Differentiation of five body fluids from forensic samples by expression analysis of four microRNAs using quantitative PCR

Advances in body fluid identification: MiRNA markers as powerful tool

Body fluids are one of the most encountered types of evidence in any crime and are commonly used for identifying a person's identity. In addition to these, they are also useful in ascertaining the nature of crime by determining the ty pe of fluid such as blood, semen, saliva, urine etc. Body fluids collected from crime scenes are mostly found in degraded, trace amounts and/or mixed with other fluids. However, the existing immunological and enzyme-based methods used for differentiating these fluids show limited specificity and sensitivity in such cases. To overcome these challenges, a new method utilizing microRNA expression of the body fluids has been proposed. This method is believed to be non-destructive as well as sensitive in nature and researches have shown promising results for highly degraded samples as well. This systematic review focuses on and explores the use and reliability of miRNAs in body fluid identification. It also summarizes the researches conducted on various aspects of miRNA in terms of body fluid examination in forensic investigations.

Analysis of MiR-20b, MIR-197 markers for differentiation between forensic body fluids encountered in sexual assault cases

Identifying body fluids can be a critical clue that aids in reconstructing the crime scene. Semen and vaginal fluid identification is crucial, especially in cases of sexual assault. The majority of forensic studies focused on identifying normal body fluids and neglected the expression variation of semen in pathology. To differentiate between vaginal fluids, fertile and infertile semen samples (oligospermia and azoospermia) using miR 20b and miR197. A total of 48 body fluid samples, divided as 16 vaginal fluids, 16 fertile semen, and 16 infertile semen samples (8 with oligospermia and 8 with azoospermia), were collected, and the expression levels of miR-20b and miR-197 were detected by the SYBR Green real-time quantitative PCR technique. Our results showed significant different expression of these miRNAs in normal semen compared to vaginal and infertile semen. Moreover, we designed a model based on Fisher's discriminant function to forecast the group affiliations of unidentified samples. With three novel equations, we were able to accurately distinguish between semen and vaginal fluid, fertile and infertile semen, and oligospermia and azoospermia semen samples with validation accuracy of 81.3%, 100%, and 100%, respectively. MiR-20b and miR-197 expression levels are efficient and appropriate markers to distinguish semen from vaginal fluid and to differentiate between fertile and infertile semen samples. However, the present study is a preliminary study based on clinical samples, and the potential role of these markers in differentiating real crime scene samples is still unknown, so we recommend further research to investigate these markers expression while using forensic samples.

Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue

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.

Body fluids should be identified before estimating the time since deposition (TsD) in microbiome-based stain analyses for forensics

Identification and the time since deposition (TsD) estimation of body fluid stains from a crime scene could provide valuable information for solving the cases and are always difficult for forensics. Microbial characteristics were considered as a promising biomarker to address the issues. However, changes in the microbiota may damage the specific characteristics of body fluids. Correspondingly, incorrect body fluid identification may result in inaccurate TsD estimation. The mutual influence is not well understood and limited the codetection. In the current study, saliva, semen, vaginal secretion, and menstrual blood samples were exposed to indoor conditions and collected at eight time points (from fresh to 30 days). High-throughput sequencing based on the 16S rRNA gene was performed to characterize the microbial communities. The results showed that a longer TsD could decrease the discrimination of different body fluid stains. However, the accuracies of identification still reached a quite high value even without knowing the TsD. Correspondingly, the mean absolute error (MAE) of TsD estimation significantly increased without distinguishing the types of body fluids. The predictive TsD of menstrual blood reached a quite low MAE (1.54 ± 0.39 d). In comparison, those of saliva (6.57 ± 1.17 d), semen (6.48 ± 1.33 d), and vaginal secretion (5.35 ± 1.11 d) needed to be further improved. The great effect of individual differences on these stains limited the TsD estimation accuracy. Overall, microbial characteristics allow for codetection of body fluid identification and TsD estimation, and body fluids should be identified before estimating TsD in microbiome-based stain analyses.IMPORTANCEEmerged evidences suggest microbial characteristics could be considered a promising tool for identification and time since deposition (TsD) estimation of body fluid stains. However, the two issues should be studied together due to a potential mutual influence. The current study provides the first evidence to understand the mutual influence and determines an optimal process for codetection of identification and TsD estimation for unknown stains for forensics. In addition, we involved aged stains into our study for identification of body fluid stains, rather than only using fresh stains like previous studies. This increased the predictive accuracy. We have preliminary verified that individual differences in microbiotas limited the predictive accuracy of TsD estimation for saliva, semen, and vaginal secretion. Microbial characteristics could provide an accurate TsD estimation for menstrual blood. Our study benefits the comprehensive understanding of microbiome-based stain analyses as an essential addition to previous studies.

Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine

At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.

Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva

Forensic trace contextualization, i.e., assessing information beyond who deposited a biological stain, has become an issue of great and steadily growing importance in forensic genetic casework and research. The human transcriptome encodes a wide variety of information and thus has received increasing interest for the identification of biomarkers for different aspects of forensic trace contextualization over the past years. Massively parallel sequencing of reverse-transcribed RNA ("RNA sequencing") has emerged as the gold standard technology to characterize the transcriptome in its entirety and identify RNA markers showing significant expression differences not only between different forensically relevant body fluids but also within a single body fluid between forensically relevant conditions of interest. Here, we analyze the quality and composition of four RNA sequencing datasets (whole transcriptome as well as miRNA sequencing) from two different research projects (the RNAgE project and the TrACES project), aiming at identifying contextualizing forensic biomarker from the forensically relevant body fluid saliva. We describe and characterize challenges of RNA sequencing of saliva samples arising from the presence of oral bacteria, the heterogeneity of sample composition, and the confounding factor of degradation. Based on these observations, we formulate recommendations that might help to improve RNA biomarker discovery from the challenging but forensically relevant body fluid saliva.

A combined molecular approach utilizing microbial DNA and microRNAs in a qPCR multiplex for the classification of five forensically relevant body fluids

Body fluid identification is an essential step in the forensic biology workflow that can assist DNA analysts in determining where to collect DNA evidence. Current presumptive tests lack the specificity that molecular techniques can achieve; therefore, molecular methods, including microRNA (miRNA) and microbial signature characterization, have been extensively researched in the forensic community. Limitations of each method suggest combining molecular markers to increase the discrimination efficiency of multiple body fluids from a single assay. While microbial signatures have been successful in identifying fluids with high bacterial abundances, microRNAs have shown promise in fluids with low microbial abundance (blood and semen). This project synergized the benefits of microRNAs and microbial DNA to identify multiple body fluids using DNA extracts. A reverse transcription (RT)-qPCR duplex targeting miR-891a and let-7g was validated, and miR-891a differential expression was significantly different between blood and semen. The miRNA duplex was incorporated into a previously reported qPCR multiplex targeting 16S rRNA genes of Lactobacillus crispatus, Bacteroides uniformis, and Streptococcus salivarius to presumptively identify vaginal/menstrual secretions, feces, and saliva, respectively. The combined classification regression tree model resulted in the presumptive classification of five body fluids with 94.6% overall accuracy, now including blood and semen identification. These results provide proof of concept that microRNAs and microbial DNA can classify multiple body fluids simultaneously at the quantification step of the current forensic DNA workflow.

Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study

Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.

Rapid and visual detection of specific bacteria for saliva and vaginal fluid identification with the lateral flow dipstick strategy

Identification of body fluids is critical for crime scene reconstruction, and a source of investigation source of investigative leads. In recent years, microbial DNA analysis using sequencing and quantitative real-time polymerase chain reaction have been used to identify body fluids. However, these techniques are time-consuming, expensive, and require complex workflows. In this study, a new method for simultaneous detection of Streptococcus salivarius and Lactobacillus crispatus using polymerase chain reaction (PCR) in combination with a lateral flow dipstick (LFD) was developed to identify saliva and vaginal fluid in forensic samples. LFD results can be observed with the naked eye within 3 min with a sensitivity of 0.001 ng/µL DNA. The PCR-LFD assay was successfully used to detect S. salivarius and L. crispatus in saliva and vaginal fluid respectively, and showed negative results in blood, semen, nasal fluid, and skin. Moreover, saliva and vaginal fluid were detectable even at an extremely high mixing ratio of sample DNA (1:999). Saliva and vaginal fluid were identified in various mock forensic samples. These results indicate that saliva and vaginal fluid can be effectively detected by identifying S. salivarius and L. crispatus, respectively. Furthermore, we have shown that DNA samples used to identify saliva and vaginal fluid can also provide a complete short tandem repeat (STR) profile when used as source material for forensic STR profiling. In summary, our results suggest that PCR-LFD is a promising assay for rapid, simple, reliable, and efficient identification of body fluids.

