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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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Kim BM, Park SU, Schmelzer L, Yang SB, Lee SD, Kim MY, Naue J, Lee HY. DNA methylation-based organ tissue identification: Marker identification, SNaPshot multiplex assay development, and interlaboratory comparison. Forensic Sci Int Genet 2024; 71:103052. [PMID: 38678764 DOI: 10.1016/j.fsigen.2024.103052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024]
Abstract
Identifying body fluids and organ tissues is highly significant as they can offer crucial evidence in criminal investigations and aid the court in making informed decisions, primarily through evaluating the biological source and possibly at the activity level up to death or fatal damage. In this study, organ tissue-specific CpG markers were identified from Illumina's methylation EPIC array data of nine organ tissues, including epidermis, dermis, heart, skeletal muscle, blood, kidney, brain, lung, and liver, from autopsies of 10 Koreans. Through the validation test using 43 samples, 18 hypomethylation markers, with two markers for each organ tissue type, were selected to construct a SNaPshot assay. Two multiplex assays involving forward and reverse SBE primers were designed to help investigators accurately determine the organ origin of the analyzed tissue samples through repeated analysis of the same PCR products for markers. The developed multiplex demonstrated high accuracy, achieving 100.0 % correct detection of the presence of nine organ tissue types in 88 samples from autopsies of 10 Asians. However, two lung samples showed additional positive indications of the presence of blood. An interlaboratory comparison using 80 autopsy samples (heart, skeletal muscle, blood, kidney cortex, kidney medulla, brain, lung, and liver) from 10 individuals in Germany revealed overall comparable results with correct detection of the presence of eight organ tissue types in 92.5 % samples (74 of 80 samples). In the case of six samples, it was impossible to determine the correct tissue successfully due to drop-outs of unmethylation signals at target tissue marker loci. One of these lung samples revealed only non-intended off-target signals for blood. The observed differences might be due to differences in sample collection during routine autopsy, technical differences due to the PCR cycler, and the threshold used for signal calling. Indicating the presence of additional tissue type and off-target unmethylation signals seems alleviated by applying more stringent hypomethylation thresholds. Therefore, the developed SNaPshot multiplex assays will be valuable for forensic investigators dealing with organ tissue identification, as well as for prosecutors and defense aiming to establish the circumstances that occurred at the crime scene.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Laura Schmelzer
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Young Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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Wohlfahrt D, Tan-Torres AL, Green R, Brim K, Bradley N, Brand A, Abshier E, Nogales F, Babcock K, Brooks J, Seashols-Williams S, Singh B. A bacterial signature-based method for the identification of seven forensically relevant human body fluids. Forensic Sci Int Genet 2023; 65:102865. [PMID: 37004371 DOI: 10.1016/j.fsigen.2023.102865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023]
Abstract
Detection and identification of body fluids plays a crucial role in criminal investigation, as it provides information on the source of the DNA as well as corroborative evidence regarding the crime committed, scene, and/or association with persons of interest. Historically, forensic serological methods have been chemical, immunological, catalytic, spectroscopic, and/or microscopic in nature. However, most of these methods are presumptive, with few robust confirmatory exceptions. In recent years several new molecular methods (mRNA, miRNA, DNA methylation, etc.) have been proposed; although promising, these methods require high quality human DNA or RNA. Additional steps are required in RNA based methods. Additionally, RNA based methods cannot be used for old cases where only DNA extracts remain to sample from. In this study, a novel non-human DNA (microbiome) based method was developed for the identification of the majority of forensically relevant human biological samples. Eight hundred and twelve (n = 812) biological samples (semen, vaginal fluid, menstrual blood, saliva, feces, urine, and blood) were collected and preserved using methods commonly used in forensic laboratories for evidence collection. Variable region four (V4) of 16 S ribosomal DNA (16 S rDNA) was amplified using a dual-indexing strategy and then sequenced on the MiSeq FGx sequencing platform using the MiSeq Reagent Kit v2 (500 cycles) and following the manufacturer's protocol. Machine learning prediction models were used to assess the classification accuracy of the newly developed method. As there was no significant difference in bacterial communities between vaginal fluid, menstrual blood, and female urine, these were combined as female intimate samples. Except in urine, the bacterial structures associated with male and female body fluid samples were not significantly different from one another. The newly developed method accurately identified human body fluid samples with an overall accuracy of more than 88%. This newly developed bacterial signature-based method is fast (no additional steps are needed as the same DNA can be used for both body fluid identification and STR typing), efficient (consume less sample as a single test can identify all major body fluids), sensitive (needs only 5 pg of bacterial DNA), accurate, and can be easily added into a forensic high throughput sequencing (HTS) panel.
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Jiang Z, Lu Y, Shi M, Li H, Duan J, Huang J. Effects of storage temperature, storage time, and hemolysis on the RNA quality of blood specimens: A systematic quantitative assessment. Heliyon 2023; 9:e16234. [PMID: 37260878 PMCID: PMC10227325 DOI: 10.1016/j.heliyon.2023.e16234] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Blood samples are the most common biospecimen in biobanks, and RNA from such blood samples is an important material for biomedical research. High-quality RNA is essential for consistent, reliable results. Preanalytical environmental conditions can affect the quality of blood RNA. Here, we carried out a quantitative assessment of the influence of storage temperature, storage time, and hemolysis on the RNA quality of blood specimens in biobanks. Methods Before RNA purification, blood samples from volunteers were exposed to 4 °C for 2, 6, 12, 24, or 48 h, 3 days, or 1 week, or exposed to room temperature (22-30 °C) for 1, 2, 6, 12, or 24 h. Hemolyzed samples were collected from laboratory department and some of them were prepared using the freeze-thaw method. After exposure to different preanalytical environmental conditions, the RNA simple Total RNA Kit was used to purify the RNA, following which a NanoDrop™ One and Qsep 100 Bio-Fragment Analyzer were used to assess RNA concentration, purity, and integrity. In addition, a part of the RNA was immediately reverse transcribed into cDNA when it was purified, then the relative expression levels of 18S, ACTB, HIF1α, HMOX1, and MKI67 were determined by real-time quantitative PCR. Finally, 30 blood samples were collected from the surplus samples in our laboratory department to assess their RNA quality without knowledge of their storage conditions (duration/temperature). Results For blood samples stored at 4 °C, there was a significant difference between the RNA integrity after 1 week compared to after 2 h. For blood samples stored at room temperature (22-30 °C), the RNA integrity was also significantly different at 6 h and 0 h. Hemolysis caused by freeze-thawing severely affected RNA quality, whereas clinical hemolysis generally produced no significant effects. Moreover, expression of 18S, ACTB, HIF1α, HMOX1, and MKI67 in whole blood stored under different conditions showed irregular changes, suggesting that preservation conditions are also important for gene expression. Conclusion RNA integrity was qualified for blood samples stored at 4 °C for up to 72 h or at room temperature (22-30 °C) for up to 2 h. Hemolysis usually does not affect the RNA quality of blood samples unless the hemolysis method damages leukocytes.
