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Akutsu T, Minegishi S, Watanabe K, Toyomane K, Yamagishi T, Sakurada K. Quantitative evaluation of endometrium-expressed mRNAs for the purpose of discriminating between menstruation and traumatic vaginal injury in sexual assault cases. Int J Legal Med 2024; 138:1245-1254. [PMID: 38409607 DOI: 10.1007/s00414-024-03199-y] [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: 12/13/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
In sexual assault cases, it is crucial to discriminate between peripheral blood and menstrual blood to provide evidence for vaginal intercourse with traumatic injury. In this study, the menstrual blood mRNA markers progestagen-associated endometrial protein (PAEP), matrix metallopeptidase 7 (MMP7), and left-right determination factor 2 (LEFTY2) were evaluated by quantitative RT-PCR (RT-qPCR) for the discrimination of menstrual blood from peripheral blood and vaginal fluid. As a result, all markers with cutoff delta cycle quantification (ΔCq) values were specifically determined in menstrual blood among forensically relevant body fluids. Even though the changes in the expression levels of each marker differed during the menstrual cycle, all markers were determined to be positive in most of the randomly collected menstrual blood samples that were analyzed. Additionally, the markers with proposed cutoff ΔCq values could discriminate between menstrual blood and peripheral blood-mixed vaginal fluid samples. The determination of positive markers was less affected by storage temperature under dry conditions than under wet conditions, while PAEP was detectable in samples stored below room temperature under wet conditions. The detectability of PAEP was considered to be the result of its higher expression level compared with MMP7 and LEFTY2. In conclusion, menstrual blood markers for the RT-qPCR procedure evaluated in this study were highly specific for menstrual blood. The proposed procedure could be useful for discriminating between menstruation and traumatic bleeding in the female genital tract. In particular, PAEP is expected to be applicable to forensic casework samples because of its high specificity and robustness.
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Affiliation(s)
- Tomoko Akutsu
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
| | - Saki Minegishi
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Ken Watanabe
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Kochi Toyomane
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Takayuki Yamagishi
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Koichi Sakurada
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
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Xiao Y, Tan M, Song J, Huang Y, Lv M, Liao M, Yu Z, Gao Z, Qu S, Liang W. Developmental validation of an mRNA kit: A 5-dye multiplex assay designed for body-fluid identification. Forensic Sci Int Genet 2024; 71:103045. [PMID: 38615496 DOI: 10.1016/j.fsigen.2024.103045] [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: 11/03/2023] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024]
Abstract
Identifying the sources of biosamples found at crime scenes is crucial for forensic investigations. Among the markers used for body fluid identification (BFI), mRNA has emerged as a well-studied marker because of its high specificity and remarkable stability. Despite this potential, commercially available mRNA kits specifically designed for BFI are lacking. Therefore, we developed an mRNA kit that includes 21 specific mRNA markers of body fluids, along with three housekeeping genes for BFI, to identify four forensic-relevant fluids (blood, semen, saliva, and vaginal fluids). In this study, we tested 451 single-body-fluid samples, validated the universality of the mRNA kit, and obtained a gene expression profile. We performed the validation studies in triplicates and determined the sensitivity, specificity, stability, precision, and repeatability of the mRNA kit. The sensitivity of the kit was found to be 0.1 ng. Our validation process involved the examination of 59 RNA mixtures, 60 body fluids mixtures, and 20 casework samples, which further established the reliability of the kit. Furthermore, we constructed five classifiers that can handle single-body fluids and mixtures using this kit. The classifiers output possibility values and identify the specific body fluids of interest. Our results showed the reliability and suitability of the BFI kit, and the Random Forest classifier performed the best, with 94% precision. In conclusion, we developed an mRNA kit for BFI which can be a promising tool for forensic practice.
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Affiliation(s)
- Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jinlong Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yihang Huang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Zailiang Yu
- Suzhou Microread Genetics Co.,Ltd, Suzhou, Jiangsu, PR China
| | - Zhixiao Gao
- Suzhou Microread Genetics Co.,Ltd, Suzhou, Jiangsu, PR China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China.
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3
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Liu Z, Wang J, Li L, Yang H, Yu H, Fan J, Zhang M, Zhang Y, Liu J, Li Z, Zhang G. Identification of the body fluid donor in mixtures through target mRNA cSNP sequencing. Forensic Sci Int Genet 2024; 71:103066. [PMID: 38833776 DOI: 10.1016/j.fsigen.2024.103066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/08/2024] [Accepted: 05/26/2024] [Indexed: 06/06/2024]
Abstract
In forensic practice, mixture stains containing various body fluids are common, presenting challenges for interpretation, particularly in multi-contributor mixtures. Traditional STR profiles face difficulties in such scenarios. Over recent years, RNA has emerged as a promising biomarker for body fluid identification, and mRNA polymorphism has shown excellent performance in identifying body fluid donors in previous studies. In this study, a massively parallel sequencing assay was developed, encompassing 202 coding region SNPs (cSNPs) from 45 body fluid/tissue-specific genes to identify both body fluid/tissue origin and the respective donors, including blood, saliva, semen, vaginal secretion, menstrual blood, and skin. The specificity was evaluated by examining the single-source body fluids/tissue and revealed that the same body fluid exhibited similar expression profiles and the tissue origin could be identified. For laboratory-generated mixtures containing 2-6 different components and mock case mixtures, the donor of each component could be successfully identified, except for the skin donor. The discriminatory power for all body fluids ranged from 0.997176329 (menstrual blood) to 0.99999999827 (blood). The concordance of DNA typing and mRNA typing for the cSNPs in this system was also validated. This cSNP typing system exhibits excellent performance in mixture deconvolution.