Identification of Mixtures of Two Types of Body Fluids Using the Multiplex Methylation System and Random Forest Models

OBJECTIVE

Body fluid mixtures are complex biological samples that frequently occur in crime scenes, and can provide important clues for criminal case analysis. DNA methylation assay has been applied in the identification of human body fluids, and has exhibited excellent performance in predicting single-source body fluids. The present study aims to develop a methylation SNaPshot multiplex system for body fluid identification, and accurately predict the mixture samples. In addition, the value of DNA methylation in the prediction of body fluid mixtures was further explored.

METHODS

In the present study, 420 samples of body fluid mixtures and 250 samples of single body fluids were tested using an optimized multiplex methylation system. Each kind of body fluid sample presented the specific methylation profiles of the 10 markers.

RESULTS

Significant differences in methylation levels were observed between the mixtures and single body fluids. For all kinds of mixtures, the Spearman's correlation analysis revealed a significantly strong correlation between the methylation levels and component proportions (1:20, 1:10, 1:5, 1:1, 5:1, 10:1 and 20:1). Two random forest classification models were trained for the prediction of mixture types and the prediction of the mixture proportion of 2 components, based on the methylation levels of 10 markers. For the mixture prediction, Model-1 presented outstanding prediction accuracy, which reached up to 99.3% in 427 training samples, and had a remarkable accuracy of 100% in 243 independent test samples. For the mixture proportion prediction, Model-2 demonstrated an excellent accuracy of 98.8% in 252 training samples, and 98.2% in 168 independent test samples. The total prediction accuracy reached 99.3% for body fluid mixtures and 98.6% for the mixture proportions.

CONCLUSION

These results indicate the excellent capability and powerful value of the multiplex methylation system in the identification of forensic body fluid mixtures.

Raman ConvMSANet: A High-Accuracy Neural Network for Raman Spectroscopy Blood and Semen Identification

Animal blood and semen analysis plays a significant role in national biological resource management, wildlife conservation, and customs security quarantine. Traditional blood analysis methods have disadvantages, such as complex sample preparation, time consumption, and false positives. Therefore, proposing a rapid and highly accurate analysis method is highly valuable. Raman spectroscopy has been widely used in blood analysis, and efficient and accurate analysis results can be obtained through the machine learning algorithm feature extraction. Recently, the transformer network structure was applied to Raman spectroscopy recognition. However, the multihead self-attention mechanism does not perform well in extracting local feature peaks, although it obtains global feature relations. This paper proposes a neural network based on the combination of one-dimensional convolution and multihead self-attention mechanism (Raman ConvMSANet) to identify 52 species of blood and semen Raman spectra. The network can achieve reliable identification effects in multiclassification and sample imbalance situations, and the average identification accuracy of blood and semen can reach more than 98.5%. The proposed network model can be applied not only to blood and semen identification but also to other biological fields.

The potential of using non-coding RNAs in forensic science applications

With the continuous development and integration of molecular biology and forensic science, non-coding RNAs (ncRNAs), especially ncRNAs with regulatory functions such as microRNA, long non-coding RNA, and circular RNA, have recently been actively explored by forensic scholars. In this study, we review the literature on these ncRNAs in various fields of forensic science, including postmortem interval determination, wound age estimation, forensic age assessment, cause of death analysis, and body fluid identification, aiming to evaluate the current research and provide a perspective for future applications.

From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom

Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.

Identification of blood species based on surface-enhanced Raman scattering spectroscopy and convolutional neural network

The identification of blood species is of great significance in many aspects such as forensic science, wildlife protection, and customs security and quarantine. Conventional Raman spectroscopy combined with chemometrics is an established method for identification of blood species. However, the Raman spectrum of trace amount of blood could hardly be obtained due to the very small cross-section of Raman scattering. In order to overcome this limitation, surface-enhanced Raman scattering (SERS) was adopted to analyze trace amount of blood. The 785 nm laser was selected as the optimal laser to acquire the SERS spectra, and the blood SERS spectra of 19 species were measured. The convolutional neural network (CNN) was used to distinguish the blood of 19 species including human. The recognition accuracy of the blood species was obtained with 98.79%. Our study provides an effective and reliable method for identification and classification of trace amount of blood.

