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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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Wang S, Jiang T, Yuan C, Wu L, Zhen X, Lei Y, Xie B, Tao R, Li C. An mRNA profiling assay incorporating coding region InDels for body fluid identification and the inference of the donor in mixed samples. Forensic Sci Int Genet 2024; 69:102979. [PMID: 38043150 DOI: 10.1016/j.fsigen.2023.102979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023]
Abstract
Biological traces discovered at crime scenes hold significant significance in forensic investigations. In cases involving mixed body fluid stains, the evidentiary value of DNA profiles depends on the type of body fluid from which the DNA was obtained. Recently, coding region polymorphism analysis has proved to be a promising method for directly linking specific body fluids to their respective DNA contributors in mixtures, which may help to avoid "association fallacy" between separate DNA and RNA evidence. In this study, we present an update on previously reported coding region Single Nucleotide Polymorphisms (cSNPs) by exploring the potential application of coding region Insertion/Deletion polymorphisms (cInDels). Nine promising cInDels, selected from 70 mRNA markers based on stringent screening criteria, were integrated into an existing mRNA profiling assay. Subsequently, the body fluid specificity of our cInDel assay and the genotyping consistency between complementary DNA (cDNA) and genomic DNA (gDNA) were examined. Our study demonstrates that cInDels can function as important multifunctional genetic markers, as they provide not only the ability to confirm the presence of forensically relevant body fluids, but also the ability to associate/dissociate specific body fluids with particular donors.
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Affiliation(s)
- Shouyu Wang
- Department of Forensic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Tingting Jiang
- Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
| | - Chunyan Yuan
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China
| | - Liming Wu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China
| | - Xiaoyuan Zhen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China
| | - Yinlei Lei
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China
| | - Baoyan Xie
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China; Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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3
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Song B, Qian J, Fu J. Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine. Int J Legal Med 2024; 138:329-350. [PMID: 37770641 DOI: 10.1007/s00414-023-03091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.
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Affiliation(s)
- Binghui Song
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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4
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Dawnay N, Sheppard K. From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom. Sci Justice 2023; 63:206-228. [PMID: 36870701 DOI: 10.1016/j.scijus.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.
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Affiliation(s)
- Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.
| | - Kayleigh Sheppard
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
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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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Establishment of a co-analysis system for personal identification and body fluid identification: a preliminary report. Int J Legal Med 2022; 136:1565-1575. [PMID: 36076078 DOI: 10.1007/s00414-022-02886-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 08/24/2022] [Indexed: 10/14/2022]
Abstract
Analysis of genetic markers can provide clues for case investigation. Short tandem repeat (STR) detection and analysis are widely used for both personal identification and parentage testing. However, DNA analysis currently cannot provide sufficient information for body fluid identification. Tissue or cell sources of samples can be identified by detecting body fluid-specific mRNA markers, which have been studied thoroughly. Integrating STR profiling and mRNA expression patterns can provide more information than conventional methods for investigations and the reconstruction of crime scenes; this can be achieved by DNA/RNA co-extraction technology, which is economical, efficient, and suitable for low-template samples. Here, we propose a co-analysis system based on the PowerPlex 16 kit. This system can simultaneously amplify 25 markers, including 15 STRs, one non-STR amelogenin, and nine mRNA markers (three blood-specific, two saliva-specific, two semen-specific, and two housekeeping gene markers). The specificity and sensitivity of the co-analysis system were determined and aged and degraded samples were used to validate the stability of the co-analysis system. Finally, different DNA/RNA ratios and various carriers were evaluated. The results showed that the DNA/RNA co-analysis system correctly identified different types of body fluid stains. The STR profiles obtained using the co-analysis system were identical to those obtained using the PP16 kit, which demonstrates that the mRNA primers used did not affect STR profiling. Complete STR and mRNA profiles could be obtained from 1/8 portions of buccal swabs, 1/16 portions of swabs of blood and semen samples, 0.1 cm2 of blood samples, 0.25 cm2 of semen samples, and 1.0 cm2 saliva samples. Additionally, our findings indicate that complete STR and mRNA profiles can be obtained with this system from blood and semen samples when the DNA/RNA ratio is 1:1/32. This study suggests that the co-analysis system could be used for simultaneous personal identification and body fluid identification.