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Affiliation(s)
- Zhijun Jiang
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Yi Lu
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Manying Shi
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Hong Li
- Central Laboratory, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Junkai Duan
- Pediatric Heart Disease Treatment Center, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Jiyi Huang
- Biobank, Jiangxi Provincial Children's Hospital, Nanchang, China
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Wenzlow N, Mills D, Byrd J, Warren M, Long MT. Review of the current and potential use of biological and molecular methods for the estimation of the postmortem interval in animals and humans. J Vet Diagn Invest 2023; 35:97-108. [PMID: 36744749 PMCID: PMC9999395 DOI: 10.1177/10406387231153930] [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] [Indexed: 02/07/2023] Open
Abstract
We provide here an overview of the state of applied techniques in the estimation of the early period of the postmortem interval (PMI). The biological methods included consist of body cooling, CSF potassium, body cooling combined with CSF potassium, and tissue autolysis. For each method, we present its application in human and veterinary medicine and provide current methodology, strengths, and weaknesses, as well as target areas for improvement. We examine current and future molecular methods as they pertain to DNA and primarily to messenger RNA degradation for the estimation of the PMI, as well as the use of RNA in aging wounds, aging blood stains, and the identification of body fluids. Various types of RNA have different lengths, structures, and functions in cells. These differences in RNAs determine various intrinsic properties, such as their half-lives in cells, and, hence, their decay rate as well as their unique use for specific forensic tests. Future applications and refinements of RNA-based techniques provide opportunities for the use of molecular methods in the estimation of PMI and other general forensic applications.
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Affiliation(s)
- Nanny Wenzlow
- Louisiana Animal Disease Diagnostic Laboratory, Louisiana State University, Baton Rouge, LA, USA
| | - DeEtta Mills
- Department of Biological Sciences and International Forensic Research Institute, Florida International University, Miami, FL, USA
| | - Jason Byrd
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Mike Warren
- Maples Center for Forensic Medicine, University of Florida, Gainesville, FL, USA
| | - Maureen T. Long
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, Gainesville, FL, USA
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Kubo S, Niimi H, Kitajima I. Improved reverse transcription-recombinase polymerase amplification assay for blood mRNA screening: comparison with one-step RT-qPCR assay. Forensic Sci Int Genet 2023; 63:102808. [PMID: 36462298 DOI: 10.1016/j.fsigen.2022.102808] [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: 07/07/2022] [Revised: 10/07/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022]
Abstract
mRNA profiling is effective for body fluid identification because of its sensitivity, specificity, and multiplexing capability. Body fluid mRNA markers can typically be detected using RT-qPCR, RT-PCR followed by capillary electrophoresis, or targeted RNA sequencing. However, due to the multiple handling steps involved, the analysis of many forensic samples using these methods requires time and effort. Here, we describe a rapid and simple method for detecting the blood mRNA marker hemoglobin β (HBB), intended for use in screening before definitive blood identification. We employed a reverse transcription-recombinase polymerase amplification (RT-RPA) assay that can detect target mRNA within 20 min in a single tube. For comparison, we used a one-step RT-qPCR assay. We optimized the RT-RPA assay and found that it could detect HBB from 10-3-10-4 ng of leukocyte RNA and approximately 10-3 µL of blood. The sensitivity was 10-fold lower than that of the one-step RT-qPCR assay but higher than that of the comprehensive analysis methods for definitive blood identification. Thus, the rapidity and sensitivity of the RT-RPA assay support its use as a screening tool. We also found that the RT-RPA assay was highly tolerant to common inhibitors such as humic acid, hematin, tannic acid, and melanin. Considering the inhibitor tolerability, we integrated a simple lysis method (addition of TCEP/EDTA and heating at 95 °C for 5 min) without the RNA purification process into the RT-RPA assay. This direct assay successfully detected HBB in crude blood samples. Our findings suggest that the RT-RPA assay for HBB is a promising strategy for mRNA-based blood screening.
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Affiliation(s)
- Seiji Kubo
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan.
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Isao Kitajima
- Administrative office, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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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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Unlocking the potential of forensic traces: Analytical approaches to generate investigative leads. Sci Justice 2022; 62:310-326. [PMID: 35598924 DOI: 10.1016/j.scijus.2022.03.005] [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: 04/29/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/21/2022]
Abstract
Forensic investigation involves gathering the information necessary to understand the criminal events as well as linking objects or individuals to an item, location or other individual(s) for investigative purposes. For years techniques such as presumptive chemical tests, DNA profiling or fingermark analysis have been of great value to this process. However, these techniques have their limitations, whether it is a lack of confidence in the results obtained due to cross-reactivity, subjectivity and low sensitivity; or because they are dependent on holding reference samples in a pre-existing database. There is currently a need to devise new ways to gather as much information as possible from a single trace, particularly from biological traces commonly encountered in forensic casework. This review outlines the most recent advancements in the forensic analysis of biological fluids, fingermarks and hair. Special emphasis is placed on analytical methods that can expand the information obtained from the trace beyond what is achieved in the usual practices. Special attention is paid to those methods that accurately determine the nature of the sample, as well as how long it has been at the crime scene, along with individualising information regarding the donor source of the trace.