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Affiliation(s)
- Zidong Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Jiaqi Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Lishan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Hailing Yang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Huan Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Jiajia Fan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Mingming Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Yuxin Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, China.
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4
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Liu Z, Yang J, Wang N, Liu J, Geng J, Zhu J, Cong B, Sun H, Wu R. Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue. Int J Legal Med 2024; 138:731-742. [PMID: 37994925 DOI: 10.1007/s00414-023-03131-w] [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: 06/19/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized their overall profiles in forensic science. In this study, we sequenced the transcriptomes of 30 samples from venous blood, menstrual blood, semen, saliva, vaginal secretion, and skin tissue, obtaining a comprehensive picture of mRNA, lncRNA, and circRNA profiles. A total of 90,305 mRNAs, 102,906 lncRNAs (including 19,549 novel lncRNAs), and 40,204 circRNAs were detected. RNA type distribution, length distribution, and expression distribution were presented according to their annotation and expression level, and many novel body fluid/tissue-specific RNA markers were identified. Furthermore, the cognate relations among the three RNAs were analyzed according to gene annotations. Finally, SNPs and InDels from RNA transcripts were genotyped, and 21,611 multi-SNP and 4,471 multi-InDel transcriptomic microhaplotypes (tMHs) were identified. These results provide a comprehensive understanding of transcriptome profiles, which could provide new avenues for tracing the origin of the body fluid/tissue and identifying an individual.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
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Zhang J, Yu D, Wang T, Gao N, Shi L, Wang Y, Huo Y, Ji Z, Li J, Zhang X, Zhang L, Yan J. Body fluids should be identified before estimating the time since deposition (TsD) in microbiome-based stain analyses for forensics. Microbiol Spectr 2024; 12:e0248023. [PMID: 38470485 PMCID: PMC10986545 DOI: 10.1128/spectrum.02480-23] [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: 06/14/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Identification and the time since deposition (TsD) estimation of body fluid stains from a crime scene could provide valuable information for solving the cases and are always difficult for forensics. Microbial characteristics were considered as a promising biomarker to address the issues. However, changes in the microbiota may damage the specific characteristics of body fluids. Correspondingly, incorrect body fluid identification may result in inaccurate TsD estimation. The mutual influence is not well understood and limited the codetection. In the current study, saliva, semen, vaginal secretion, and menstrual blood samples were exposed to indoor conditions and collected at eight time points (from fresh to 30 days). High-throughput sequencing based on the 16S rRNA gene was performed to characterize the microbial communities. The results showed that a longer TsD could decrease the discrimination of different body fluid stains. However, the accuracies of identification still reached a quite high value even without knowing the TsD. Correspondingly, the mean absolute error (MAE) of TsD estimation significantly increased without distinguishing the types of body fluids. The predictive TsD of menstrual blood reached a quite low MAE (1.54 ± 0.39 d). In comparison, those of saliva (6.57 ± 1.17 d), semen (6.48 ± 1.33 d), and vaginal secretion (5.35 ± 1.11 d) needed to be further improved. The great effect of individual differences on these stains limited the TsD estimation accuracy. Overall, microbial characteristics allow for codetection of body fluid identification and TsD estimation, and body fluids should be identified before estimating TsD in microbiome-based stain analyses.IMPORTANCEEmerged evidences suggest microbial characteristics could be considered a promising tool for identification and time since deposition (TsD) estimation of body fluid stains. However, the two issues should be studied together due to a potential mutual influence. The current study provides the first evidence to understand the mutual influence and determines an optimal process for codetection of identification and TsD estimation for unknown stains for forensics. In addition, we involved aged stains into our study for identification of body fluid stains, rather than only using fresh stains like previous studies. This increased the predictive accuracy. We have preliminary verified that individual differences in microbiotas limited the predictive accuracy of TsD estimation for saliva, semen, and vaginal secretion. Microbial characteristics could provide an accurate TsD estimation for menstrual blood. Our study benefits the comprehensive understanding of microbiome-based stain analyses as an essential addition to previous studies.
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Affiliation(s)
- Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Linyu Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Yaya Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
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6
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Zhang J, Yan M, Ji A, Sun Q, Ying W. Mass spectrometry-based proteomic analysis of biological stains identifies body fluids specific markers. Forensic Sci Int 2024; 357:112008. [PMID: 38522320 DOI: 10.1016/j.forsciint.2024.112008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
The identification of biological stains and their tissue resource is an important part of forensic research. Current methods suffer from several limitations including poor sensitivity and specificity, trace samples, and sample destruction. In this study, we profiled the proteomes of menstrual blood, peripheral blood, saliva, semen, and vaginal fluid with mass spectrometry technology. Tissue-enhanced and tissue-specific proteins of each group have been proposed as potential biomarkers. These candidate proteins were further annotated and screened through the combination with the Human Protein Atlas database. Our data not only validates the protein biomarkers reported in previous studies but also identifies novel candidate biomarkers for human body fluids. These candidates lay the foundation for the development of rapid and specific forensic examination methods.
