNA and RNA profiling in a case of sexual assault in a 3-year-old child: Forensic genetics solves the crime. Leg Med (Tokyo) 2020; 47:101727. [DOI: 10.1016/j.legalmed.2020.101727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/02/2019] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
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25
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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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26
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Akutsu T, Watanabe K. A Proposed Procedure for Discriminating between Nasal Secretion and Saliva by RT-qPCR. Diagnostics (Basel) 2020; 10:E519. [PMID: 32722656 PMCID: PMC7460356 DOI: 10.3390/diagnostics10080519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022] Open
Abstract
In forensic casework, nasal secretion can be a good source of DNA. Moreover, saliva can prove useful in cases of sexual assault. However, discriminating between these body fluids is often difficult because of cross-reactivity between them on presumptive and confirmatory tests. Therefore, an RT-qPCR procedure was developed to discriminate between nasal secretion and saliva. Characteristic genes in nasal secretion and/or saliva (BPIFA1, STATH, HTN3, and PRH2) were selected as candidates. Discrimination criteria were established based on the expression levels of these markers in various body fluids. In addition, a flowchart was proposed and used to discriminate among nasal secretion, saliva, and other body fluids in various forensic samples. BPIFA1 was highly expressed in nasal secretion but was also expressed in saliva, semen, and vaginal fluid at trace levels. STATH was expressed in nasal secretion and saliva but not in other body fluids. HTN3 was specifically expressed in most of the saliva samples, as reported previously. Unexpectedly, PRH2 was expressed in only a few saliva samples. Using the proposed criteria and flowchart, nasal secretion and saliva were successfully discriminated among the various body fluids tested. The developed procedure could be useful in forensic casework.
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Affiliation(s)
- Tomoko Akutsu
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa-shi, Chiba 277-0882, Japan;
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27
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Tozzo P, Gabbin A, Politi C, Da Pian M, Caenazzo L, Causin V. Combined Statistical Analyses of Forensic Evidence in Sexual Assault: A Case Report and Brief Review of the Literature. J Forensic Sci 2020; 65:1767-1773. [PMID: 32615002 DOI: 10.1111/1556-4029.14487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022]
Abstract
DNA analysis has been widely used in the forensic field in order to contribute to identifying the perpetrator of a crime. Forensic investigation in sexual assaults usually focuses on locating and identifying biological fluids, followed by DNA analysis. The identification of certain compounds present in condoms can be useful to reconstruct the occurred event, especially in cases of sexual assaults where the DNA analysis did not show the presence of a male profile and where RNA analysis did not show the presence of sperm markers. Herein we describe the case of a woman reporting to be victim of sexual assault, who was not able to provide accurate information concerning the dynamics of the event; she remembered only forced penile-vaginal penetration by a single perpetrator. We performed short tandem repeat (STR) analyses and mRNA typing for forensic genetics testing on vaginal and rectal swabs collected on the victim, and Fourier-transform infrared spectroscopy (FTIR) followed by chromatographic analyses for the detection of condom compounds on the same swabs. The STR analysis showed only the victim's genetic profile, and RNA analysis showed only the presence of vaginal and skin markers. In this situation, the identification of condom compounds residues on vaginal swabs became important as it complemented other collected evidences allowing the Court to reconstruct the events. A proposal of likelihood ratio (LR) calculation for the assessment of the weight of evidence in this case is described.