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Kubo S, Niimi H, Kitajima I. Rapid detection of blood and semen mRNA markers by reverse transcription-recombinase polymerase amplification. Forensic Sci Int Genet 2022; 58:102665. [DOI: 10.1016/j.fsigen.2022.102665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
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Vibrational spectroscopic approaches for semen analysis in forensic investigation: State of the art and way forward. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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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[The influence of peripheral blood sample storage and delivery on the quantitative detection result of BCR-ABL (P210) transcript levels]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:224-229. [PMID: 33910308 PMCID: PMC8081946 DOI: 10.3760/cma.j.issn.0253-2727.2021.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
目的 探索慢性髓性白血病(CML)患者外周血样本的存储和运输对实时定量PCR(RQ-PCR)检测BCR-ABL(P210)转录本水平的影响。 方法 采集84例CML患者外周血样本,根据储存时间(0、6、12、24、48和72 h)、温度[室温(18~24 °C)和低温(2~8 °C)]以及振荡条件(振荡时长3、6和12 h)设置不同分组,RQ-PCR法检测不同条件下外周血样本BCR-ABL(P210)转录本水平。本研究将BCR-ABL拷贝数、ABL拷贝数和BCR-ABL(P210)转录本水平等原始数据进行对数转化(log10N)。 结果 ①琼脂糖凝胶电泳结果显示:室温条件下,储存48、72 h的样本RNA出现显著降解;②储存温度方面,总体样本中,室温储存48、72 h的样本BCR-ABL拷贝数检测水平显著低于低温储存的样本(P<0.05);然而BCR-ABL(P210)转录本水平在低温储存与室温储存条件下检测结果差异无统计学意义(P>0.05);③储存时间方面,与基线的3.35±1.60相比,总体样本的BCR-ABL拷贝数检测结果仅在室温储存储存下48 h(2.93±1.59)和72 h(2.79±1.42)显著下降(P<0.05);与基线的5.47±0.35相比,总体样本中ABL拷贝数检测结果在48 h(低温5.29±0.30,室温5.06±0.38)和72 h(低温5.11±0.54,室温4.64±0.79)均显著下降(P<0.05)。但是,与基线的−0.56±1.51相比,无论低温或室温条件下,不同储存时间(6、12、24、48和72 h)的样本BCR-ABL(P210)转录本水平检测结果无显著改变(P>0.05);④振荡方面,与基线的−0.60±1.37相比,振荡3、6、12 h的样本BCR-ABL(P210)转录本水平检测结果无显著改变(P>0.05)。 结论 样本储存时间、储存温度及运输振荡因素可以影响BCR-ABL、ABL拷贝数的检测结果,但对BCR-ABL(P210)转录本水平定量检测结果无显著影响。
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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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Murahashi M, Makinodan M, Yui M, Hibi T, Kobayashi M. Immunochromatographic detection of human hemoglobin from deteriorated bloodstains due to methamphetamine contamination, aging, and heating. Anal Bioanal Chem 2020; 412:5799-5809. [PMID: 32642837 DOI: 10.1007/s00216-020-02802-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 11/29/2022]
Abstract
Japanese police conduct highly sensitive and quick blood tests to detect human hemoglobin (Hb), because bloodstains left at a crime scene have probative value of circumstantial evidence in a criminal investigation. Although DNA detection from a bloodstain is a useful tool to identify an individual, doing so requires evidence that the bloodstain is of human origin. Stimulant drug abuse and dependence causes major social problems and crimes in Japan, and bloodstains are often found inside syringes seized from drug abusers. In this case, Hb often cannot be detected by conventional testing as high concentrations of stimulants, such as methamphetamine hydrochloride (MA), in blood trigger polymerization of Hb molecules, which become insoluble under non-reducing conditions and can no longer be detected by immunochromatographic detection kits. To overcome this problem, we analyzed methods to detect denatured Hb from bloodstains contaminated with MA. Reduction of polymerized Hb with a strong denaturing agent was required to solubilize polymers into monomers, suggesting that Hb aggregation is caused by aberrant formation of disulfide bonds. Based on these results, we established a pretreatment method, called Fukui's Reduction and Eiken's Dilution (FRED), that enables highly sensitive detection of human Hb from bloodstains mixed with MA by reducing and refolding of denatured Hb. This powerful method can be applied to blood that has been boiled or has otherwise deteriorated for over 20 years.
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Affiliation(s)
- Masataka Murahashi
- Forensic Science Laboratory, Fukui Prefectural Police Headquarters, 3-17-1 Ote, Fukui, 910-8515, Japan. .,Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Fukui, 910-1193, Japan.
| | - Mitsuru Makinodan
- Biochemical Research Laboratory I, Eiken Chemical Co., Ltd., 143 Nogi, Nogimachi, Tochigi, 329-0114, Japan
| | - Megumi Yui
- Biochemical Research Laboratory I, Eiken Chemical Co., Ltd., 143 Nogi, Nogimachi, Tochigi, 329-0114, Japan
| | - Takao Hibi
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjyojima, Eiheiji, Fukui, 910-1195, Japan
| | - Motohiro Kobayashi
- Department of Tumor Pathology, Faculty of Medical Sciences, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji, Fukui, 910-1193, Japan
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15
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Song J, Zhou J. Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens. PeerJ 2020; 8:e8940. [PMID: 32309050 PMCID: PMC7153556 DOI: 10.7717/peerj.8940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/18/2020] [Indexed: 11/30/2022] Open
Abstract
A prolonged preservation duration of blood specimens at 4 °C may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses. However, effects of preservation durations at 4 °C on RNA quality in blood specimens need to be studied. We collected rabbit blood using EDTA tubes and stored them at 4 °C for different preservation durations. Then, we examined the quality of RNA from whole blood and leukocytes isolated from rabbit blood. Our results show that the purity of whole blood RNA and leukocyte RNA does not indicate significant change after rabbit blood is stored at 4 °C for different preservation durations (from 1 h to 7 days). The integrity of leukocyte RNA indicates the same result as above, but the integrity of whole blood RNA is significantly decreased after rabbit blood is stored at 4 °C for over 3 days. Moreover, expression of SMAD7, MKI67, FOS, TGFβ1 and HIF1α of whole blood RNA and leukocyte RNA remains basically stable, but PCNA expression of whole blood RNA or leukocyte RNA is significantly decreased after rabbit blood is stored at 4 °C for over 24 h or 7 days. Therefore, these results suggest that high-quality RNA is obtained from the fresher blood specimens and if blood specimens are stored for over 3 days at 4 °C, the quality of leukocyte RNA is more stable and of better quality than that of whole blood RNA.
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Affiliation(s)
- Jiaojiao Song
- Children's Hospital of Shanghai, Shanghai, China.,Children's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Junmei Zhou
- Children's Hospital of Shanghai, Shanghai, China.,Children's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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16
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Alshehhi S, Haddrill PR. Evaluating the effect of body fluid mixture on the relative expression ratio of blood-specific RNA markers. Forensic Sci Int 2019; 307:110116. [PMID: 31881371 DOI: 10.1016/j.forsciint.2019.110116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/09/2019] [Accepted: 12/08/2019] [Indexed: 11/15/2022]
Abstract
The estimation of the time elapsed since a biological stain was deposited at a crime scene can provide crucial information to a forensic investigation, indicating either when a crime was committed, or whether the biological evidence was deposited at the time of a known crime event. This would enable the investigators to limit the number of suspects and to assess alibis. The relative expression ratios (RERs) of body fluid-specific RNA markers are promising molecular tools for indicating the age of biological stains. However, the nature of some forensic samples found at crime scenes could be challenging, as they frequently occur in a mixture of different body fluid types. The research presented here has utilised reverse transcription quantitative PCR (RT-qPCR) to explore the impact of bloodstains being present in mixtures with other body fluids (saliva or semen) on the resulting RERs of blood-specific markers. The expression level of three blood-specific markers (HBA, HBB and miR16) along with two reference genes (18S and U6) were analysed across multiple ageing time points in pure and mixed bloodstains. For some markers, no significant differences were found when comparing RERs in pure and mixed bloodstains, however some RERs were altered in mixed stains. This indicates that the presence of body fluid mixtures may have a significant effect on the RERs of some blood-specific markers. This should therefore be considered when selecting markers for estimating the age of stains, particularly when multiple body fluids are thought to be present.
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Affiliation(s)
- Suaad Alshehhi
- Centre for Forensic Science, University of Strathclyde (Glasgow), UK; General Department of Forensic Science and Criminology, Dubai Police, United Arab Emirates.