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Affiliation(s)
- Jian Zhang
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China; State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Meng Yan
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Anquan Ji
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China
| | - Qifan Sun
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China.
| | - Wantao Ying
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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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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8
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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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9
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Lynch C, Fleming R. Partial validation of multiplexed real-time quantitative PCR assays for forensic body fluid identification. Sci Justice 2023; 63:724-735. [PMID: 38030341 DOI: 10.1016/j.scijus.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 09/04/2023] [Accepted: 10/15/2023] [Indexed: 12/01/2023]
Abstract
Confirmatory body fluid identification using messenger RNA (mRNA) is a well-established technique to address issues encountered with conventional testing - such as poor sensitivity, specificity, and a lack of available tests for all body fluids of interest. For over a decade, endpoint reverse-transcription polymerase chain reaction (RT-PCR) assays have been used in forensic casework for such purposes. However, in comparison with real-time quantitative RT-PCR (RT-qPCR), endpoint RT-PCR has lower sensitivity, precision, and linear dynamic range. This research details the multiplexing and partial validation of confirmatory RT-qPCR assays. We have previously described novel assays for a range of body fluid targets and identified an optimal commercial kit for their amplification. Here, multiplexing was undertaken to form three assays: circulatory blood (SLC4A1) and menstrual fluid (STC1), saliva (HTN3) and vaginal material (CYP2B7P), and spermatozoa (PRM1) and seminal fluid (KLK2), all including a synthetic internal control RNA. Partial validation of the multiplexed assays incorporated the MIQE guidelines, ISO requirements, and SWGDAM guidelines. Using receiver operating characteristic (ROC) curves, each marker was significantly different from an uninformative assay and optimal cut-offs were all above 35 cycles. All assays showed a wide LDR (ranging from 3 to 5 logs with most R2 > 0.99), and high precision (most mean CV < 1 %). STC1 showed some instances of sporadic expression in blood, semen, and vaginal material at high CT values. CYP2B7P showed off-target expression in semen and blood. The sensitivities were approximated as; saliva: 1 in 1,000 dilution of a whole buccal swab, circulatory blood: 0.01-0.1 µL blood, menstrual fluid: 1 in 10,000 dilution of a whole menstrual swab, spermatozoa: 0.001 µL semen, seminal fluid: 0.01 µL semen, and vaginal material: 1 in 1,000 dilution of a whole vaginal swab. A total of 16 mock body fluid extract mixtures and 18 swab mixtures were tested and had 100% and 99% detection of target markers below each specific cut-off, respectively. Some mixtures containing high volumes of blood and semen showed off-target CYP2B7P expression. The successful application of a probabilistic model to the RT-qPCR data was also demonstrated. Further work will involve full developmental validation.
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Affiliation(s)
- Courtney Lynch
- Forensic Science Programme, School of Chemical Sciences, The University of Auckland, Auckland, New Zealand; Forensic Research and Development Team, Institute of Environmental Science and Research Ltd, Auckland, New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd, Auckland, New Zealand.
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10
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Chierto E, Alessandrini F, Bini C, Carnevali E, Fabbri M, Fattorini P, Grignani P, Scarnicci F, Tozzo P, Verzeletti A, Pelotti S, Buscemi L, Robino C. An mRNA Profiling Study of Vaginal Swabs from Pre- and Postmenopausal Women. Curr Issues Mol Biol 2023; 45:6526-6537. [PMID: 37623230 PMCID: PMC10453267 DOI: 10.3390/cimb45080411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Body fluid identification by means of mRNA profiling provides valuable supplementary information in forensic investigations. In particular, the detection of vaginal mucosa mRNA markers is highly relevant in sexual assault cases. Although the vagina undergoes characteristic age-related physiological changes over a lifetime, few studies have evaluated the efficacy of vaginal mRNA markers in women of different ages. In this multicentric study, a 19-plex mRNA profiling assay including vaginal-specific markers (CYP2B7P1, MUC4, MYOZ1) was tested in a collection of 6-20-month-old vaginal swabs obtained from pre- (n = 84) and postmenopausal (n = 55) female volunteer donors. Overall, participating laboratories were able to correctly identify ~85% of samples as vaginal mucosa by mRNA profiling. The assay's success rate did not differ between the two age groups and was not affected by the time interval between swab collection and RNA analysis. MYOZ1 resulted a less sensitive vaginal marker compared to MUC4 and CYP2B7P1. A significant relative increase in the contribution to the total amplification signal was observed for MUC4, compared to CYP2B7P1 and MYOZ1, in postmenopausal women. Observation of other body fluids and tissues different from vaginal mucosa was also evaluated in connection to information on previous sexual activity and menstrual cycle phase at the time of sampling.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy;
| | - Federica Alessandrini
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Eugenia Carnevali
- Unità Operativa Semplice Laboratory of Forensic Science, Section of Legal Medicine, Department of Medicine and Surgery, S. Maria Hospital, University of Perugia, 05100 Terni, Italy
| | - Matteo Fabbri
- Section of Legal Medicine, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, 34129 Trieste, Italy
| | - Pierangela Grignani
- Section of Legal Medicine and Forensic Sciences, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Francesca Scarnicci
- Section of Legal Medicine, Department of Health Surveillance and Bioethics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Pamela Tozzo
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Forensic Medicine Unit, University of Brescia, 25123 Brescia, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Loredana Buscemi
- AOU Ospedali Riuniti Ancona, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy;
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11
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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: 0] [Impact Index Per Article: 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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12
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Al-Hazani TMI, Al-Qahtani WS, Abboosh TS, Safhi FA, Alshaya DS, Jalal AS, Al-Shamrani SM, Al-Ghamdi NA, Alotaibi AM, Alotaibi MA, Alghamdi HS, Alafari HA, ALMatrafi TA, Alshehri E. Detecting STR profiles from degrading menstrual blood samples and their use as possible evidence in forensic investigations. Forensic Sci Int 2023; 343:111562. [PMID: 36657183 DOI: 10.1016/j.forsciint.2023.111562] [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: 11/08/2022] [Revised: 12/29/2022] [Accepted: 01/05/2023] [Indexed: 01/08/2023]
Abstract
This research explores DNA consistency and attempts to detect STR profiles from the degrading menstrual blood samples (MBS) as reliable forensic evidence. Peripheral (PBS) and MBS of 30 healthy fertile females were taken on the menstrual cycle's second day. They were obtained at different time periods (0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 24, and 48 h) at 25 °C. DNA evaluation was fulfilled to analyze DNA profiles. A considerable elevation in the median concentrations of DNA between 0 and 14-h intervals were documented, whereas decreased extents were registered between 16 and 48 h. Moreover, complete STR profiles (24/24) for DNA were discovered in all the intervals (0, 2, and 48 h). Periods of 0-8 h demonstrated the maximum extents of DNA materials. Full STR were discovered in all the intervals (0, 2, and 48 h). Eventually, MBS can be utilized as forensic evidence.
