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Fernandez-Tejero N, Gauthier Q, Cho S, McCord BR. High-resolution melt analysis for the detection of skin/sweat via DNA methylation. Electrophoresis 2023; 44:371-377. [PMID: 36480207 DOI: 10.1002/elps.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The determination of tissue type is important when reconstructing a crime scene as skin cells may indicate innocent contact, whereas other types of cells, such as blood and semen, may indicate foul play. Up to now, there has been no specific DNA methylation-based marker to distinguish skin cell DNA from other body fluids. The goal of this study is to develop a DNA methylation-based assay to detect and identify skin cells collected at forensic crime scenes for use in DNA typing. For this reason, we have utilized a DNA methylation chip array-based genome-wide association study to identify skin-specific DNA methylation markers. DNA obtained from skin along with other body fluids, such as semen, saliva, blood, and vaginal epithelia, were tested using five genes that were identified as sites for potential new epigenetic skin markers. Samples were collected, bisulfite converted, and subjected to real-time polymerase chain reaction (PCR) with high-resolution melt analysis. In our studies, when using WDR11, PON2, and NHSL1 assays with bisulfite-modified PCR, skin/sweat amplicons melted at lower temperatures compared to blood, saliva, semen, and vaginal epithelia. One-way analysis of variance demonstrates that these three skin/sweat markers are significantly different when compared with other body fluids (p < 0.05). These results demonstrate that high-resolution melt analysis is a promising technology to detect and identify skin/sweat DNA from other body fluids.
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Affiliation(s)
- Nicole Fernandez-Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Quentin Gauthier
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Bruce R McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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2
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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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3
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Bart G, Fischer D, Samoylenko A, Zhyvolozhnyi A, Stehantsev P, Miinalainen I, Kaakinen M, Nurmi T, Singh P, Kosamo S, Rannaste L, Viitala S, Hiltunen J, Vainio SJ. Characterization of nucleic acids from extracellular vesicle-enriched human sweat. BMC Genomics 2021; 22:425. [PMID: 34103018 PMCID: PMC8188706 DOI: 10.1186/s12864-021-07733-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07733-9.
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Affiliation(s)
- Geneviève Bart
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Daniel Fischer
- Production Systems, Natural Resources Institute Finland (LUKE), 31600, Jokioinen, Finland
| | - Anatoliy Samoylenko
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Artem Zhyvolozhnyi
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Pavlo Stehantsev
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Ilkka Miinalainen
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Mika Kaakinen
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Tuomas Nurmi
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Prateek Singh
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland.,Present Address: Finnadvance, Aapistie 5, 90220, Oulu, Finland
| | - Susanna Kosamo
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland
| | - Lauri Rannaste
- Biosensors, VTT, Technical Research Center of Finland Ltd, Kaitoväylä 1, 90570, Oulu, Finland
| | - Sirja Viitala
- Production Systems, Natural Resources Institute Finland (LUKE), 31600, Jokioinen, Finland
| | - Jussi Hiltunen
- Biosensors, VTT, Technical Research Center of Finland Ltd, Kaitoväylä 1, 90570, Oulu, Finland
| | - Seppo J Vainio
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Laboratory of Developmental Biology, Kvantum Institute, Infotech Oulu, University of Oulu, 90014 University of Oulu, Oulu, Finland.
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Valentine JL, Presler-Jur P, Mills H, Miles S. Evidence Collection and Analysis for Touch Deoxyribonucleic Acid in Groping and Sexual Assault Cases. JOURNAL OF FORENSIC NURSING 2021; 17:67-75. [PMID: 33843809 PMCID: PMC8140663 DOI: 10.1097/jfn.0000000000000324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Historically, evidence collection in sexual assault cases focused on obtaining foreign contributor bodily fluids through swab collection. With improvements in deoxyribonucleic acid (DNA) analysis methods, DNA profiles can be developed from touch DNA and applied to sexual assault cases. Following a literature review on factors affecting touch DNA transfer, a groping case study with innovative evidence collection is presented to support the expansion of touch DNA evidence collection in sexual assault cases. The groping case led to the development of a statewide sexual assault touch DNA form to guide evidence collection. DNA findings from additional groping sexual assault cases are reported to further show and justify the importance of evidence collection in groping cases. Implications on multidisciplinary practices are summarized to promote evidence collection and analysis in groping sexual assault cases. As forensic nurses are educated to accurately collect DNA evidence and provide trauma-informed, patient-centered care, they are best suited to provide nursing care for patients who have experienced groping sexual assaults. Optimal DNA findings in groping and sexual assault cases are best achieved through development of strong multidisciplinary, collaborative relationships between forensic nurses and forensic scientists.
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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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6
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Fujimoto S, Manabe S, Morimoto C, Ozeki M, Hamano Y, Hirai E, Kotani H, Tamaki K. Distinct spectrum of microRNA expression in forensically relevant body fluids and probabilistic discriminant approach. Sci Rep 2019; 9:14332. [PMID: 31586097 PMCID: PMC6778116 DOI: 10.1038/s41598-019-50796-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/19/2019] [Indexed: 11/09/2022] Open
Abstract
MicroRNA is attracting worldwide attention as a new marker for the identification of forensically relevant body fluids. A probabilistic discriminant model was constructed to identify venous blood, saliva, semen, and vaginal secretion, based on microRNA expression assessed via RT-qPCR. We quantified 15 candidate microRNAs in four types of body fluids by RT-qPCR and found that miR-144-3p, miR-451a-5p, miR-888-5p, miR-891a-5p, miR-203a-3p, miR-223-3p and miR-1260b were helpful to discriminate body fluids. Using the relative expression of seven candidate microRNAs in each body fluid, we implemented a partial least squares-discriminant analysis (PLS-DA) as a probabilistic discriminant model and distinguished four types of body fluids. Of 14 testing samples, 13 samples were correctly identified with >90% posterior probability. We also investigated the effects of microRNA expression in skin, semen infertility, and vaginal secretion during different menstrual phases. Semen infertility and menstrual phases did not affect our body fluid identification system. Therefore, the selected microRNAs were effective in identifying the four types of body fluids, indicating that probabilistic evaluation may be practical in forensic casework.
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Affiliation(s)
- Shuntaro Fujimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Sho Manabe
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Chie Morimoto
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Munetaka Ozeki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuya Hamano
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Forensic Science Laboratory, Kyoto Prefectural Police Headquaters, 85-3, 85-4, Yabunouchi-cho, Kamigyo-ku, Kyoto, 602-8550, Japan
| | - Eriko Hirai
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirokazu Kotani
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Keiji Tamaki
- Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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7
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Immunohistochemical staining of skin-expressed proteins to identify exfoliated epidermal cells for forensic purposes. Forensic Sci Int 2019; 303:109940. [DOI: 10.1016/j.forsciint.2019.109940] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/05/2019] [Accepted: 08/22/2019] [Indexed: 12/21/2022]
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8
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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van Oorschot RA, Szkuta B, Meakin GE, Kokshoorn B, Goray M. DNA transfer in forensic science: A review. Forensic Sci Int Genet 2019; 38:140-166. [DOI: 10.1016/j.fsigen.2018.10.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
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