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Wei Y, Wang J, Wang Q, Cong B, Li S. The estimation of bloodstain age utilizing circRNAs and mRNAs biomarkers. Forensic Sci Int 2022; 338:111408. [PMID: 35901585 DOI: 10.1016/j.forsciint.2022.111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/19/2022]
Abstract
Determining the time since deposition (TsD) of bloodstains can provide forensic investigators with additional clues, as it can corroborate eyewitness accounts, limit the number of suspects, and help confirm alibis. Bloodstains are the most common bodily fluid stains at crime scenes. In this study, we examined the relative expression levels (REs) of circRNAs and mRNAs data in bloodstains over ten time points by Real-time quantitative polymerase chain reaction (qPCR), to determine the utility of the relative expression levels of RNA markers for TsD estimation. Forensic samples more than just appear in indoor settings, we also evaluated the use of RNA degradation rate to indicate the age of bloodstains in different environments including indoor and outdoor conditions. The expression levels of six blood-specific mRNA markers (GYPA, CD93, ALAS2, SPTB, HBB, HBA), three highly expressed circRNAs in human peripheral blood (hsa_circ_0001445, hsa_circ_0000972, hsa_circ_0000095) and three reference genes (18 S, ACTB and U6) were analyzed across numerous ageing time points. Analysis of the degradation rates of individual RNAs under indoor and outdoor conditions showed that they exhibited a unique degradation profile during the four-month storage interval, with both circRNAs and mRNAs linearly showing continuous degradation, while U6 is more stable than other reference gene markers. In the current study, we firstly used circRNAs as additional novel biomarkers for bloodstain age estimation, and at the same time proved that different environments had a significant impact on the REs of certain blood biomarkers, and sex differences did not affect the age estimation of bloodstains. The REs of the selected RNA molecules in this study showed a non-linear relationship with bloodstain age and the mathematical formula for estimating the bloodstain age based on the relative expression levels of hsa_circ_0001445, ALAS2 and HBB can be used to estimate the TsD of bloodstains from the REs of bloodstains of unknown age, which represent a potentially effective approach to looking for time-dependent changes and TsD estimation.
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Affiliation(s)
- Yangyan Wei
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Junyan Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Shujin Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
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8
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Vibrational spectroscopic approaches for semen analysis in forensic investigation: State of the art and way forward. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Developments in forensic DNA analysis. Emerg Top Life Sci 2021; 5:381-393. [PMID: 33792660 PMCID: PMC8457771 DOI: 10.1042/etls20200304] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022]
Abstract
The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.
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10
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Salzmann AP, Arora N, Russo G, Kreutzer S, Snipen L, Haas C. Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers. Forensic Sci Int Genet 2021; 53:102537. [PMID: 34090061 DOI: 10.1016/j.fsigen.2021.102537] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 01/16/2023]
Abstract
Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples.
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Affiliation(s)
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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Salzmann AP, Russo G, Kreutzer S, Haas C. Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces. Forensic Sci Int Genet 2021; 53:102524. [PMID: 34015741 DOI: 10.1016/j.fsigen.2021.102524] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation.
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Affiliation(s)
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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Liu J, Cheng X, Liu F, Hao T, Wang J, Guo J, Li J, Liu Z, Li W, Shi J, Zhang X, Li J, Yan J, Zhang G. Identification of coding region SNPs from specific and sensitive mRNA biomarkers for the deconvolution of the semen donor in a body fluid mixture. Forensic Sci Int Genet 2021; 52:102483. [PMID: 33610949 DOI: 10.1016/j.fsigen.2021.102483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 11/29/2022]
Abstract
mRNA markers provide a very promising method for the identification of human body fluids or tissues in the context of forensic investigations. Previous studies have shown that different body fluids can be distinguished from each other according to their specific mRNA biomarkers. In this study, we evaluated eight semen-specific mRNA markers (KLK3, NKX3-1, CKB, KLK2, PRAC1, SEMG1, TGM4, and SORD) that encompass 12 coding single nucleotide polymorphisms (cSNPs) to identify the semen contributor in a mixed stain. Five highly specific and sensitive mRNA markers for blood, menstrual blood, saliva, vaginal secretions, and skin were also incorporated into the PCR system as body fluid-positive controls. Reverse transcription polymerase chain reaction (RT-PCR), multiplex PCR and SNaPshot mini-sequencing assays were established for the identification of semen-specific mRNA. The amplicon size ranged from 133 to 337 bp. The semen-specific system was examined against blood, menstrual blood, saliva, vaginal secretions, and skin swabs. The eight mRNA biomarkers were semen-specific and could be successfully typed in laboratory-generated mixtures composed of different body fluids supplemented with 1 ng of semen cDNA. This system possessed a high sensitivity that ranged from 1:10-1:100 for detecting trace amounts of semen in semen-containing body fluid mixtures. Additionally, our results demonstrated that the cSNPs polymorphisms included in the mRNA markers were concordant with genomic DNA (gDNA). Despite the presence of other body fluids, the system exhibited high sensitivity and specificity to the semen in the mixture. In future studies, we will add other cSNPs from the semen-specific genes using massively parallel sequencing to further improve our system.