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Affiliation(s)
- Tahani Mohamed Ibrahim Al-Hazani
- Department of Biology, College of Sciences and Humanities, Prince Sattam Bin Abdulaziz University, P.O. Box: 83, Al-Kharj 11940, Saudi Arabia.
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, P.O. Box 6830, Riyadh 11452, Saudi Arabia.
| | - Tahani Saeed Abboosh
- Ministry of Interior, Public Security, Forensic Evidence Laboratories, Criminal Examinations, Riyadh, Saudi Arabia.
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Dalal S Alshaya
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Areej Saud Jalal
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Salha M Al-Shamrani
- University of Jeddah, College of Science, Department of Biology, P.O. Box 13151, Jeddah 21493, Saudi Arabia.
| | | | | | | | - Hanan S Alghamdi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
| | - Hayat Ali Alafari
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | | | - Eman Alshehri
- Department of Zoology, College of Science, King Saud University, Saudi Arabia.
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13
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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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14
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Layne TR, Nouwairi RL, Fleming R, Blair H, Landers JP. Rapid Microchip Electrophoretic Separation of Novel Transcriptomic Body Fluid Markers for Forensic Fluid Profiling. MICROMACHINES 2022; 13:1657. [PMID: 36296010 PMCID: PMC9609788 DOI: 10.3390/mi13101657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Initial screening of criminal evidence often involves serological testing of stains of unknown composition and/or origin discovered at a crime scene to determine the tissue of origin. This testing is presumptive but critical for contextualizing the scene. Here, we describe a microfluidic approach for body fluid profiling via fluorescent electrophoretic separation of a published mRNA panel that provides unparalleled specificity and sensitivity. This centrifugal microfluidic approach expedites and automates the electrophoresis process by allowing for simple, rotationally driven flow and polymer loading through a 5 cm separation channel; with each disc containing three identical domains, multi-sample analysis is possible with a single disc and multi-sample detection per disc. The centrifugal platform enables a series of sequential unit operations (metering, mixing, aliquoting, heating, storage) to execute automated electrophoretic separation. Results show on-disc fluorescent detection and sizing of amplicons to perform comparably with a commercial 'gold standard' benchtop instrument and permitted sensitive, empirical discrimination between five distinct body fluids in less than 10 min. Notably, our microfluidic platform represents a faster, simpler method for separation of a transcriptomic panel to be used for forensically relevant body fluid identification.
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Affiliation(s)
- Tiffany R. Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - Renna L. Nouwairi
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - Rachel Fleming
- Institute of Environmental Science and Research Limited, Auckland 1025, New Zealand
| | - Haley Blair
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
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15
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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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16
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Johannessen H, Gill P, Shanthan G, Fonneløp AE. Transfer, persistence and recovery of DNA and mRNA vaginal mucosa markers after intimate and social contact with Bayesian network analysis for activity level reporting. Forensic Sci Int Genet 2022; 60:102750. [PMID: 35914368 DOI: 10.1016/j.fsigen.2022.102750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/25/2023]
Abstract
In sexual assault cases, it can be challenging to identify the type of body fluids/ cell types present in a crime scene sample, especially the origin of epithelial cells. Therefore, more labs are applying mRNA body fluid analysis for saliva, skin and vaginal mucosa markers. To address activity level propositions, it is necessary to assign probabilities of transfer, persistence, prevalence and recovery of DNA and mRNA markers. In this study we analysed 158 samples (fingernail swabs, penile swabs and boxershorts) from 12 couples collected at different time points post intimate contact and after non-intimate contact in order to detect DNA from the person of interest (POI) and mRNA vaginal mucosa markers. Samples were DNA and RNA co-extracted and analysed with PowerPlex®Fusion 6C System and 19-plex mRNA primer mix respectively, using Endpoint PCR and the CE platform. Vaginal mucosa was detected up to 36 h post intimate contact, but also detected in one non-intimate contact sample. In 94% of intimate contact and 50 % of non-intimate contact samples the DNA results support the proposition that POI is the donor (LR ≥ 10,000). There was a strong association between the detection of vaginal mucosa and the average RFU value of the POI. The data were used to instantiate a comprehensive Bayesian network to evaluate the evidence at activity level, given alternate propositions conditioned upon indirect or direct transfer events. It is shown that the value of the evidence is mainly affected by the high DNA quantity (measured as mean RFU) that is recovered from the POI. The detection of vaginal mucosa had low impact upon the resultant likelihood ratio.
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Affiliation(s)
| | - Peter Gill
- Department of Forensic Medicine, University of Oslo, Norway; Department of Forensic Sciences, Oslo University Hospital, Norway
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17
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Identification of the vaginal secretion donor in mixture stains using polymorphic cSNPs on mRNA biomarkers. Forensic Sci Int Genet 2022; 59:102703. [DOI: 10.1016/j.fsigen.2022.102703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023]
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18
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Dørum G, Bleka Ø, Gill P, Haas C. Source level interpretation of mixed biological stains using coding region SNPs. Forensic Sci Int Genet 2022; 59:102685. [DOI: 10.1016/j.fsigen.2022.102685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
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19
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Development of a combined differential DNA/RNA co-extraction protocol and its application in forensic casework. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2022. [DOI: 10.1016/j.fsir.2022.100261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Sijen T, Harbison S. On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime. Genes (Basel) 2021; 12:1728. [PMID: 34828334 PMCID: PMC8617621 DOI: 10.3390/genes12111728] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.