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Affiliation(s)
- Pamela Tozzo
- Laboratory of Forensic Genetics, Department of Molecular Medicine, University of Padova, Via Falloppio 50, Padova, 35121, Italy
| | - Andrea Gabbin
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Falloppio 50, Padova, 35121, Italy
| | - Caterina Politi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Falloppio 50, Padova, 35121, Italy
| | - Marta Da Pian
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
| | - Luciana Caenazzo
- Laboratory of Forensic Genetics, Department of Molecular Medicine, University of Padova, Via Falloppio 50, Padova, 35121, Italy
| | - Valerio Causin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
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28
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Chirnside O, Lemalu A, Fleming R. Identification of nasal mucosa markers for forensic mRNA body fluid determination. Forensic Sci Int Genet 2020; 48:102317. [PMID: 32563047 DOI: 10.1016/j.fsigen.2020.102317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/10/2020] [Accepted: 05/26/2020] [Indexed: 01/26/2023]
Abstract
Biological fluids are commonly encountered as a form of evidence within forensic science, and can often provide important information relating to events which may have occurred. Over the years, significant advancements have been made with DNA profiling techniques, allowing for links to be made between an individual and cellular material recovered from a crime scene. While this DNA analysis can aid in linking an individual to a crime, it can often be beneficial to also determine the body fluid source of the DNA obtained from the sample in question for case context. One increasing area within the forensic field is the use of mRNA profiling for the identification of body fluids. The analysis of gene expression patterns can give information on cell function, and ultimately the body fluid source of the DNA in a sample. Over time this has led to the development of mRNA reverse transcriptase PCR assays to detect body fluid specific RNA transcripts for casework. During the use of these techniques nasal mucosa has been observed to give rise to false positive results. We report here on the identification of promising markers using RNA sequencing for the detection of nasal mucosa, with the aim to incorporate these markers into existing assays to assist in the identification of nasal mucosa and to assist in the interpretation of possible false positive results.
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Affiliation(s)
- Olivia Chirnside
- Forensic Science Program, Department of Chemistry, University of Auckland, New Zealand
| | - Anna Lemalu
- Institute of Environmental Science and Research Ltd (ESR), Mt Albert Science Centre, Hampstead Road, Private Bag, 92021, Auckland, New Zealand
| | - Rachel Fleming
- Institute of Environmental Science and Research Ltd (ESR), Mt Albert Science Centre, Hampstead Road, Private Bag, 92021, Auckland, New Zealand.
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29
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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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30
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Díez López C, Montiel González D, Haas C, Vidaki A, Kayser M. Microbiome-based body site of origin classification of forensically relevant blood traces. Forensic Sci Int Genet 2020; 47:102280. [PMID: 32244163 DOI: 10.1016/j.fsigen.2020.102280] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Human blood traces are amongst the most commonly encountered biological stains collected at crime scenes. Identifying the body site of origin of a forensic blood trace can provide crucial information in many cases, such as in sexual and violent assaults. However, means for reliably and accurately identifying from which body site a forensic blood trace originated are missing, but would be highly valuable in crime scene investigations. With this study, we introduce a taxonomy-independent deep neural network approach based on massively parallel microbiome sequencing, which delivers accurate body site of origin classification of forensically-relevant blood samples, such as menstrual, nasal, fingerprick, and venous blood. A total of 50 deep neural networks were trained using a large 16S rRNA gene sequencing dataset from 773 reference samples, including 220 female urogenital tract, 190 nasal cavity, 213 skin, and 150 venous blood samples. Validation was performed with de-novo generated 16S rRNA gene massively parallel sequencing (MPS) data from 94 blood test samples of four different body sites, and achieved high classification accuracy with AUC values at 0.992 for menstrual blood (N = 23), 0.978 for nasal blood (N = 16), 0.978 for fingerprick blood (N = 30), and 0.990 for venous blood (N = 25). The obtained highly accurate classification of menstrual blood was independent of the day of the menses, as established in additional 86 menstrual blood test samples. Accurate body site of origin classification was also revealed for 45 fresh and aged mock casework blood samples from all four body sites. Our novel microbiome approach works based on the assumption that a sample is from blood, as can be obtained in forensic practise from prior presumptive blood testing, and provides accurate information on the specific body source of blood, with high potentials for future forensic applications.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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31