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17
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Sharma S, Singh R. Detection and discrimination of seminal fluid using attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy combined with chemometrics. Int J Legal Med 2019; 134:411-432. [PMID: 31814056 DOI: 10.1007/s00414-019-02222-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
Semen is most frequently encountered body fluid in forensic cases apart from blood especially in sexual assault cases. The presence and absence of semen can help in conviction or exoneration of a suspect by either confirming or refuting the claims put forward by the suspect and the victim. However, in the wake of limited studies on non-destructive and rapid analysis of semen, it is fairly difficult. Therefore, it is an increasing demand to pioneer the application of available analytical methods in such manner that non-destructive, automated, rapid, and reliable identification and discrimination of body fluids can be established. In the present study, such a methodological application of attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy has been put forward as one of the initial steps towards the identification and discrimination/classification of seminal fluid from vaginal fluid and other human biological as well as non-biological look-alike semen substances using chemometric tools which are principal component analysis (PCA), partial least square regression (PLSR), and linear discriminant analysis (LDA). Effect of other simulated factors such as substrate interference, mixing with other body fluids, dilutions, and washing and chemical treatments to the samples has been studied. PCA resulted in 98.8% of accuracy for the discrimination of seminal fluid from vaginal fluid whilst 100% accuracy was obtained using LDA method. One hundred percent discrimination was achieved to discriminate semen from other biological fluids using PLSR and LDA, and from non-biological substances using PCA-LDA models. Furthermore, results of the effect of substrates, chemical treatment, mixing with vaginal secretions, and dilution have also been described.
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Affiliation(s)
- Sweety Sharma
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India
| | - Rajinder Singh
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India.
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Watanabe K, Akutsu T. Evaluation of a co-extraction kit for mRNA, miRNA and DNA methylation-based body fluid identification. Leg Med (Tokyo) 2019; 42:101630. [PMID: 31751797 DOI: 10.1016/j.legalmed.2019.101630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023]
Abstract
Recently, messenger RNA (mRNA), micro RNA (miRNA), and DNA methylation (DNAm) have been reported as novel markers for body fluid identification (BFID). Comprehensive analysis of these markers should be a flexible and reliable BFID method for various types of forensic samples. However, independent extraction of all targets can be difficult depending on the usable amounts of samples. In this study, the applicability of a co-extraction kit for these molecules, the AllPrep DNA/RNA/miRNA Universal Kit (APU), was evaluated by comparing RNA and DNA extracted from blood and saliva stains by the APU with those extracted by standard kits for each molecule and by previously reported methods for mRNA/DNA or miRNA/DNA co-extraction. Electrophoresis using the Bioanalyzer platform and real-time PCR analysis revealed that the APU performed almost equivalently to each standard kit in the quality of RNA or DNA extracted and extraction efficiency of mRNAs, miRNAs, and DNA. Moreover, the APU outperformed the co-extraction methods, especially in RNA integrity and miRNA extraction efficiency. In addition, pyrosequencing revealed that the methylation ratios of DNA extracted by the APU were not different from those extracted by standard DNA extraction kits. Overall, the APU is applicable to comprehensive analysis of mRNA/miRNA/DNAm markers for BFID analysis. Because the DNA eluate can also be used for DNA typing, the APU may be among the best choices for forensic examination of body fluid samples in terms of its flexibility and reliability in BFID and efficiency in sample consumption.
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Affiliation(s)
- Ken Watanabe
- National Research Institute of Police Science, Chiba 277-0882, Japan.
| | - Tomoko Akutsu
- National Research Institute of Police Science, Chiba 277-0882, Japan
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19
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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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20
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Gauthier QT, Cho S, Carmel JH, McCord BR. Development of a body fluid identification multiplex via DNA methylation analysis. Electrophoresis 2019; 40:2565-2574. [DOI: 10.1002/elps.201900118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/05/2019] [Accepted: 06/25/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Quentin T. Gauthier
- Department of Chemistry and BiochemistryFlorida International University Miami FL USA
| | - Sohee Cho
- Department of Chemistry and BiochemistryFlorida International University Miami FL USA
- Institute of Forensic ScienceSeoul National University College of Medicine Seoul South Korea
| | - Justin H. Carmel
- Department of Chemistry and BiochemistryFlorida International University Miami FL USA
| | - Bruce R. McCord
- Department of Chemistry and BiochemistryFlorida International University Miami FL USA
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Jung L, Hogan ME, Sun Y, Liang BM, Hayward JA. Rapid authentication of pharmaceuticals via DNA tagging and field detection. PLoS One 2019; 14:e0218314. [PMID: 31194827 PMCID: PMC6564018 DOI: 10.1371/journal.pone.0218314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 05/26/2019] [Indexed: 11/23/2022] Open
Abstract
A small PCR-generated DNA fragment was introduced into a pharmaceutical grade ink as a molecular taggant, and the DNA tagged ink was delivered onto the surface of capsules by standard high-speed offset printing. The amount of DNA in the ink on each capsule is roughly 10−12 fold lower than that allowed as safe by the United States Food and Drug Administration (FDA) and the WHO with regards to acceptable limits of residual DNA. The printed ink on the capsule surface was sampled by swabbing, followed by direct analysis of the DNA-swab complex, without subsequent DNA purification. It was shown that DNA recovered from the ink by swabbing was suitable for PCR-CE analysis—a widely used method in forensic science and was also suitable for qPCR and isothermal DNA amplification, when coupled with portable devices similar to those used for environmental sampling and food safety testing. The data set a precedent: A small DNA fragment could be introduced as an excipient into a pharmaceutical application, and thereafter tracked through the pharmaceutical supply chain via forensic DNA authentication.
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Affiliation(s)
- Lawrence Jung
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
- * E-mail: (MEH); (LJ)
| | - Michael E. Hogan
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
- * E-mail: (MEH); (LJ)
| | - Yuhua Sun
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
| | | | - James A. Hayward
- Applied DNA Sciences, Inc. Stony Brook, New York, United States of America
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22
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Acute Spinal Cord Injury: A Systematic Review Investigating miRNA Families Involved. Int J Mol Sci 2019; 20:ijms20081841. [PMID: 31013946 PMCID: PMC6515063 DOI: 10.3390/ijms20081841] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/06/2019] [Accepted: 04/10/2019] [Indexed: 02/07/2023] Open
Abstract
Acute traumatic spinal cord injury (SCI) involves primary and secondary injury mechanisms. The primary mechanism is related to the initial traumatic damage caused by the damaging impact and this damage is irreversible. Secondary mechanisms, which begin as early as a few minutes after the initial trauma, include processes such as spinal cord ischemia, cellular excitotoxicity, ionic dysregulation, and free radical-mediated peroxidation. SCI is featured by different forms of injury, investigating the pathology and degree of clinical diagnosis and treatment strategies, the animal models that have allowed us to better understand this entity and, finally, the role of new diagnostic and prognostic tools such as miRNA could improve our ability to manage this pathological entity. Autopsy could benefit from improvements in miRNA research: the specificity and sensitivity of miRNAs could help physicians in determining the cause of death, besides the time of death.