Rapid Microchip Electrophoretic Separation of Novel Transcriptomic Body Fluid Markers for Forensic Fluid Profiling

Initial screening of criminal evidence often involves serological testing of stains of unknown composition and/or origin discovered at a crime scene to determine the tissue of origin. This testing is presumptive but critical for contextualizing the scene. Here, we describe a microfluidic approach for body fluid profiling via fluorescent electrophoretic separation of a published mRNA panel that provides unparalleled specificity and sensitivity. This centrifugal microfluidic approach expedites and automates the electrophoresis process by allowing for simple, rotationally driven flow and polymer loading through a 5 cm separation channel; with each disc containing three identical domains, multi-sample analysis is possible with a single disc and multi-sample detection per disc. The centrifugal platform enables a series of sequential unit operations (metering, mixing, aliquoting, heating, storage) to execute automated electrophoretic separation. Results show on-disc fluorescent detection and sizing of amplicons to perform comparably with a commercial 'gold standard' benchtop instrument and permitted sensitive, empirical discrimination between five distinct body fluids in less than 10 min. Notably, our microfluidic platform represents a faster, simpler method for separation of a transcriptomic panel to be used for forensically relevant body fluid identification.

Attenuated total reflection-Fourier transform infrared spectroscopy: a universal analytical technique with promising applications in forensic analyses

Contemporary criminal investigations are based on the statements made by the victim and the eyewitnesses. They also rely on the physical evidences found in the crime scene. These evidences, and more particularly biological ones, have a great judicial value in the courtroom. They are usually used to revoke the suspect’s allegations and confirm or refute the statements made by the victim and the witnesses. Stains of body fluids are biological evidences highly sought by forensic investigators. In many criminal cases, the success of the investigation relies on the correct identification and classification of these stains. Therefore, the adoption of reliable and accurate forensic analytical methods seems to be of vital importance to attain this objective. Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) is a modern and universal analytical technique capable of fingerprint recognition of the analyte using minimal amount of the test sample. The current systematic review aims to through light on the fundamentals of this technique and to illustrate its wide range of applications in forensic investigations. ATR-FTIR is a nondestructive technique which has demonstrated an exceptional efficiency in detecting, identifying and discriminating between stains of various types of body fluids usually encountered in crime scenes. The ATR-FTIR spectral data generated from bloodstains can be used to deduce a wealth of information related to the donor species, age, gender, and race. These data can also be exploited to discriminate between stains of different types of bloods including menstrual and peripheral bloods. In addition, ATR-FTIR has a great utility in the postmortem investigations. More particularly, in estimating the postmortem interval and diagnosing death caused by extreme weather conditions. It is also useful in diagnosing some ambiguous death causes such as fatal anaphylactic shock and diabetic ketoacidosis.

A Comprehensive Characterization of Small RNA Profiles by Massively Parallel Sequencing in Six Forensic Body Fluids/Tissue

Body fluids/tissue identification (BFID) is an essential procedure in forensic practice, and RNA profiling has become one of the most important methods. Small non-coding RNAs, being expressed in high copy numbers and resistant to degradation, have great potential in BFID but have not been comprehensively characterized in common forensic stains. In this study, the miRNA, piRNA, snoRNA, and snRNA were sequenced in 30 forensic relevant samples (menstrual blood, saliva, semen, skin, venous blood, and vaginal secretion) using the BGI platform. Based on small RNA profiles, relative specific markers (RSM) and absolute specific markers (ASM) were defined, which can be used to identify a specific body fluid/tissue out of two or six, respectively. A total of 5204 small RNAs were discovered including 1394 miRNAs (including 236 novel miRNA), 3157 piRNAs, 636 snoRNAs, and 17 snRNAs. RSMs for 15 pairwise body fluid/tissue groups were discovered by differential RNA analysis. In addition, 90 ASMs that were specifically expressed in a certain type of body fluid/tissue were screened, among them, snoRNAs were reported first in forensic genetics. In brief, our study deepened the understanding of small RNA profiles in forensic stains and offered potential BFID markers that can be applied in different forensic scenarios.