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Fattorini P, Bonin S, Marrubini G, Bertoglio B, Grignani P, Recchia E, Pitacco P, Zupanič Pajnič I, Sorçaburu-Ciglieri S, Previderè C. Highly degraded RNA can still provide molecular information: An in vitro approach. Electrophoresis 2020; 41:386-393. [PMID: 31967656 DOI: 10.1002/elps.201900200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/01/2023]
Abstract
The long-term survival of RNA in postmortem tissues is a tricky topic. Many aged/forensic specimens show, in fact, high rates of null/inconclusive PCR-based results, while reliable outcomes were sometimes achieved from archaeological samples. On the other hand, several data show that the RNA is a molecule that survives even to several physical-chemical stresses. In the present study, a simple protocol, which was already developed for the prolonged hydrolysis of DNA, was applied to a RNA sample extracted from blood. This protocol is based on the heat-mediated (70°C) hydrolysis for up to 36 h using ultrapure water and di-ethyl-pyro-carbonate-water as hydrolysis medium. Measurable levels of depurination were not found even if microfluidic devices showed a progressive pattern of degradation. The reverse transcription/quantitative PCR analysis of two (60 bp long) housekeeping targets (glyceraldehyde-3-phosphate dehydrogenase and porphobilinogen deaminase) showed that the percentage of amplifiable target (%AT) decreased in relation to the duration of the damaging treatment (r2 > 0.973). The comparison of the %AT in the degraded RNA and in the DNA samples that underwent the same damaging treatment showed that the %AT is always higher in RNA, reaching up to three orders of magnitude. Lastly, even the end-point PCR of blood-specific markers gave reliable results, which is in agreement with the body fluid origin of the sample. In conclusion, all the PCR-based results show that RNA maintains the ability to be retro-transcribed in short cDNA fragments even after 36 h of incubation at 70°C in mildly acidic buffers. It is therefore likely that the long-term survival of RNA samples depends mainly on the protection against RNAase attacks rather than on environmental factors (such as humidity and acidity) that are instead of great importance for the stability of DNA. As a final remark, our results suggest that the RNA analysis can be successfully performed even when DNA profiling failed.
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Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | | | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Elisa Recchia
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Paola Pitacco
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
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32
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Robino C, Chierto E, Alessandrini F, Bini C, Carnevali E, Fabbri M, Fattorini P, Grignani P, Scarnicci F, Tozzo P, Verzeletti A, Pelotti S, Buscemi L. Evaluation of vaginal mRNA markers in women from different age groups: A GeFI collaborative study. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Watanabe K, Akutsu T. Evaluation of a co-extraction kit for mRNA, miRNA and DNA methylation-based body fluid identification. Leg Med (Tokyo) 2019; 42:101630. [PMID: 31751797 DOI: 10.1016/j.legalmed.2019.101630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023]
Abstract
Recently, messenger RNA (mRNA), micro RNA (miRNA), and DNA methylation (DNAm) have been reported as novel markers for body fluid identification (BFID). Comprehensive analysis of these markers should be a flexible and reliable BFID method for various types of forensic samples. However, independent extraction of all targets can be difficult depending on the usable amounts of samples. In this study, the applicability of a co-extraction kit for these molecules, the AllPrep DNA/RNA/miRNA Universal Kit (APU), was evaluated by comparing RNA and DNA extracted from blood and saliva stains by the APU with those extracted by standard kits for each molecule and by previously reported methods for mRNA/DNA or miRNA/DNA co-extraction. Electrophoresis using the Bioanalyzer platform and real-time PCR analysis revealed that the APU performed almost equivalently to each standard kit in the quality of RNA or DNA extracted and extraction efficiency of mRNAs, miRNAs, and DNA. Moreover, the APU outperformed the co-extraction methods, especially in RNA integrity and miRNA extraction efficiency. In addition, pyrosequencing revealed that the methylation ratios of DNA extracted by the APU were not different from those extracted by standard DNA extraction kits. Overall, the APU is applicable to comprehensive analysis of mRNA/miRNA/DNAm markers for BFID analysis. Because the DNA eluate can also be used for DNA typing, the APU may be among the best choices for forensic examination of body fluid samples in terms of its flexibility and reliability in BFID and efficiency in sample consumption.