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23
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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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24
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Kaczor-Urbanowicz KE, Trivedi HM, Lima PO, Camargo PM, Giannobile WV, Grogan TR, Gleber-Netto FO, Whiteman Y, Li F, Lee HJ, Dharia K, Aro K, Carerras-Presas CM, Amuthan S, Vartak M, Akin D, Al-adbullah H, Bembey K, Klokkevold PR, Elashoff D, Barnes VM, Richter R, DeVizio W, Masters JG, Wong DTW. Salivary exRNA biomarkers to detect gingivitis and monitor disease regression. J Clin Periodontol 2018; 45:806-817. [PMID: 29779262 PMCID: PMC6023773 DOI: 10.1111/jcpe.12930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/14/2018] [Accepted: 05/13/2018] [Indexed: 12/15/2022]
Abstract
AIM This study tests the hypothesis that salivary extracellular RNA (exRNA) biomarkers can be developed for gingivitis detection and monitoring disease regression. MATERIALS AND METHODS Salivary exRNA biomarker candidates were developed from a total of 100 gingivitis and non-gingivitis individuals using Affymetrix's expression microarrays. The top 10 differentially expressed exRNAs were tested in a clinical cohort to determine whether the discovered salivary exRNA markers for gingivitis were associated with clinical gingivitis and disease regression. For this purpose, unstimulated saliva was collected from 30 randomly selected gingivitis subjects, the gingival and plaque indexes scores were taken at baseline, 3 and 6 weeks and salivary exRNAs were assayed by means of reverse transcription quantitative polymerase chain reaction. RESULTS Eight salivary exRNA biomarkers developed for gingivitis were statistically significantly changed over time, consistent with disease regression. A panel of four salivary exRNAs [SPRR1A, lnc-TET3-2:1, FAM25A, CRCT1] can detect gingivitis with a clinical performance of 0.91 area under the curve, with 71% sensitivity and 100% specificity. CONCLUSIONS The clinical values of the developed salivary exRNA biomarkers are associated with gingivitis regression. They offer strong potential to be advanced for definitive validation and clinical laboratory development test.
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Affiliation(s)
| | - Harsh M. Trivedi
- Colgate Palmolive Co., Early Research Oral Care, New Jersey, 909
River Road, Piscataway, New Jersey, USA 08855
| | - Patricia O. Lima
- Center for Oral/Head & Neck Oncology Research, UCLA School
of Dentistry, University of California at Los Angeles, California, USA
- Department of Physiological Sciences, Piracicaba Dental School,
University of Campinas, Piracicaba, São Paulo, Brazil
| | - Paulo M. Camargo
- Section of Periodontics, UCLA School of Dentistry, University of
California at Los Angeles, California, USA
| | - William V. Giannobile
- Department of Periodontics and Oral Medicine, School of Dentistry,
University of Michigan, Ann Arbor, Michigan, USA
| | - Tristan R. Grogan
- Department of Biostatistics, University of California at Los
Angeles, California, USA
| | - Frederico O. Gleber-Netto
- Medical Genomics Laboratory, Centro Internacional de Pesquisa e
Ensino (CIPE), AC Camargo Cancer Center, São Paulo, Brazil
| | - Yair Whiteman
- Center for Esthetic Dentistry, UCLA School of Dentistry, University
of California at Los Angeles, California, USA
| | - Feng Li
- Center for Oral/Head & Neck Oncology Research, UCLA School
of Dentistry, University of California at Los Angeles, California, USA
| | - Hyo Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National
University Bundang Hospital, Seoul, Korea
| | - Karan Dharia
- UCLA School of Dentistry, University of California at Los Angeles,
California, USA
| | - Katri Aro
- Center for Oral/Head & Neck Oncology Research, UCLA School
of Dentistry, University of California at Los Angeles, California, USA
| | | | - Saarah Amuthan
- UCLA School of Dentistry, University of California at Los Angeles,
California, USA
| | - Manjiri Vartak
- UCLA School of Dentistry, University of California at Los Angeles,
California, USA
| | - David Akin
- Center for Oral/Head & Neck Oncology Research, UCLA School
of Dentistry, University of California at Los Angeles, California, USA
| | - Hiba Al-adbullah
- UCLA School of Dentistry, University of California at Los Angeles,
California, USA
| | - Kanika Bembey
- UCLA School of Dentistry, University of California at Los Angeles,
California, USA
| | - Perry R. Klokkevold
- Section of Periodontics, UCLA School of Dentistry, University of
California at Los Angeles, California, USA
| | - David Elashoff
- Department of Biostatistics, University of California at Los
Angeles, California, USA
| | - Virginia Monsul Barnes
- Colgate Palmolive Co., Clinical Research Oral Care, New Jersey, 909
River Road, Piscataway, New Jersey, USA 08855
| | - Rose Richter
- Colgate Palmolive Co., Clinical Research Oral Care, New Jersey, 909
River Road, Piscataway, New Jersey, USA 08855
| | - William DeVizio
- Colgate Palmolive Co., Clinical Research Oral Care, New Jersey, 909
River Road, Piscataway, New Jersey, USA 08855
| | - James G. Masters
- Colgate Palmolive Co., Early Research Oral Care, New Jersey, 909
River Road, Piscataway, New Jersey, USA 08855
| | - David T. W. Wong
- Center for Oral/Head & Neck Oncology Research, UCLA School
of Dentistry, University of California at Los Angeles, California, USA
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25
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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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26
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Satoh T, Kouroki S, Ogawa K, Tanaka Y, Matsumura K, Iwase S. Development of mRNA-based body fluid identification using reverse transcription loop-mediated isothermal amplification. Anal Bioanal Chem 2018; 410:4371-4378. [PMID: 29696299 DOI: 10.1007/s00216-018-1088-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 11/24/2022]
Abstract
Identifying body fluids from forensic samples can provide valuable evidence for criminal investigations. Messenger RNA (mRNA)-based body fluid identification was recently developed, and highly sensitive parallel identification using reverse transcription polymerase chain reaction (RT-PCR) has been described. In this study, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a simple, rapid assay for identifying three common forensic body fluids, namely blood, semen, and saliva, and evaluated its specificity and sensitivity. Hemoglobin beta (HBB), transglutaminase 4 (TGM4), and statherin (STATH) were selected as marker genes for blood, semen, and saliva, respectively. RT-LAMP could be performed in a single step including both reverse transcription and DNA amplification under an isothermal condition within 60 min, and detection could be conveniently performed via visual fluorescence. Marker-specific amplification was performed in each assay, and no cross-reaction was observed among five representative forensically relevant body fluids. The detection limits of the assays were 0.3 nL, 30 nL, and 0.3 μL for blood, semen, and saliva, respectively, and their sensitivities were comparable with those of RT-PCR. Furthermore, RT-LAMP assays were applicable to forensic casework samples. It is considered that RT-LAMP is useful for body fluid identification.