MicroRNAs in Various Body Fluids and its importance in Forensic Medicine

MicroRNAs (miRNAs) are a class of noncoding RNAs which regulate gene expression. miRNAs have tissue-specific expression and are also present in various extracellular body fluids, including blood, tears, semen, vaginal fluid and urine. Additionally, expression of miRNAs in body fluids is linked to various pathological diseases, including cancer and neurodegenerative diseases. Examination of body fluids is important in forensic medicine as they serve as a valuable form of evidence. Due to its stability, miRNA offers an advantage for body fluid identification, which can be detected even after several months or from compromised samples. Identification of unique miRNA profiles for different body fluids enable the identification of these body fluid. Furthermore, miRNAs profiling can be used to estimate post-mortem interval. Various biochemical and molecular methods have been used for identification of miRNAs have shown promising results. We discuss different miRNAs as specific biomarkers and their clinical importance regarding different pathological conditions, as well as their medico-legal importance.

Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences

The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.

A new strategy for distinguishing menstrual blood from peripheral blood by the miR-451a/miR-21-5p ratio

Distinction between menstrual blood and peripheral blood is vital for forensic casework, as it could provide strong evidence to figure out the nature of some criminal cases. However, to date no single blood-specific gene, including the most variable microRNAs (miRNAs) could work well in identification of blood source. In this study, we developed a new strategy for identification of human blood samples by using the copy number ratios of miR-451a to miR-21-5p based on 133 samples, including 56 menstrual blood and 47 peripheral blood, as well as 30 non-blood samples of saliva (10), semen (10) and vaginal secretion (10). The cut-off value and efficacy of the identification strategy were determined through receiver operating characteristic (ROC) analysis. Our results showed that when the miR-451a/miR-21-5p ratio below 0.929, the sample should be non-blood. In contrast, when the miR-451a/miR-21-5p ratio above 0.929 and below 10.201, the sample should be menstrual blood; and when this ratio above 10.201, the sample should be peripheral blood. External validation using 86 samples (62 menstrual blood and 24 peripheral blood samples) fully supported this strategy with the 100% sensitivity and 100% specificity. We confirmed that this result accuracy was not affected by various potential confounding factors of samples and different experimental platforms. We showed that 0.2 ng of total RNA from menstrual blood and peripheral blood was sufficient for qPCR quantification. In conclusion, our results provide an accurate reference to distinguish menstrual blood from peripheral blood for forensic authentication.

Developments in forensic DNA analysis

The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

Feasibility of using probabilistic methods to analyse microRNA quantitative data in forensically relevant body fluids: a proof-of-principle study

Several studies have confirmed that microRNAs (miRNAs) are promising markers for body fluid identification since they were introduced to this field. However, there is no consensus on the choice of reference genes and identification strategies. In this study, 13 potential candidate miRNAs were screened from three forensically relevant body fluid datasets, and the expression of 12 markers in five body fluids was determined using a real-time quantitative method. Two probabilistic approaches, Naive Bayes (NB) and partial least squares discriminant analysis (PLS-DA), were then applied to predict the origin of the samples to determine whether probabilistic methods are helpful in body fluid identification using miRNA quantitative data. Furthermore, 14 reference combinations were used to validate the influence of different reference choices on the predicted results simultaneously. Our results showed that in the NB model, leave-one-out cross-validation (LOOCV) achieved 100% accuracy and the prediction accuracy of the test set was 100% in most reference combinations. In the PLS-DA model, the first two components could interpret about 80% expression variance and LOOCV achieved 100% accuracy when miR-92a-3p was used as the reference. This study preliminarily proved that probabilistic approaches hold huge potential in miRNA-based body fluid identification, and the choice of references influences the prediction results to a certain extent.

A novel multiplex assay system based on 10 methylation markers for forensic identification of body fluids

Identifying the source of body fluids found at a crime scene is an essential forensic step. Some methods based on DNA methylation played significant role in body fluids identification. Since DNA methylation is related to multiple factors, such as race, age, and diseases, it is necessary to know the methylation profile of a given population. In this study, we tested 19 body fluid-specific methylation markers in a Chinese Han population. A novel multiplex assay system based on the selected markers with smaller variation in methylation and stronger tissue-specific methylation were developed for the identification of body fluids. The multiplex assay were tested in 265 body fluid samples. A random forest model was established to predict the tissue source based on the methylation data of the 10 markers. The multiplex assay was evaluated by testing the sensitivity, the mixtures, and old samples. For the result, the novel multiplex assay based on 10 selected methylation markers presented good methylation profiles in all tested samples. The random forest model worked extremely well in predicting the source of body fluids, with an accuracy of 100% and 97.5% in training data and test data, respectively. The multiplex assay could accurately predict the tissue source from 0.5 ng genomic DNA, six-months-old samples and distinguish the minor component from a mixture of two components. Our results indicated that the methylation multiplex assay and the random forest model could provide a convenient tool for forensic practitioners in body fluid identification.