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Affiliation(s)
- Titia Sijen
- Division Human Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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21
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Li Z, Chen D, Wang Q, Tian H, Tan M, Peng D, Tan Y, Zhu J, Liang W, Zhang L. mRNA and microRNA stability validation of blood samples under different environmental conditions. Forensic Sci Int Genet 2021; 55:102567. [PMID: 34403952 DOI: 10.1016/j.fsigen.2021.102567] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/29/2021] [Accepted: 08/01/2021] [Indexed: 01/10/2023]
Abstract
RNA molecules, including mRNAs and microRNAs (miRNAs), have been used for forensic body fluid identification. Specific body fluids present unique mRNA expression patterns, while miRNAs identifying body fluids are mainly differentially expressed. miRNAs are thought to be more stable than mRNAs, although this lacks adequate supporting data. In this study, we addressed perceived concerns regarding the stability of miRNAs and mRNAs in blood samples. The samples used in this study involved three groups. First, environmentally-degraded blood stain samples were exposed to a range of environmental conditions over 1-360 days to degrade naturally. Second, simulated-degraded samples were prepared using RNase A or high temperature (80 °C). Furthermore, two authentic casework samples that were proven to be degraded from short tandem repeat (STR) profiles were analyzed. mRNAs and miRNAs present in the same blood samples were simultaneously detected through reverse transcriptase qPCR (RT-qPCR). Furthermore, mRNAs expression was determined by an mRNA multiplex PCR system. Our results showed that both mRNAs and miRNAs were stable in dry environments. The stability of miRNAs was relatively higher than that of mRNAs in humid environments or at high temperature. RNase A had the most serious impact on RNA stability, both mRNA profiles and miRNAs expression patterns were altered. The results of this study provide data and support to demonstrate that miRNAs represent more stable RNA molecules in body fluid identification compared to mRNAs.
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Affiliation(s)
- Zhilong Li
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qian Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Huan Tian
- Department of Obstetric and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Duo Peng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yu Tan
- Department of Obstetric and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jing Zhu
- Department of Criminal Science and Technology, Sichuan Police College, Luzhou, Sichuan 646000, P.R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China.
| | - Lin Zhang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China; Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China.
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22
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Díez López C, Kayser M, Vidaki A. Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study. Front Microbiol 2021; 12:647933. [PMID: 34149638 PMCID: PMC8206545 DOI: 10.3389/fmicb.2021.647933] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
Information on the time when a stain was deposited at a crime scene can be valuable in forensic investigations. It can link a DNA-identified stain donor with a crime or provide a post-mortem interval estimation in cases with cadavers. The available methods for estimating stain deposition time have limitations of different types and magnitudes. In this proof-of-principle study we investigated for the first time the use of microbial DNA for this purpose in human saliva stains. First, we identified the most abundant and frequent bacterial species in saliva using publicly available 16S rRNA gene next generation sequencing (NGS) data from 1,848 samples. Next, we assessed time-dependent changes in 15 identified species using de-novo 16S rRNA gene NGS in the saliva stains of two individuals exposed to indoor conditions for up to 1 year. We selected four bacterial species, i.e., Fusobacterium periodonticum, Haemophilus parainfluenzae, Veillonella dispar, and Veillonella parvula showing significant time-dependent changes and developed a 4-plex qPCR assay for their targeted analysis. Then, we analyzed the saliva stains of 15 individuals exposed to indoor conditions for up to 1 month. Bacterial counts generally increased with time and explained 54.9% of the variation (p = <2.2E–16). Time since deposition explained ≥86.5% and ≥88.9% of the variation in each individual and species, respectively (p = <2.2E–16). Finally, based on sample duplicates we built and tested multiple linear regression models for predicting the stain deposition time at an individual level, resulting in an average mean absolute error (MAE) of 5 days (ranging 3.3–7.8 days). Overall, the deposition time of 181 (81.5%) stains was correctly predicted within 1 week. Prediction models were also assessed in stains exposed to similar conditions up to 1 month 7 months later, resulting in an average MAE of 8.8 days (ranging 3.9–16.9 days). Our proof-of-principle study suggests the potential of the DNA profiling of human commensal bacteria as a method of estimating saliva stains time since deposition in the forensic scenario, which may be expanded to other forensically relevant tissues. The study considers practical applications of this novel approach, but various forensic developmental validation and implementation criteria will need to be met in more dedicated studies in the future.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
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Bamberg M, Dierig L, Kulstein G, Kunz SN, Schmidt M, Hadrys T, Wiegand P. Development and validation of an mRNA-based multiplex body fluid identification workflow and a rectal mucosa marker pilot study. Forensic Sci Int Genet 2021; 54:102542. [PMID: 34098418 DOI: 10.1016/j.fsigen.2021.102542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 01/26/2023]
Abstract
Molecular identification of body fluids and tissues is crucial in order to understand the circumstances of crimes. For that reason, molecular investigations used to identify body fluids/tissues have increasingly been examined recently. Various studies have proved that messenger RNA (mRNA) profiling is a sensitive and robust method for body fluid/tissue identification. The forensically relevant body fluids/tissues blood, semen, saliva, vaginal secretion, menstrual blood and skin have all been detected successfully by applying suitable mRNA assay. However, rectal mucosa, which can be found as evidence in sexual assault cases, has been neglected in forensic investigations. So far there is no mRNA marker to detect rectal mucosa, although anal penetration occurs in a large number of sexual assaults (23.2% of female victims and 50% of male victims). In this study, specific and sensitive mRNA markers for forensically relevant body fluids were adapted and validated in an mRNA multiplex assay for routine casework. This included the implementation of a DNA/RNA re-extraction method for automated extraction that can be integrated into casework without loss of DNA. This re-extraction method and the mRNA multiplex assay were tested using casework samples. PCR-primers were designed for the identification of rectal mucosa and the more effective marker MUC12 was integrated into an extended multiplex assay. The result of our study is a highly specific and sensitive mRNA multiplex assay plus an automated DNA/RNA re-extraction method, that can be integrated into casework and identify rectal mucosa for the first time.