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Affiliation(s)
- Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiaojuan Cheng
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Ting Hao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangling Guo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jintao Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Wenyan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jie Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Xiuying Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jing Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
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13
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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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14
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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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15
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Liu Z, Gao Z, Wang J, Shi J, Liu J, Chen D, Li W, Guo J, Cheng X, Hao T, Li Z, Li Y, Yan J, Zhang G. A method of identifying the blood contributor in mixture stains through detecting blood‐specific mRNA polymorphism. Electrophoresis 2020; 41:1364-1373. [DOI: 10.1002/elps.202000053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/31/2020] [Accepted: 05/04/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Zidong Liu
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Zhe Gao
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiaqi Wang
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jie Shi
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jinding Liu
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Deqing Chen
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Wenyan Li
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiangling Guo
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Xiaojuan Cheng
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Ting Hao
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Zeqin Li
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Yanhua Li
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Jiangwei Yan
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
| | - Gengqian Zhang
- School of Forensic MedicineShanxi Medical University Jinzhong Shanxi P. R. China
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16
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Liu B, Yang Q, Meng H, Shao C, Jiang J, Xu H, Sun K, Zhou Y, Yao Y, Zhou Z, Li H, Shen Y, Zhao Z, Tang Q, Xie J. Development of a multiplex system for the identification of forensically relevant body fluids. Forensic Sci Int Genet 2020; 47:102312. [PMID: 32480323 DOI: 10.1016/j.fsigen.2020.102312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Currently, mRNA profiling is widely investigated for forensic body fluid identification, while it is still required to advance the approach for those casework samples of limited quantity or low quality. The inclusion of circular RNAs (circRNAs) can facilitate the detection of mRNA markers in forensic body fluid identification. In this study, a multiplex assay for forensic body fluid identification (F18plex assay) was developed by incorporating 14 tissue-specific mRNA markers with circRNAs expression, 2 mRNA markers with high abundance and 2 housekeeping markers for the discrimination of the most common forensic body fluids, including blood, menstrual blood, saliva, vaginal secretion, semen and urine. The markers employed in the F18plex assay show similar specificity to previous reports. Additionally, even if all linear transcripts were completely erased, the expected markers in target biofluids could still be identified, which should help the discrimination of those aged biological stains. Results from sensitivity testing and the detection of mixtures demonstrate good sensitivity of the multiplex assay. Generally, full biomarker profiles could be obtained with ≥1 μl of blood, saliva, or semen, and ≥1 ng of total RNAs from menstrual blood, vaginal secretion, or urine samples, respectively, using this multiplex assay under the established conditions. Collectively, the newly established multiplex assay can assist in determining the biological origin of forensic stains.
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Affiliation(s)
- Baonian Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jieqing Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Kuan Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxiang Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Yiwen Shen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ziqin Zhao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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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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18
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Wang S, Wang Z, Tao R, Song F, Hou Y. Validating the consistency of cSNPs analysis results between DNA and RNA using SNaPshot method. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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19
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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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20
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Salzmann AP, Russo G, Aluri S, Haas C. Transcription and microbial profiling of body fluids using a massively parallel sequencing approach. Forensic Sci Int Genet 2019; 43:102149. [DOI: 10.1016/j.fsigen.2019.102149] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022]
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21
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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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22
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Wang S, Wang Z, Tao R, Wang M, Liu J, He G, Yang Y, Xie M, Zou X, Hou Y. Expression profile analysis of piwi-interacting RNA in forensically relevant biological fluids. Forensic Sci Int Genet 2019; 42:171-180. [DOI: 10.1016/j.fsigen.2019.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/21/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
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23
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The potential use of Piwi-interacting RNA biomarkers in forensic body fluid identification: A proof-of-principle study. Forensic Sci Int Genet 2019; 39:129-135. [DOI: 10.1016/j.fsigen.2019.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/14/2018] [Accepted: 01/07/2019] [Indexed: 12/21/2022]