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Affiliation(s)
- Tetsuya Satoh
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan.
| | - Seiya Kouroki
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Keita Ogawa
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Yorika Tanaka
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Kazutoshi Matsumura
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Susumu Iwase
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
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27
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Zou Y, Yang F, Yuan X, Ma K, Li H, Zhao X, Cai N, Huang X, Liu W. An efficient sodium citrate-promoted synthetic method for the preparation of AuNPs@mesoSiO 2 for surface enhanced Raman spectroscopy in the detection of diluted blood. JOURNAL OF SAUDI CHEMICAL SOCIETY 2017. [DOI: 10.1016/j.jscs.2017.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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28
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Holtkötter H, Schwender K, Wiegand P, Peiffer H, Vennemann M. Improving body fluid identification in forensic trace evidence—construction of an immunochromatographic test array to rapidly detect up to five body fluids simultaneously. Int J Legal Med 2017; 132:83-90. [DOI: 10.1007/s00414-017-1724-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
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29
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Abstract
In forensic investigations, the identification of the cellular or body fluid source of biological evidence can provide crucial probative information for the court. Messenger RNA (mRNA) profiling has become a valuable tool for body fluid and cell type identification due to its high sensitivity and compatibility with DNA analysis. However, using a single marker to determine the somatic origin of a sample can lead to misinterpretation as a result of cross-reactions. While false positives may be avoided through the simultaneous detection of multiple markers per body fluid, this approach is currently limited by the small number of known differentially expressed mRNAs. Here we characterise six novel mRNAs, partly identified from RNA-Seq, which can supplement existing markers for the detection of circulatory blood, semen (with and without spermatozoa), and menstrual fluid: HBD and SLC4A1 for blood, TNP1 for spermatozoa, KLK2 for seminal fluid, and MMP3 and STC1 for menstrual fluid. Respective expression profiles were evaluated by singleplex endpoint reverse transcription polymerase chain reaction (RT-PCR). HBD, SLC4A1, and KLK2 were specific to their target body fluids. TNP1, MMP3, and STC1 each cross-reacted with two non-target samples; however, these signals were below 350RFU, not reproducible, and likely resulted from large body fluid inputs. All candidates were more sensitive for the detection of their target body fluids than corresponding well-known mRNAs, in particular those for menstrual fluid. The increased sensitivities were statistically significant, except for KLK2. Thus, the new mRNAs introduced here are promising new targets for improved body fluid profiling.
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Affiliation(s)
- Patricia P Albani
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand; The Institute of Environmental Science and Research Ltd. (ESR), Auckland, New Zealand
| | - Rachel Fleming
- The Institute of Environmental Science and Research Ltd. (ESR), Auckland, New Zealand.
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30
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Lin YC, Tsai LC, Lee JCI, Su CW, Tzen JTC, Linacre A, Hsieh HM. Novel identification of biofluids using a multiplex methylation sensitive restriction enzyme-PCR system. Forensic Sci Int Genet 2016; 25:157-165. [DOI: 10.1016/j.fsigen.2016.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/28/2016] [Accepted: 08/31/2016] [Indexed: 12/22/2022]
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31
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Seashols-Williams S, Lewis C, Calloway C, Peace N, Harrison A, Hayes-Nash C, Fleming S, Wu Q, Zehner ZE. High-throughput miRNA sequencing and identification of biomarkers for forensically relevant biological fluids. Electrophoresis 2016; 37:2780-2788. [DOI: 10.1002/elps.201600258] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/14/2016] [Accepted: 08/17/2016] [Indexed: 12/18/2022]
Affiliation(s)
| | - Carolyn Lewis
- Department of Forensic Science; Virginia Commonwealth University; Richmond VA USA
| | - Chelsea Calloway
- Department of Forensic Science; Virginia Commonwealth University; Richmond VA USA
| | - Nerissa Peace
- Department of Forensic Science; Virginia Commonwealth University; Richmond VA USA
| | - Ariana Harrison
- Department of Forensic Science; Virginia Commonwealth University; Richmond VA USA
| | - Christina Hayes-Nash
- Department of Forensic Science; Virginia Commonwealth University; Richmond VA USA
| | - Samantha Fleming
- Department of Forensic Science; Virginia Commonwealth University; Richmond VA USA
| | - Qianni Wu
- Department of Biochemistry and Molecular Biology; Virginia Commonwealth University; Richmond VA USA
| | - Zendra E. Zehner
- Department of Biochemistry and Molecular Biology; Virginia Commonwealth University; Richmond VA USA
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Watanabe K, Akutsu T, Takamura A, Sakurada K. Evaluation of a blood-specific DNA methylated region and trial for allele-specific blood identification from mixed body fluid DNA. Leg Med (Tokyo) 2016; 22:49-53. [DOI: 10.1016/j.legalmed.2016.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/27/2016] [Accepted: 08/10/2016] [Indexed: 02/07/2023]
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33
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Michailidou E, Tzimagiorgis G, Chatzopoulou F, Vahtsevanos K, Antoniadis K, Kouidou S, Markopoulos A, Antoniades D. Salivary mRNA markers having the potential to detect oral squamous cell carcinoma segregated from oral leukoplakia with dysplasia. Cancer Epidemiol 2016; 43:112-8. [DOI: 10.1016/j.canep.2016.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/15/2016] [Accepted: 04/15/2016] [Indexed: 01/28/2023]
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34
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A 17-month time course study of human RNA and DNA degradation in body fluids under dry and humid environmental conditions. Int J Legal Med 2016; 130:1431-1438. [DOI: 10.1007/s00414-016-1373-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/29/2016] [Indexed: 12/20/2022]
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35
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Malentacchi F, Pizzamiglio S, Wyrich R, Verderio P, Ciniselli C, Pazzagli M, Gelmini S. Effects of Transport and Storage Conditions on Gene Expression in Blood Samples. Biopreserv Biobank 2016; 14:122-8. [DOI: 10.1089/bio.2015.0037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Francesca Malentacchi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | | | | | - Paolo Verderio
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Mario Pazzagli
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | - Stefania Gelmini
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
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36
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Matsumura S, Matsusue A, Waters B, Kashiwagi M, Hara K, Kubo SI. Application of mRNA Expression Analysis to Human Blood Identification in Degenerated Samples that were False-negative by Immunochromatography,,. J Forensic Sci 2016; 61:903-12. [DOI: 10.1111/1556-4029.13045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 06/25/2015] [Accepted: 07/03/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Shusaku Matsumura