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Affiliation(s)
- Ken Watanabe
- National Research Institute of Police Science, Chiba 277-0882, Japan.
| | - Tomoko Akutsu
- National Research Institute of Police Science, Chiba 277-0882, Japan
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34
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Fujimoto S, Manabe S, Morimoto C, Ozeki M, Hamano Y, Hirai E, Kotani H, Tamaki K. Distinct spectrum of microRNA expression in forensically relevant body fluids and probabilistic discriminant approach. Sci Rep 2019; 9:14332. [PMID: 31586097 PMCID: PMC6778116 DOI: 10.1038/s41598-019-50796-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/19/2019] [Indexed: 11/09/2022] Open
Abstract
MicroRNA is attracting worldwide attention as a new marker for the identification of forensically relevant body fluids. A probabilistic discriminant model was constructed to identify venous blood, saliva, semen, and vaginal secretion, based on microRNA expression assessed via RT-qPCR. We quantified 15 candidate microRNAs in four types of body fluids by RT-qPCR and found that miR-144-3p, miR-451a-5p, miR-888-5p, miR-891a-5p, miR-203a-3p, miR-223-3p and miR-1260b were helpful to discriminate body fluids. Using the relative expression of seven candidate microRNAs in each body fluid, we implemented a partial least squares-discriminant analysis (PLS-DA) as a probabilistic discriminant model and distinguished four types of body fluids. Of 14 testing samples, 13 samples were correctly identified with >90% posterior probability. We also investigated the effects of microRNA expression in skin, semen infertility, and vaginal secretion during different menstrual phases. Semen infertility and menstrual phases did not affect our body fluid identification system. Therefore, the selected microRNAs were effective in identifying the four types of body fluids, indicating that probabilistic evaluation may be practical in forensic casework.
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Affiliation(s)
- Shuntaro Fujimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Sho Manabe
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Chie Morimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Munetaka Ozeki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuya Hamano
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Forensic Science Laboratory, Kyoto Prefectural Police Headquaters, 85-3, 85-4, Yabunouchi-cho, Kamigyo-ku, Kyoto, 602-8550, Japan
| | - Eriko Hirai
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirokazu Kotani
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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35
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Charles DD, Fisher JR, Hoskinson SM, Medina-Colorado AA, Shen YC, Chaaban MR, Widen SG, Eaves-Pyles TD, Maxwell CA, Miller AL, Popov VL, Pyles RB. Development of a Novel ex vivo Nasal Epithelial Cell Model Supporting Colonization With Human Nasal Microbiota. Front Cell Infect Microbiol 2019; 9:165. [PMID: 31165051 PMCID: PMC6536665 DOI: 10.3389/fcimb.2019.00165] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/01/2019] [Indexed: 12/19/2022] Open
Abstract
The nasal mucosa provides first line defense against inhaled pathogens while creating a unique microenvironment for bacterial communities. Studying the impact of microbiota in the nasal cavity has been difficult due to limitations with current models including explant cultures, primary cells, or neoplastic cell lines. Most notably, none have been shown to support reproducible colonization by bacterial communities from human donors. Therefore, to conduct controlled studies of the human nasal ecosystem, we have developed a novel ex vivo mucosal model that supports bacterial colonization of a cultured host mucosa created by immortalized human nasal epithelial cells (NEC). For this model, immortalized NEC established from 5 male and 5 female donors were cultured with an air-interfaced, apical surface on a porous transwell membrane. NEC were grown from nasal turbinate tissues harvested from willed bodies or from discarded tissue collected during sinonasal procedures. Immortalized cells were evaluated through molecular verification of cell type, histological confirmation of tissue differentiation including formation of tight junctions, NEC multilayer viability, metabolism, physiology and imaging of the luminal surface by scanning electron microscopy. Results showed proper differentiation and multilayer formation at seven to 10 days after air interface that was maintained for up to 3 weeks. The optimized mucosal cultures created an environment necessary to sustain colonization by nasal microbiomes (NMBs) that were collected from healthy volunteers, cryogenically preserved and characterized with customized quantitative polymerase chain reaction (qPCR) arrays. Polymicrobial communities of nasal bacteria associated with healthy and inflamed states were consistently reproduced in matured NEC co-cultures by transplant of NMBs from multiple community types. The cultured NMBs were stable after an initial period of bacterial replication and equilibration. This novel ex vivo culture system is the first model that supports controlled cultivation of NMBs, allowing for lab-based causation studies and further experimentation to explore the complexities of host-microbe and microbe-microbe interactions.