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24
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A review of trace “Touch DNA” deposits: Variability factors and an exploration of cellular composition. Forensic Sci Int Genet 2019; 39:8-18. [DOI: 10.1016/j.fsigen.2018.11.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/14/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023]
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25
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Blackman S, Stafford-Allen B, Hanson EK, Panasiuk M, Brooker AL, Rendell P, Ballantyne J, Wells S. Developmental validation of the ParaDNA® Body Fluid ID System—A rapid multiplex mRNA-profiling system for the forensic identification of body fluids. Forensic Sci Int Genet 2018; 37:151-161. [DOI: 10.1016/j.fsigen.2018.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 06/01/2018] [Accepted: 08/22/2018] [Indexed: 11/28/2022]
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26
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Dørum G, Ingold S, Hanson E, Ballantyne J, Snipen L, Haas C. Predicting the origin of stains from next generation sequencing mRNA data. Forensic Sci Int Genet 2018; 34:37-48. [DOI: 10.1016/j.fsigen.2018.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/30/2017] [Accepted: 01/05/2018] [Indexed: 01/27/2023]
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27
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Hanson E, Ingold S, Haas C, Ballantyne J. Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing. Forensic Sci Int Genet 2018; 34:206-221. [DOI: 10.1016/j.fsigen.2018.02.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/16/2018] [Accepted: 02/27/2018] [Indexed: 10/17/2022]
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28
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Ingold S, Dørum G, Hanson E, Berti A, Branicki W, Brito P, Elsmore P, Gettings K, Giangasparo F, Gross T, Hansen S, Hanssen E, Kampmann ML, Kayser M, Laurent FX, Morling N, Mosquera-Miguel A, Parson W, Phillips C, Porto M, Pośpiech E, Roeder A, Schneider P, Schulze Johann K, Steffen C, Syndercombe-Court D, Trautmann M, van den Berge M, van der Gaag K, Vannier J, Verdoliva V, Vidaki A, Xavier C, Ballantyne J, Haas C. Body fluid identification using a targeted mRNA massively parallel sequencing approach – results of a EUROFORGEN/EDNAP collaborative exercise. Forensic Sci Int Genet 2018; 34:105-115. [DOI: 10.1016/j.fsigen.2018.01.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 01/05/2018] [Indexed: 11/30/2022]
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29
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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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30
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Abstract
In forensic investigations, the identification of the cellular or body fluid source of biological evidence can provide crucial probative information for the court. Messenger RNA (mRNA) profiling has become a valuable tool for body fluid and cell type identification due to its high sensitivity and compatibility with DNA analysis. However, using a single marker to determine the somatic origin of a sample can lead to misinterpretation as a result of cross-reactions. While false positives may be avoided through the simultaneous detection of multiple markers per body fluid, this approach is currently limited by the small number of known differentially expressed mRNAs. Here we characterise six novel mRNAs, partly identified from RNA-Seq, which can supplement existing markers for the detection of circulatory blood, semen (with and without spermatozoa), and menstrual fluid: HBD and SLC4A1 for blood, TNP1 for spermatozoa, KLK2 for seminal fluid, and MMP3 and STC1 for menstrual fluid. Respective expression profiles were evaluated by singleplex endpoint reverse transcription polymerase chain reaction (RT-PCR). HBD, SLC4A1, and KLK2 were specific to their target body fluids. TNP1, MMP3, and STC1 each cross-reacted with two non-target samples; however, these signals were below 350RFU, not reproducible, and likely resulted from large body fluid inputs. All candidates were more sensitive for the detection of their target body fluids than corresponding well-known mRNAs, in particular those for menstrual fluid. The increased sensitivities were statistically significant, except for KLK2. Thus, the new mRNAs introduced here are promising new targets for improved body fluid profiling.
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Affiliation(s)
- Patricia P Albani
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand; The Institute of Environmental Science and Research Ltd. (ESR), Auckland, New Zealand
| | - Rachel Fleming
- The Institute of Environmental Science and Research Ltd. (ESR), Auckland, New Zealand.
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31
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Evaluation of the inclusion of circular RNAs in mRNA profiling in forensic body fluid identification. Int J Legal Med 2017; 132:43-52. [PMID: 28948359 DOI: 10.1007/s00414-017-1690-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023]
Abstract
The use of messenger RNA (mRNA) profiling is considered a promising method in the identification of forensically relevant body fluids which can provide crucial information for reconstructing a potential crime. However, casework samples are usually of limited quantity or have been subjected to degradation, which requires improvement of body fluid identification. Circular RNAs (circRNAs), a class of products from the backsplicing of pre-mRNAs, are shown to have high abundance, remarkable stability, and cell type-specific expression in human cells. In this study, we investigated whether the inclusion of circRNAs in mRNA profiling improve the detection of biomarkers including δ-aminolevulinate synthase 2 (ALAS2) and matrix metallopeptidase 7 (MMP7) in body fluid identification. The major circRNAs of ALAS2 and MMP7 were first identified and primer sets for the simultaneous detection of linear and circular transcripts were developed. The inclusion of circRNAs in mRNA profiling showed improved detection sensitivity and stability of biomarkers revealed by using serial dilutions, mixed samples, and menstrual bloodstains as well as degraded and aged samples. Therefore, the inclusion of circRNAs in mRNA profiling should facilitate the detection of mRNA markers in forensic body fluid identification.