- Forensic Science Laboratory; Fukuoka Prefectural Police Headquarters; 7-7 Higashikoen Hakata-ku Fukuoka 812-8576 Japan
- Department of Forensic Medicine; Faculty of Medicine; Fukuoka University; 7-45-1 Nanakuma Jonan-ku Fukuoka 814-0180 Japan
| | - Aya Matsusue
- Department of Forensic Medicine; Faculty of Medicine; Fukuoka University; 7-45-1 Nanakuma Jonan-ku Fukuoka 814-0180 Japan
| | - Brian Waters
- Department of Forensic Medicine; Faculty of Medicine; Fukuoka University; 7-45-1 Nanakuma Jonan-ku Fukuoka 814-0180 Japan
| | - Masayuki Kashiwagi
- Department of Forensic Medicine; Faculty of Medicine; Fukuoka University; 7-45-1 Nanakuma Jonan-ku Fukuoka 814-0180 Japan
| | - Kenji Hara
- Department of Forensic Medicine; Faculty of Medicine; Fukuoka University; 7-45-1 Nanakuma Jonan-ku Fukuoka 814-0180 Japan
| | - Shin-ichi Kubo
- Department of Forensic Medicine; Faculty of Medicine; Fukuoka University; 7-45-1 Nanakuma Jonan-ku Fukuoka 814-0180 Japan
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37
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Song F, Luo H, Hou Y. Developed and evaluated a multiplex mRNA profiling system for body fluid identification in Chinese Han population. J Forensic Leg Med 2015; 35:73-80. [PMID: 26311108 DOI: 10.1016/j.jflm.2015.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
In forensic casework, identification the cellular origin from a biological sample is crucial to the case investigation and reconstruction in crime scene. DNA/RNA co-extraction for STR typing and human body fluids identification has been proposed as an efficient and comprehensive assay for forensic analysis. Several cell-specific messenger RNA (mRNA) markers for identification of the body fluids have been proposed by previous studies. In this study, a novel multiplex mRNA profiling system included 19 markers was developed and performed by reverse transcription endpoint polymerase chain reaction (RT-PCR). The multiplex combined 3 housekeeping gene markers and 16 cell-specific markers that have been used to identify five types of human body fluids: peripheral blood, semen, saliva, vaginal secretions and menstrual blood. The specificity, sensitivity, stability and detectability of the mixture were explored in our study. Majority of the cell-specific mRNA markers showed high specificity, although cross-reactivity was observed sporadically. Specific profiling for per body fluid was obtained. Moreover, the interpretation guidelines for inference of body fluid types were performed according to the A. Lindenbergh et al. The scoring guidelines can be applied to any RNA multiplex, which was based on six different scoring categories (observed, observed and fits, sporadically observed and fits, not observed, sporadically observed, not reliable, and non-specific due to high input). The simultaneous extraction of DNA showed positive full or partial profiling results of all samples. It demonstrated that the approach of combined STR-profiling and RNA profiling was suitable and reliable to detect the donor and origin of human body fluids in Chinese Han population.
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Affiliation(s)
- Feng Song
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China.
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38
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Lin MH, Jones DF, Fleming R. Transcriptomic analysis of degraded forensic body fluids. Forensic Sci Int Genet 2015; 17:35-42. [DOI: 10.1016/j.fsigen.2015.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/06/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
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39
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Haas C, Hanson E, Banemann R, Bento A, Berti A, Carracedo Á, Courts C, Cock GD, Drobnic K, Fleming R, Franchi C, Gomes I, Hadzic G, Harbison S, Hjort B, Hollard C, Hoff-Olsen P, Keyser C, Kondili A, Maroñas O, McCallum N, Miniati P, Morling N, Niederstätter H, Noël F, Parson W, Porto M, Roeder A, Sauer E, Schneider P, Shanthan G, Sijen T, Syndercombe Court D, Turanská M, van den Berge M, Vennemann M, Vidaki A, Zatkalíková L, Ballantyne J. RNA/DNA co-analysis from human skin and contact traces – results of a sixth collaborative EDNAP exercise. Forensic Sci Int Genet 2015; 16:139-147. [DOI: 10.1016/j.fsigen.2015.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/12/2014] [Accepted: 01/04/2015] [Indexed: 11/25/2022]
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40
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Grabmüller M, Madea B, Courts C. Comparative evaluation of different extraction and quantification methods for forensic RNA analysis. Forensic Sci Int Genet 2015; 16:195-202. [DOI: 10.1016/j.fsigen.2015.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/20/2014] [Accepted: 01/15/2015] [Indexed: 12/31/2022]
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41
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Lee HY, An JH, Jung SE, Oh YN, Lee EY, Choi A, Yang WI, Shin KJ. Genome-wide methylation profiling and a multiplex construction for the identification of body fluids using epigenetic markers. Forensic Sci Int Genet 2015; 17:17-24. [PMID: 25796047 DOI: 10.1016/j.fsigen.2015.03.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/06/2015] [Accepted: 03/10/2015] [Indexed: 11/26/2022]
Abstract
The identification of body fluids found at crime scenes can contribute to solving crimes by providing important insights into crime scene reconstruction. In the present study, body fluid-specific epigenetic marker candidates were identified from genome-wide DNA methylation profiling of 42 body fluid samples including blood, saliva, semen, vaginal fluid and menstrual blood using the Illumina Infinium HumanMethylation450 BeadChip array. A total of 64 CpG sites were selected as body fluid-specific marker candidates by having more than 20% discrepancy in DNA methylation status between a certain type of body fluid and other types of body fluids and to have methylation or unmethylation pattern only in a particular type of body fluid. From further locus-specific methylation analysis in additional samples, 1 to 3 CpG sites were selected for each body fluid. Then, a multiplex methylation SNaPshot reaction was constructed to analyze methylation status of 8 body fluid-specific CpG sites. The developed multiplex reaction positively identifies blood, saliva, semen and the body fluid which originates from female reproductive organ in one reaction, and produces successful DNA methylation profiles in aged or mixed samples. Although it remains to be investigated whether this approach is more sensitive, more practical than RNA- or peptide-based assays and whether it can be successfully applied to forensic casework, the results of the present study will be useful for the forensic investigators dealing with body fluid samples.
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Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.
| | - Ja Hyun An
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Sang-Eun Jung
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Yu Na Oh
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Eun Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Ajin Choi
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Woo Ick Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
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42
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Donfack J, Wiley A. Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification. Forensic Sci Int Genet 2015; 16:112-120. [PMID: 25594487 DOI: 10.1016/j.fsigen.2014.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
Abstract
Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework.