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Affiliation(s)
- Malte Bamberg
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Lisa Dierig
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | | | - Sebastian N Kunz
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Max Schmidt
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, DNA Department, Maillingerstr. 15, 80636 Munich, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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24
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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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25
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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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26
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Haas C, Neubauer J, Salzmann AP, Hanson E, Ballantyne J. Forensic transcriptome analysis using massively parallel sequencing. Forensic Sci Int Genet 2021; 52:102486. [PMID: 33657509 DOI: 10.1016/j.fsigen.2021.102486] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
The application of transcriptome analyses in forensic genetics has experienced tremendous growth and development in the past decade. The earliest studies and main applications were body fluid and tissue identification, using targeted RNA transcripts and a reverse transcription endpoint PCR method. A number of markers have been identified for the forensically most relevant body fluids and tissues and the method has been successfully used in casework. The introduction of Massively Parallel Sequencing (MPS) opened up new perspectives and opportunities to advance the field. Contrary to genomic DNA where two copies of an autosomal DNA segment are present in a cell, abundant RNA species are expressed in high copy numbers. Even whole transcriptome sequencing (RNA-Seq) of forensically relevant body fluids and of postmortem material was shown to be possible. This review gives an overview on forensic transcriptome analyses and applications. The methods cover whole transcriptome as well as targeted MPS approaches. High resolution forensic transcriptome analyses using MPS are being applied to body fluid/ tissue identification, determination of the age of stains and the age of the donor, the estimation of the post-mortem interval and to post mortem death investigations.
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Affiliation(s)
- Cordula Haas
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland.
| | - Jacqueline Neubauer
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland
| | - Andrea Patrizia Salzmann
- University of Zurich, Zurich Institute of Forensic Medicine, Forensic Genetics, Winterthurerstrasse 190/52, CH-8057 Zurich, Switzerland
| | - Erin Hanson
- National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA; Department of Chemistry, National Center for Forensic Science, University of Central Florida, 12354 Research Parkway, Suite 225, Orlando, FL 32826, USA
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27
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Mistek-Morabito E, Lednev IK. Discrimination of menstrual and peripheral blood traces using attenuated total reflection Fourier transform-infrared (ATR FT-IR) spectroscopy and chemometrics for forensic purposes. Anal Bioanal Chem 2021; 413:2513-2522. [PMID: 33580831 DOI: 10.1007/s00216-021-03206-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/23/2020] [Accepted: 01/29/2021] [Indexed: 12/22/2022]
Abstract
Body fluid traces can provide highly valuable clues in forensic investigations. In particular, bloodstains are a common occurrence in criminal investigation, and the discrimination of menstrual and peripheral blood is a crucial step for casework involving rape and sexual assault. Most of the current protocols require the detection of characteristic menstrual blood components using sophisticated procedures that need to be performed in a laboratory. The present study uses attenuated total reflection Fourier transform-infrared (ATR FT-IR) spectroscopy as a nondestructive technique for discriminating menstrual and peripheral blood traces. This method incorporates statistical analysis and was evaluated by internal and external validation testing. A partial least squares discriminant analysis (PLSDA) classification model was created for differentiating the two types of blood in a binary manner. Excellent separation between menstrual and peripheral blood samples was achieved during internal validation. External validation resulted in 100% accuracy for predicting a sample as peripheral or menstrual blood. This study demonstrates that ATR FT-IR spectroscopy combined with chemometrics is a reliable approach for rapid and nondestructive discrimination of menstrual and peripheral bloodstains. It offers a significant advantage to forensic science due to the availability of portable instruments and the potential for bloodstain analysis at a crime scene. Graphical abstract.
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Affiliation(s)
- Ewelina Mistek-Morabito
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Igor K Lednev
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.
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28
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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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29
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Sakurada K, Watanabe K, Akutsu T. Current Methods for Body Fluid Identification Related to Sexual Crime: Focusing on Saliva, Semen, and Vaginal Fluid. Diagnostics (Basel) 2020; 10:diagnostics10090693. [PMID: 32937964 PMCID: PMC7555023 DOI: 10.3390/diagnostics10090693] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/25/2022] Open
Abstract
Although, DNA typing plays a decisive role in the identification of persons from blood and body fluid stains in criminal investigations, clarifying the origin of extracted DNA has also been considered an essential task in proving a criminal act. This review introduces the importance of developing precise methods for body fluid identification. Body fluid identification has long relied on enzymatic methods as a presumptive assay and histological or serological methods as a confirmatory assay. However, because the latest DNA typing methods can rapidly obtain results from very small and even old, poorly preserved samples, the development of a novel corresponding body fluid identification method is required. In particular, an immunochromatographic method has been introduced to identify saliva and semen from sexual crimes. In addition, for vaginal fluid identification, attempts have been made in the past decade to introduce a method relying on body fluid-specific mRNA expression levels. At present, the development of molecular biological methods involving microRNA, DNA methylation, and resident bacterial DNA is ongoing. Therefore, in criminal investigations, body fluid identification is an essential task for correctly applying the results of DNA typing, although further research and development are required.