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32
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Zhao H, Wang C, Yao L, Lin Q, Xu X, Hu L, Li W. Identification of aged bloodstains through mRNA profiling: Experiments results on selected markers of 30- and 50-year-old samples. Forensic Sci Int 2017; 272:e1-e6. [DOI: 10.1016/j.forsciint.2017.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 12/28/2016] [Accepted: 01/06/2017] [Indexed: 02/05/2023]
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33
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Jung SE, Cho S, Antunes J, Gomes I, Uchimoto ML, Oh YN, Di Giacomo L, Schneider PM, Park MS, van der Meer D, Williams G, McCord B, Ahn HJ, Choi DH, Lee YH, Lee SD, Lee HY. A collaborative exercise on DNA methylation based body fluid typing. Electrophoresis 2016; 37:2759-2766. [DOI: 10.1002/elps.201600256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/01/2016] [Accepted: 07/10/2016] [Indexed: 01/25/2023]
Affiliation(s)
- Sang-Eun Jung
- Department of Forensic Medicine; Yonsei University College of Medicine; Seoul South Korea
| | - Sohee Cho
- Institute of Forensic Science; Seoul National University College of Medicine; Seoul South Korea
| | - Joana Antunes
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Iva Gomes
- Institute of Legal Medicine, Faculty of Medicine; University of Cologne; Cologne Germany
| | - Mari L. Uchimoto
- Forensic and Analytical Research Centre; University of Huddersfield; Queensgate Huddersfield West Yorkshire UK
- School of Biomedical and Forensic Science; Anglia Ruskin University, Cambridge Campus; East Road Cambridge UK
| | - Yu Na Oh
- Division of DNA Analysis, Department of Forensic Medicine, Scientific Investigation Laboratory, Criminal Investigation Command; Ministry of National Defense; Seoul South Korea
| | - Lisa Di Giacomo
- Institute of Legal Medicine, Faculty of Medicine; University of Cologne; Cologne Germany
| | - Peter M. Schneider
- Institute of Legal Medicine, Faculty of Medicine; University of Cologne; Cologne Germany
| | - Min Sun Park
- Forensic DNA Division; National Forensic Service; Wonju Gangwon-do South Korea
| | - Dieudonne van der Meer
- Forensic and Analytical Research Centre; University of Huddersfield; Queensgate Huddersfield West Yorkshire UK
| | - Graham Williams
- Forensic and Analytical Research Centre; University of Huddersfield; Queensgate Huddersfield West Yorkshire UK
| | - Bruce McCord
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Hee-Jung Ahn
- Division of DNA Analysis, Department of Forensic Medicine, Scientific Investigation Laboratory, Criminal Investigation Command; Ministry of National Defense; Seoul South Korea
| | - Dong Ho Choi
- Forensic DNA Division; National Forensic Service; Wonju Gangwon-do South Korea
| | - Yang Han Lee
- Forensic DNA Division; National Forensic Service; Wonju Gangwon-do South Korea
| | - Soong Deok Lee
- Institute of Forensic Science; Seoul National University College of Medicine; Seoul South Korea
| | - Hwan Young Lee
- Department of Forensic Medicine; Yonsei University College of Medicine; Seoul South Korea
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Watanabe K, Akutsu T, Takamura A, Sakurada K. Evaluation of a blood-specific DNA methylated region and trial for allele-specific blood identification from mixed body fluid DNA. Leg Med (Tokyo) 2016; 22:49-53. [DOI: 10.1016/j.legalmed.2016.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/27/2016] [Accepted: 08/10/2016] [Indexed: 02/07/2023]
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35
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Zou KN, Ren LJ, Ping Y, Ma K, Li H, Cao Y, Zhou HG, Wei YL. Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population. J Forensic Leg Med 2016; 43:126-131. [PMID: 27570236 DOI: 10.1016/j.jflm.2016.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/14/2016] [Accepted: 08/11/2016] [Indexed: 10/21/2022]
Abstract
In recent years, forensic scientists have focused on the discrimination of body fluids using microbial signatures. In this study, we performed PCR-based detection of microbial signatures of vaginal fluid, saliva, and feces in a Han Chinese population. We investigated the 16S rRNA genes of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae in vaginal fluid, the 16S rRNA and the glucosyltransferase enzyme genes of Streptococcus salivarius and Streptococcus mutans in saliva, and the 16S rRNA genes of Enterococcus species, the RNA polymerase β-subunit gene of Bacteroides uniformis and Bacteroides vulgatus, and the α-1-6 mannanase gene of Bacteroides thetaiotaomicron in feces. As a result, the detection proportions of L. crispatus, L. gasseri, L. jensenii, L. iners, and A. vaginae were 15/16, 5/16, 8/16, 14/16, and 3/16 in 16 vaginal fluid donors, respectively. L. crispatus and L. jensenii were specifically detected in vaginal fluid; L. gasseri, L. iners, and A. vaginae were also detected in non-vaginal fluid. S. salivarius and S. mutans were not specifically detected in saliva. The detection proportions of Enterococcus species, B. uniformis, B. vulgatus, and B. thetaiotaomicron in 16 feces samples were 16/16, 12/16, 15/16, and 11/16, respectively. B. uniformis and B. thetaiotaomicron were specifically detected in feces. In addition, DNA samples prepared for the identification of body fluid can also be used for individual identification by short tandem repeat typing. The mean detection sensitivities of L. crispatus and L. jensenii were 0.362 and 0.249 pg/uL, respectively. In conclusion, L. crispatus, L. jensenii, B. uniformis, and B. thetaiotaomicron can be used as effective markers for forensic identification of vaginal fluid and feces.