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Affiliation(s)
- Joseph Donfack
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Anissa Wiley
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA 22135, USA
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43
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Akutsu T, Kitayama T, Watanabe K, Sakurada K. Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids. Forensic Sci Int Genet 2015; 14:11-7. [DOI: 10.1016/j.fsigen.2014.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/10/2014] [Accepted: 09/08/2014] [Indexed: 01/21/2023]
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44
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Danaher P, White RL, Hanson EK, Ballantyne J. Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets. Forensic Sci Int Genet 2015; 14:18-30. [DOI: 10.1016/j.fsigen.2014.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/27/2014] [Accepted: 09/07/2014] [Indexed: 11/25/2022]
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45
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Malentacchi F, Pazzagli M, Simi L, Orlando C, Wyrich R, Günther K, Verderio P, Pizzamiglio S, Ciniselli CM, Zhang H, Korenková V, Rainen L, Bar T, Kubista M, Gelmini S. SPIDIA-RNA: second external quality assessment for the pre-analytical phase of blood samples used for RNA based analyses. PLoS One 2014; 9:e112293. [PMID: 25384019 PMCID: PMC4226503 DOI: 10.1371/journal.pone.0112293] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 10/11/2014] [Indexed: 11/19/2022] Open
Abstract
One purpose of the EC funded project, SPIDIA, is to develop evidence-based quality guidelines for the pre-analytical handling of blood samples for RNA molecular testing. To this end, two pan-European External Quality Assessments (EQAs) were implemented. Here we report the results of the second SPIDIA-RNA EQA. This second study included modifications in the protocol related to the blood collection process, the shipping conditions and pre-analytical specimen handling for participants. Participating laboratories received two identical proficiency blood specimens collected in tubes with or without an RNA stabilizer. For pre-defined specimen storage times and temperatures, laboratories were asked to perform RNA extraction from whole blood according to their usual procedure and to return extracted RNA to the SPIDIA facility for further analysis. These RNA samples were evaluated for purity, yield, integrity, stability, presence of interfering substances, and gene expression levels for the validated markers of RNA stability: FOS, IL1B, IL8, GAPDH, FOSB and TNFRSF10c. Analysis of the gene expression results of FOS, IL8, FOSB, and TNFRSF10c, however, indicated that the levels of these transcripts were significantly affected by blood collection tube type and storage temperature. These results demonstrated that only blood collection tubes containing a cellular RNA stabilizer allowed reliable gene expression analysis within 48 h from blood collection for all the genes investigated. The results of these two EQAs have been proposed for use in the development of a Technical Specification by the European Committee for Standardization.
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Affiliation(s)
- Francesca Malentacchi
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
- * E-mail:
| | - Mario Pazzagli
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Lisa Simi
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Claudio Orlando
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | | | | | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Maura Ciniselli
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Vlasta Korenková
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lynne Rainen
- Becton Dickinson (BD), Franklin Lakes, New Jersey, United States of America
| | - Tzachi Bar
- Labonnet Ltd, St. Ramat-Hasharon, Israel
| | - Mikael Kubista
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- TATAA Biocenter AB, Gothenburg, Sweden
| | - Stefania Gelmini
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
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46
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Lee SB, McCord B, Buel E. Advances in forensic DNA quantification: a review. Electrophoresis 2014; 35:3044-52. [PMID: 25088961 DOI: 10.1002/elps.201400187] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/27/2014] [Accepted: 07/27/2014] [Indexed: 01/11/2023]
Abstract
This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification.
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Affiliation(s)
- Steven B Lee
- Department of Justice Studies, San Jose State University, San Jose, CA, USA
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47
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Hanson EK, Mirza M, Rekab K, Ballantyne J. The identification of menstrual blood in forensic samples by logistic regression modeling of miRNA expression. Electrophoresis 2014; 35:3087-95. [DOI: 10.1002/elps.201400171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/04/2014] [Accepted: 08/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
| | - Mohid Mirza
- Molecular Biology and Microbiology (Biomedical Sciences) Undergraduate Program; University of Central Florida; Orlando FL USA
| | - Kamel Rekab
- University of Missouri-Kansas City; Kansas City MO USA
| | - Jack Ballantyne
- National Center for Forensic Science; Orlando FL USA
- Department of Chemistry; University of Central Florida; Orlando FL USA
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48
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Balamurugan K, Bombardi R, Duncan G, McCord B. Identification of spermatozoa by tissue-specific differential DNA methylation using bisulfite modification and pyrosequencing. Electrophoresis 2014; 35:3079-86. [DOI: 10.1002/elps.201400175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 11/12/2022]
Affiliation(s)
| | - Robin Bombardi
- School of Criminal Justice; The University of Southern Mississippi; Hattiesburg MS USA
| | - George Duncan
- DNA Unit; Broward County Sheriff's Office; Fort Lauderdale FL USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
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49
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Identification of body fluid-specific DNA methylation markers for use in forensic science. Forensic Sci Int Genet 2014; 13:147-53. [PMID: 25128690 DOI: 10.1016/j.fsigen.2014.07.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/04/2014] [Accepted: 07/19/2014] [Indexed: 12/31/2022]
Abstract
DNA methylation, which occurs at the 5'-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers, but DNA methylation differences are sometimes low in saliva and vaginal secretions. Moreover, specific DNA methylation markers in four types of body fluids (blood, saliva, semen, and vaginal secretions) have not been investigated with genome-wide profiling. Here, we investigated novel DNA methylation markers for identification of body fluids for use in forensic science using the Illumina HumanMethylation 450K bead array, which contains over 450,000 CpG sites. Using methylome data from 16 samples of blood, saliva, semen, and vaginal secretions, we first selected 2986 hypermethylated or hypomethylated regions that were specific for each type of body fluid. We then selected eight CpG sites as novel, forensically relevant DNA methylation markers: cg06379435 and cg08792630 for blood, cg26107890 and cg20691722 for saliva, cg23521140 and cg17610929 for semen, and cg01774894 and cg14991487 for vaginal secretions. These eight selected markers were evaluated in 80 body fluid samples using pyrosequencing, and all showed high sensitivity and specificity for identification of the target body fluid. We suggest that these eight DNA methylation markers may be good candidates for developing an effective molecular assay for identification of body fluids in forensic science.
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Park JL, Park SM, Kwon OH, Lee HC, Kim JY, Seok HH, Lee WS, Lee SH, Kim YS, Woo KM, Kim SY. Microarray screening and qRT-PCR evaluation of microRNA markers for forensic body fluid identification. Electrophoresis 2014; 35:3062-8. [PMID: 24915788 DOI: 10.1002/elps.201400075] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 11/08/2022]
Abstract
MicroRNAs (miRNA) are a class of small (∼22 nucleotides) noncoding RNAs that regulate diverse biological processes at the post-transcriptional level. MiRNAs have great potential for forensic body fluid identification because they are expressed in a tissue specific manner and are less prone to degradation. Previous studies reported several miRNAs as body fluid specific, but there are few overlaps among them. Here, we used a genome-wide miRNA microarray containing over 1700 miRNAs to assay 20 body fluid samples and identify novel miRNAs useful for forensic body fluid identification. Based on Shannon Entropy and Q-statistics, 203 miRNAs specifically expressed in each body fluid were first selected. Eight miRNAs were then selected as novel forensically relevant miRNA markers: miR-484 and miR-182 for blood, miR-223 and miR-145 for saliva, miR-2392 and miR-3197 for semen, and miR-1260b and miR-654-5p for vaginal secretions. When the eight selected miRNAs were evaluated in 40 additional body fluid samples by qRT-PCR, they showed high sensitivity and specificity for the identification of the target body fluid. We suggest that the eight miRNAs may be candidates for developing an effective molecular assay for forensic body fluid identification.
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Affiliation(s)
- Jong-Lyul Park
- Medical Genomics Research Center, KRIBB, Daejeon, Republic of Korea; Department of Functional Genomics, University of Science of Technology, Daejeon, Republic of Korea
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