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Affiliation(s)
- Derald D Charles
- School of Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - James R Fisher
- School of Medicine, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Sarah M Hoskinson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | | | - Yi C Shen
- School of Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | - Mohamad R Chaaban
- Department of Otolaryngology, University of Texas Medical Branch, Galveston, TX, United States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Tonyia D Eaves-Pyles
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Carrie A Maxwell
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Aaron L Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Richard B Pyles
- School of Medicine, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States.,Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States
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36
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Developmental validation of an enhanced mRNA-based multiplex system for body fluid and cell type identification. Sci Justice 2019; 59:217-227. [DOI: 10.1016/j.scijus.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/16/2018] [Accepted: 01/20/2019] [Indexed: 12/14/2022]
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37
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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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38
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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39
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The Importance of Distinguishing Menstrual and Peripheral Blood in Forensic Casework. ACTA ACUST UNITED AC 2018; 39:337-340. [DOI: 10.1097/paf.0000000000000414] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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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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41
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Fabbri M, Venturi M, Talarico A, Frisoni P, Gaudio R, Neri M. mRNA profiling in ancient blood stains. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Fabbri M, Venturi M, Talarico A, Inglese R, Gaudio R, Neri M. mRNA profiling: Application to an old casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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DNA/RNA co-analysis of seminal fluid-stained fabrics after water immersion for up to seven days. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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44
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A GEFI collaborative exercise on DNA/RNA co-analysis and mRNA profiling interpretation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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45
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Stella C, Mitchell R, van Oorschot R. Hand activities during robberies—Relevance to consideration of DNA transfer and detection. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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McColl DL, Harvey ML, van Oorschot RA. DNA transfer by different parts of a hand. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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47
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Stafford-Allen B, Dawnay N, Hanson EK, Ball G, Gupta A, Blackman S, French DJ, Duxbury N, Ballantyne J, Wells S. Development of HyBeacon ® probes for specific mRNA detection using body fluids as a model system. Mol Cell Probes 2017; 38:51-59. [PMID: 29175285 DOI: 10.1016/j.mcp.2017.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022]
Abstract
HyBeacons are linear oligonucleotides which incorporate fluorescent dyes covalently linked to internal nucleotides. They have previously been used with PCR and isothermal amplification to interrogate SNPs and STRs in fields as diverse as clinical diagnostics, food authentication, and forensic DNA profiling. This work explores their use for the identification of expressed gene sequences through mRNA profiling. The use of mRNA is becoming increasingly common in forensic casework to identify body fluids on evidence items, as it offers higher specificity and fewer false positives than current chemical presumptive testing methods. The work presented here details the development of a single-step one-tube RT-PCR assay to detect the presence of body fluids of forensic interest (saliva, blood, seminal fluid, vaginal fluid and menstrual blood) using HyBeacon® probes and melt curve analysis. Each assay shows a high degree of specificity to the target body fluid mRNA suggesting there is no requirement to remove genomic DNA prior to analysis. Of the five assays developed, four were able to detect between 10 and 100 copies of target cDNA, the fifth 1000 copies of target. The results presented here demonstrate that such an approach can be optimised for non-expert users and further areas of work are discussed.
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Affiliation(s)
- Beccy Stafford-Allen
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK.
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Erin K Hanson
- National Center for Forensic Science, PO Box 162367, Orlando, FL, 32816-2367, USA
| | - Glyn Ball
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - Ambika Gupta
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Stephen Blackman
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - David J French
- Product Development Group, LGC Ltd, Queens Road, Teddington, TW11 0LY, UK
| | - Nicola Duxbury
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - Jack Ballantyne
- National Center for Forensic Science, PO Box 162367, Orlando, FL, 32816-2367, USA; Department of Chemistry, University of Central Florida, PO Box 162366, Orlando, FL, 32816-2366, USA
| | - Simon Wells
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
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48
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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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49
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An inter-laboratory comparison study on transfer, persistence and recovery of DNA from cable ties. Forensic Sci Int Genet 2017; 31:95-104. [DOI: 10.1016/j.fsigen.2017.08.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 11/21/2022]
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50
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Kulstein G, Wiegand P. Comprehensive examination of conventional and innovative body fluid identification approaches and DNA profiling of laundered blood- and saliva-stained pieces of cloths. Int J Legal Med 2017; 132:67-81. [DOI: 10.1007/s00414-017-1691-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/12/2017] [Indexed: 01/26/2023]
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