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Affiliation(s)
- Kai-Nan Zou
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China; Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China; Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, People's Republic of China
| | - Li-Jie Ren
- The 519th Hospital of the People's Liberation Army, Wenchang, 300457, Hainan, People's Republic of China
| | - Yuan Ping
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, 200083, People's Republic of China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, 200083, People's Republic of China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China
| | - Huai-Gu Zhou
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China.
| | - Yi-Liang Wei
- Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China; Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, People's Republic of China.
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36
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A 17-month time course study of human RNA and DNA degradation in body fluids under dry and humid environmental conditions. Int J Legal Med 2016; 130:1431-1438. [DOI: 10.1007/s00414-016-1373-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/29/2016] [Indexed: 12/20/2022]
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37
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Forat S, Huettel B, Reinhardt R, Fimmers R, Haidl G, Denschlag D, Olek K. Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence. PLoS One 2016; 11:e0147973. [PMID: 26829227 PMCID: PMC4734623 DOI: 10.1371/journal.pone.0147973] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/11/2016] [Indexed: 12/14/2022] Open
Abstract
The identification of body fluids is an essential tool for clarifying the course of events at a criminal site. The analytical problem is the fact that the biological material has been very often exposed to detrimental exogenous influences. Thereby, the molecular substrates used for the identification of the traces may become degraded. So far, most protocols utilize cell specific proteins or RNAs. Instead of measuring these more sensitive compounds this paper describes the application of the differential DNA-methylation. As a result of two genome wide screenings with the Illumina HumanMethylation BeadChips 27 and 450k we identified 150 candidate loci revealing differential methylation with regard to the body fluids venous blood, menstrual blood, vaginal fluid, saliva and sperm. Among them we selected 9 loci as the most promising markers. For the final determination of the methylation degree we applied the SNuPE-method. Because the degree of methylation might be modified by various endogenous and exogenous factors, we tested each marker with approximately 100 samples of each target fluid in a validation study. The stability of the detection procedure is proved in various simulated forensic surroundings according to standardized conditions. We studied the potential influence of 12 relatively common tumors on the methylation of the 9 markers. For this purpose the target fluids of 34 patients have been analysed. Only the cervix carcinoma might have an remarkable effect because impairing the signal of both vaginal markers. Using the Illumina MiSeq device we tested the potential influence of cis acting sequence variants on the methylation degree of the 9 markers in the specific body fluid DNA of 50 individuals. For 4 marker loci we observed such an influence either by sole SNPs or haplotypes. The identification of each target fluid is possible in arbitrary mixtures with the remaining four body fluids. The sensitivity of the individual body fluid tests is in the same range as for the forensic STR-analysis. It is the first forensic body fluid protocol which considers the exogenic and endogenic parameters potentially interfering with the true results.
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Affiliation(s)
- Sophia Forat
- Labor für Abstammungsbegutachtungen GmbH, Rheinbach, Germany
- * E-mail: (KO); (SF)
| | - Bruno Huettel
- Max Planck Genome Centre Cologne Institute for Breeding Research, Cologne, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne Institute for Breeding Research, Cologne, Germany
| | - Rolf Fimmers
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Gerhard Haidl
- Department of Dermatology, Andrology Unit, University of Bonn, Bonn, Germany
| | - Dominik Denschlag
- Department of OB/GYN Hochtaunuskliniken Bad Homburg, Bad Homburg, Germany
| | - Klaus Olek
- Labor für Abstammungsbegutachtungen GmbH, Rheinbach, Germany
- * E-mail: (KO); (SF)
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38
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de Zoete J, Curran J, Sjerps M. A probabilistic approach for the interpretation of RNA profiles as cell type evidence. Forensic Sci Int Genet 2016; 20:30-44. [DOI: 10.1016/j.fsigen.2015.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/28/2015] [Accepted: 09/17/2015] [Indexed: 10/23/2022]
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39
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Abstract
RNA analysis is a valuable tool for the identification of the forensically relevant body fluids, saliva, blood, menstrual blood, cervicovaginal fluid, and semen. Multiple human mRNA and bacterial RNA markers have been identified for each of these body fluids. RNA and DNA can be coextracted from the same portion of a sample and RNA markers for different body fluids can be multiplexed in a single PCR, thereby maximizing the number of analyses that can be performed with limited sample material.