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Affiliation(s)
- Koichi Sakurada
- Department of Forensic Dentistry, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Correspondence: ; Tel.: +81-3-5803-4387
| | - Ken Watanabe
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan; (K.W.); (T.A.)
| | - Tomoko Akutsu
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan; (K.W.); (T.A.)
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30
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Akutsu T, Watanabe K. A Proposed Procedure for Discriminating between Nasal Secretion and Saliva by RT-qPCR. Diagnostics (Basel) 2020; 10:diagnostics10080519. [PMID: 32722656 PMCID: PMC7460356 DOI: 10.3390/diagnostics10080519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022] Open
Abstract
In forensic casework, nasal secretion can be a good source of DNA. Moreover, saliva can prove useful in cases of sexual assault. However, discriminating between these body fluids is often difficult because of cross-reactivity between them on presumptive and confirmatory tests. Therefore, an RT-qPCR procedure was developed to discriminate between nasal secretion and saliva. Characteristic genes in nasal secretion and/or saliva (BPIFA1, STATH, HTN3, and PRH2) were selected as candidates. Discrimination criteria were established based on the expression levels of these markers in various body fluids. In addition, a flowchart was proposed and used to discriminate among nasal secretion, saliva, and other body fluids in various forensic samples. BPIFA1 was highly expressed in nasal secretion but was also expressed in saliva, semen, and vaginal fluid at trace levels. STATH was expressed in nasal secretion and saliva but not in other body fluids. HTN3 was specifically expressed in most of the saliva samples, as reported previously. Unexpectedly, PRH2 was expressed in only a few saliva samples. Using the proposed criteria and flowchart, nasal secretion and saliva were successfully discriminated among the various body fluids tested. The developed procedure could be useful in forensic casework.
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31
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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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32
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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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33
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Akutsu T, Yokota I, Watanabe K, Sakurada K. Development of a multiplex RT-PCR assay and statistical evaluation of its use in forensic identification of vaginal fluid. Leg Med (Tokyo) 2020; 45:101715. [PMID: 32413723 DOI: 10.1016/j.legalmed.2020.101715] [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: 03/23/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 01/09/2023]
Abstract
The identification of vaginal fluid from casework samples of sexual assaults provides important probative evidence of vaginal intercourse. The aim of this study was to establish a more specific procedure for identifying vaginal fluids for forensic purposes. Vaginal fluid marker candidates have been evaluated quantitatively and five of these markers (ESR1, SERPINB13, KLK13, CYP2B7P1, MUC4) have been amplified simultaneously by a multiplex reverse transcription-polymerase chain reaction (RT-PCR) procedure. Each amplicon has been separated and quantified automatically using chip electrophoresis. Subsequently, in the present study, detectability and cross-reactivity of the developed multiplex procedure were assessed in detail using various forensically relevant body fluids. Then, a cutoff value for the positive detection of vaginal fluids was set for each marker by Youden index. The ability of the multiplex RT-PCR assay to distinguish between vaginal and other body fluids was evaluated statistically using a likelihood ratio (LR) that was estimated using a Bayesian estimation approach to consider the infrequency of detection. A high LR was obtained when all five markers showed positive results (LR = 4.33 × 109; 95% credible interval, 3.95 × 107 -2.87 × 1012). The developed procedure was validated using vaginal fluid samples under various conditions. High LRs were found for aged vaginal fluid stains, although each amplicon peak was low. It was also able to identify vaginal stains mixed with other body fluids. In conclusion, the multiplex RT-PCR-based procedure followed by the statistical evaluation using LR could be a powerful tool for the objective identification of vaginal fluids.
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Affiliation(s)
- Tomoko Akutsu
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Isao Yokota
- Department of Biostatistics, Graduate School of Medicine, Hokkaido University, Nishi 15, Kita 7, Sapporo, Hokkaido 060-8638, Japan
| | - Ken Watanabe
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Koichi Sakurada
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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34
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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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35
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Validation of a streamlined RT-qPCR method for body fluid identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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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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37
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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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38
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Lewis CA, Layne TR, Seashols-Williams SJ. Detection of microRNAs in DNA Extractions for Forensic Biological Source Identification. J Forensic Sci 2019; 64:1823-1830. [PMID: 31107550 DOI: 10.1111/1556-4029.14070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 04/12/2019] [Indexed: 11/29/2022]
Abstract
Molecular-based approaches for biological source identification are of great interest in the forensic community because of a lack of sensitivity and specificity in current methods. MicroRNAs (miRNAs) have been considered due to their robust nature and tissue specificity; however, analysis requires a separate RNA extraction, requiring an additional step in the forensic analysis workflow. The purpose of this study was to evaluate miRNA detection in blood, semen, and saliva using DNA extraction methods commonly utilized for forensic casework. RT-qPCR analysis revealed that the tested miRNAs were consistently detectable across most tested DNA extraction methods, but detection was significantly reduced compared to RNA extracts in some biological fluids. DNase treatment was not necessary to achieve miRNA-specific results. A previously developed miRNA panel for forensic body fluid identification was evaluated using DNA extracts, and largely demonstrated concordance with results from samples deriving from RNA extracts of semen, blood, and saliva.