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Affiliation(s)
- Amy D Roeder
- Cellmark, Blacklands Way, Abingdon, Oxfordshire, OX14 1DY, UK.
| | - Cordula Haas
- Institute of Legal Medicine, University of Zurich, Zürich, Switzerland
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40
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On the effect of shooting distance, ballistic model construction, doping and weapon type on the simultaneous analysis of DNA and RNA from backspatter recovered from inside surfaces of firearms. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci Int Genet 2015; 18:21-32. [DOI: 10.1016/j.fsigen.2014.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
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42
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Song F, Luo H, Hou Y. Developed and evaluated a multiplex mRNA profiling system for body fluid identification in Chinese Han population. J Forensic Leg Med 2015; 35:73-80. [PMID: 26311108 DOI: 10.1016/j.jflm.2015.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
In forensic casework, identification the cellular origin from a biological sample is crucial to the case investigation and reconstruction in crime scene. DNA/RNA co-extraction for STR typing and human body fluids identification has been proposed as an efficient and comprehensive assay for forensic analysis. Several cell-specific messenger RNA (mRNA) markers for identification of the body fluids have been proposed by previous studies. In this study, a novel multiplex mRNA profiling system included 19 markers was developed and performed by reverse transcription endpoint polymerase chain reaction (RT-PCR). The multiplex combined 3 housekeeping gene markers and 16 cell-specific markers that have been used to identify five types of human body fluids: peripheral blood, semen, saliva, vaginal secretions and menstrual blood. The specificity, sensitivity, stability and detectability of the mixture were explored in our study. Majority of the cell-specific mRNA markers showed high specificity, although cross-reactivity was observed sporadically. Specific profiling for per body fluid was obtained. Moreover, the interpretation guidelines for inference of body fluid types were performed according to the A. Lindenbergh et al. The scoring guidelines can be applied to any RNA multiplex, which was based on six different scoring categories (observed, observed and fits, sporadically observed and fits, not observed, sporadically observed, not reliable, and non-specific due to high input). The simultaneous extraction of DNA showed positive full or partial profiling results of all samples. It demonstrated that the approach of combined STR-profiling and RNA profiling was suitable and reliable to detect the donor and origin of human body fluids in Chinese Han population.
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Affiliation(s)
- Feng Song
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China.
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43
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Grabmüller M, Schyma C, Euteneuer J, Madea B, Courts C. Simultaneous analysis of nuclear and mitochondrial DNA, mRNA and miRNA from backspatter from inside parts of firearms generated by shots at "triple contrast" doped ballistic models. Forensic Sci Med Pathol 2015. [PMID: 26210238 DOI: 10.1007/s12024-015-9695-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
When a firearm projectile hits a biological target a spray of biological material (e.g., blood and tissue fragments) can be propelled from the entrance wound back towards the firearm. This phenomenon has become known as "backspatter" and if caused by contact shots or shots from short distances traces of backspatter may reach, consolidate on, and be recovered from, the inside surfaces of the firearm. Thus, a comprehensive investigation of firearm-related crimes must not only comprise of wound ballistic assessment but also backspatter analysis, and may even take into account potential correlations between these emergences. The aim of the present study was to evaluate and expand the applicability of the "triple contrast" method by probing its compatibility with forensic analysis of nuclear and mitochondrial DNA and the simultaneous investigation of co-extracted mRNA and miRNA from backspatter collected from internal components of different types of firearms after experimental shootings. We demonstrate that "triple contrast" stained biological samples collected from the inside surfaces of firearms are amenable to forensic co-analysis of DNA and RNA and permit sequence analysis of the entire mtDNA displacement-loop, even for "low template" DNA amounts that preclude standard short tandem repeat DNA analysis. Our findings underscore the "triple contrast" method's usefulness as a research tool in experimental forensic ballistics.
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Affiliation(s)
- Melanie Grabmüller
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111, Bonn, Germany
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44
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Haas C, Hanson E, Banemann R, Bento A, Berti A, Carracedo Á, Courts C, Cock GD, Drobnic K, Fleming R, Franchi C, Gomes I, Hadzic G, Harbison S, Hjort B, Hollard C, Hoff-Olsen P, Keyser C, Kondili A, Maroñas O, McCallum N, Miniati P, Morling N, Niederstätter H, Noël F, Parson W, Porto M, Roeder A, Sauer E, Schneider P, Shanthan G, Sijen T, Syndercombe Court D, Turanská M, van den Berge M, Vennemann M, Vidaki A, Zatkalíková L, Ballantyne J. RNA/DNA co-analysis from human skin and contact traces – results of a sixth collaborative EDNAP exercise. Forensic Sci Int Genet 2015; 16:139-147. [DOI: 10.1016/j.fsigen.2015.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/12/2014] [Accepted: 01/04/2015] [Indexed: 11/25/2022]
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45
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Orphanou CM, Walton-Williams L, Mountain H, Cassella J. The detection and discrimination of human body fluids using ATR FT-IR spectroscopy. Forensic Sci Int 2015; 252:e10-6. [PMID: 25944716 DOI: 10.1016/j.forsciint.2015.04.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/16/2015] [Accepted: 04/18/2015] [Indexed: 12/31/2022]
Abstract
Blood, saliva, semen and vaginal secretions are the main human body fluids encountered at crime scenes. Currently presumptive tests are routinely utilised to indicate the presence of body fluids, although these are often subject to false positives and limited to particular body fluids. Over the last decade more sensitive and specific body fluid identification methods have been explored, such as mRNA analysis and proteomics, although these are not yet appropriate for routine application. This research investigated the application of ATR FT-IR spectroscopy for the detection and discrimination of human blood, saliva, semen and vaginal secretions. The results demonstrated that ATR FT-IR spectroscopy can detect and distinguish between these body fluids based on the unique spectral pattern, combination of peaks and peak frequencies corresponding to the macromolecule groups common within biological material. Comparisons with known abundant proteins relevant to each body fluid were also analysed to enable specific peaks to be attributed to the relevant protein components, which further reinforced the discrimination and identification of each body fluid. Overall, this preliminary research has demonstrated the potential for ATR FT-IR spectroscopy to be utilised in the routine confirmatory screening of biological evidence due to its quick and robust application within forensic science.
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Affiliation(s)
- Charlotte-Maria Orphanou
- Forensic & Crime Science, Staffordshire University, Science Centre, Leek Road, Stoke-on-Trent, Staffordshire ST4 2DF, United Kingdom.
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46
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Donfack J, Wiley A. Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification. Forensic Sci Int Genet 2015; 16:112-120. [PMID: 25594487 DOI: 10.1016/j.fsigen.2014.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
Abstract
Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework.
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Affiliation(s)
- Joseph Donfack
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Anissa Wiley
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA 22135, USA
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47
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Akutsu T, Kitayama T, Watanabe K, Sakurada K. Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids. Forensic Sci Int Genet 2015; 14:11-7. [DOI: 10.1016/j.fsigen.2014.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/10/2014] [Accepted: 09/08/2014] [Indexed: 01/21/2023]
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48
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Danaher P, White RL, Hanson EK, Ballantyne J. Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets. Forensic Sci Int Genet 2015; 14:18-30. [DOI: 10.1016/j.fsigen.2014.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/27/2014] [Accepted: 09/07/2014] [Indexed: 11/25/2022]
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49
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Hanson EK, Mirza M, Rekab K, Ballantyne J. The identification of menstrual blood in forensic samples by logistic regression modeling of miRNA expression. Electrophoresis 2014; 35:3087-95. [DOI: 10.1002/elps.201400171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/04/2014] [Accepted: 08/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
| | - Mohid Mirza
- Molecular Biology and Microbiology (Biomedical Sciences) Undergraduate Program; University of Central Florida; Orlando FL USA
| | - Kamel Rekab
- University of Missouri-Kansas City; Kansas City MO USA
| | - Jack Ballantyne
- National Center for Forensic Science; Orlando FL USA
- Department of Chemistry; University of Central Florida; Orlando FL USA
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50
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Schweighardt AJ, Tate CM, Scott KA, Harper KA, Robertson JM. Evaluation of Commercial Kits for Dual Extraction of DNA and RNA from Human Body Fluids,,. J Forensic Sci 2014; 60:157-65. [DOI: 10.1111/1556-4029.12586] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 11/30/2013] [Accepted: 12/21/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Andrew J. Schweighardt
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Courtney M. Tate
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Kristina A. Scott
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Kathryn A. Harper
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - James M. Robertson
- Counterterrorism and Forensic Science Research Unit; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
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