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Affiliation(s)
- Carolyn A Lewis
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Tiffany R Layne
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
| | - Sarah J Seashols-Williams
- Department of Forensic Science, Virginia Commonwealth University, Box 843079, Richmond, Virginia, 23284-3079
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39
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Dobay A, Haas C, Fucile G, Downey N, Morrison HG, Kratzer A, Arora N. Microbiome-based body fluid identification of samples exposed to indoor conditions. Forensic Sci Int Genet 2019; 40:105-113. [DOI: 10.1016/j.fsigen.2019.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/14/2019] [Accepted: 02/10/2019] [Indexed: 12/18/2022]
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40
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Díez López C, Vidaki A, Ralf A, Montiel González D, Radjabzadeh D, Kraaij R, Uitterlinden AG, Haas C, Lao O, Kayser M. Novel taxonomy-independent deep learning microbiome approach allows for accurate classification of different forensically relevant human epithelial materials. Forensic Sci Int Genet 2019; 41:72-82. [PMID: 31003081 DOI: 10.1016/j.fsigen.2019.03.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022]
Abstract
Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and identification when using previously proposed human cell biomarkers, while their microbiota composition largely differs. By using validated 16S rRNA gene massively parallel sequencing data from the Human Microbiome Project of 1636 skin, oral and vaginal samples, 50 taxonomy-independent deep learning networks were trained to classify these three tissues. Validation testing was performed in de-novo generated high-throughput 16S rRNA gene sequencing data using the Ion Torrent™ Personal Genome Machine from 110 test samples: 56 hand skin, 31 saliva and 23 vaginal secretion specimens. Body-site classification accuracy of these test samples was very high as indicated by AUC values of 0.99 for skin, 0.99 for oral, and 1 for vaginal secretion. Misclassifications were limited to 3 (5%) skin samples. Additional forensic validation testing was performed in mock casework samples by de-novo high-throughput sequencing of 19 freshly-prepared samples and 22 samples aged for 1 up to 7.6 years. All of the 19 fresh and 20 (91%) of the 22 aged mock casework samples were correctly tissue-type classified. Moreover, comparing the microbiome results with outcomes from previous human mRNA-based tissue identification testing in the same 16 aged mock casework samples reveals that our microbiome approach performs better in 12 (75%), similarly in 2 (12.5%), and less good in 2 (12.5%) of the samples. Our results demonstrate that this new microbiome approach allows for accurate tissue-type classification of three human epithelial materials of skin, oral and vaginal origin, which is highly relevant for future forensic investigations.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Arwin Ralf
- 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
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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41
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Lynch C, Fleming R. A review of direct polymerase chain reaction of DNA and RNA for forensic purposes. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Courtney Lynch
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
- School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rachel Fleming
- Forensic Research and Development Team, Institute of Environmental Science and Research Ltd Auckland New Zealand
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42
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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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43
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Characterization of tissue-specific biomarkers with the expression of circRNAs in forensically relevant body fluids. Int J Legal Med 2019; 133:1321-1331. [PMID: 30810820 DOI: 10.1007/s00414-019-02027-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Messenger RNA (mRNA) markers have been extensively investigated for the identification of forensically relevant body fluids and tissues based on their expression profiles among cell types. As products of the backsplicing of pre-mRNAs, circular RNAs (circRNAs) share exonic sequences with their linear counterparts. The inclusion of circRNAs in mRNA profiling is shown to facilitate the detection of biomarkers in the identification of body fluids. In this study, we identified the expression of circRNAs of 14 out of 45 biomarkers from five body fluid types using outward-facing primer sets and revealed the ratio of circular to total transcripts of biomarkers by RNase R treatment. Furthermore, our results of qPCR analysis show that the inclusion of circRNAs in the detection of biomarkers, including HBA and ALAS2 for blood; MMP7 and MMP10 for menstrual blood; HTN3 for saliva; SPINK5, SERPINB3, ESR1, and CYP2B7P1 for vaginal secretions; TGM4, KLK3, and PRM2 for semen; and SLC22A6 and MIOX for urine, does not impair the specificity of these biomarkers. Additionally, a high copy number of targets from linear transcripts could be employed to increase the detection sensitivity of TGM4 and KLK3 with a low expression level of circRNAs in urine samples. Altogether, these results will help with the development of robust multiplex assays for body fluid identification.
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44
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Specific microbes of saliva and vaginal fluid of Guangdong Han females based on 16S rDNA high-throughput sequencing. Int J Legal Med 2019; 133:699-710. [DOI: 10.1007/s00414-018-1986-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023]
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45
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"The acid test"-validation of the ParaDNA® Body Fluid ID Test for routine forensic casework. Int J Legal Med 2018; 133:751-757. [PMID: 30460509 DOI: 10.1007/s00414-018-1971-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/12/2018] [Indexed: 01/18/2023]
Abstract
The identification of the cellular origin and composition of crime scene-related traces can provide crucial insight into a crime scene reconstruction. In the last decade, especially mRNA-based body fluid and tissue identification (BFI) has been vigorously examined. Besides capillary electrophoretic (CE) and real-time quantitative PCR (RT-qPCR)-based approaches for mRNA detection, melt curve analysis bears potential as a simple-to-use method for BFI. The ParaDNA® Body Fluid ID Test relies on HyBeacon® probes and was developed as a rapid test for mRNA-based BFI of six different body fluids: vaginal fluid, seminal fluid, sperm cells, saliva, menstrual, and peripheral blood. The herein presented work was performed as an "acid test" of the system and should clarify whether the approach matches the requirements of forensic routine casework in German police departments. Tested samples consisted of single source as well as of mixed samples.
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46
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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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47
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Moawad AM, zaghlol HS, Abdelsalam MH, Abdelfattah A, Sabry D, Atef A. Differential genes expression biomarkers for menstrual and peripheral blood stains analysis. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0072-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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48
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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
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49
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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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50
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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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