mRNA and microRNA stability validation of blood samples under different environmental conditions

RNA molecules, including mRNAs and microRNAs (miRNAs), have been used for forensic body fluid identification. Specific body fluids present unique mRNA expression patterns, while miRNAs identifying body fluids are mainly differentially expressed. miRNAs are thought to be more stable than mRNAs, although this lacks adequate supporting data. In this study, we addressed perceived concerns regarding the stability of miRNAs and mRNAs in blood samples. The samples used in this study involved three groups. First, environmentally-degraded blood stain samples were exposed to a range of environmental conditions over 1-360 days to degrade naturally. Second, simulated-degraded samples were prepared using RNase A or high temperature (80 °C). Furthermore, two authentic casework samples that were proven to be degraded from short tandem repeat (STR) profiles were analyzed. mRNAs and miRNAs present in the same blood samples were simultaneously detected through reverse transcriptase qPCR (RT-qPCR). Furthermore, mRNAs expression was determined by an mRNA multiplex PCR system. Our results showed that both mRNAs and miRNAs were stable in dry environments. The stability of miRNAs was relatively higher than that of mRNAs in humid environments or at high temperature. RNase A had the most serious impact on RNA stability, both mRNA profiles and miRNAs expression patterns were altered. The results of this study provide data and support to demonstrate that miRNAs represent more stable RNA molecules in body fluid identification compared to mRNAs.

The effect of infertile semen on the mRNA-based body fluid identification

In the past decade, mRNA markers have been well demonstrated as promising molecular markers in forensic body fluid identification (BFI), and successfully used in wide applications. Several studies have assessed the performance of semen-specific mRNA markers in distinguishing semen from other common body fluids at the crime scene. Infertility has been reported as a global health problem that is affecting approximately 15% of couples worldwide. Therefore, it is important for forensic researchers to consider the impact of infertility on semen identification. This study aimed to explore the effect of semen from infertile men (hereinafter "infertile semen") on BFI and to identify semen-specific mRNAs that can efficiently and accurately distinguish normal and infertile semen samples from other body fluids. Results showed that the selected five mRNAs (KLK3, TGM4, SEMG1, PRM1, and PRM2) performed a significantly high semen specificity in normal semen. Moreover, KLK3 was slightly influenced by infertile semen samples with over 98% positive results in all semen samples. The accuracy to predict normal semen reached up to 96.6% using the discrimination function Y1 with KLK3 and PRM1. However, when the infertile semen samples were included in discrimination function (function Y2 with KLK3), the accuracy rate of semen identification (including the normal and infertile semen) was down to 89.5%. Besides, the sensitivity of multiplex assay could reach down to 50pg. Our results suggest that it is important to consider the presence of infertile semen when using mRNAs to identify semen samples, which would have a far-reaching impact in forensic identification.

Multiplex and on-site PCR detection of swine diseases based on the microfluidic chip system

BACKGROUND

At present, the process of inspection and quarantine starts with sampling at the customs port, continues with transporting the samples to the central laboratory for inspection experiments, and ends with the inspected results being fed back to the port. This process had the risks of degradation of biological samples and generation of pathogenic microorganisms and did not meet the rapid on-site detection demand because it took a rather long time. Therefore, it is urgently needed to develop a rapid and high-throughput detection assay of pathogenic microorganisms at the customs port. The aim of this study was to develop a microfluidic chip to rapidly detect swine pathogenic microorganisms with high-throughput and higher accuracy. Moreover, this chip will decrease the risk of spreading infection during transportation.

RESULTS

A series of experiments were performed to establish a microfluidic chip. The resulting data showed that the positive nucleic acid of four swine viruses were detected by using a portable and rapid microfluidic PCR system, which could achieve a on-site real-time quantitative PCR detection. Furthermore, the detection results of eight clinical samples were obtained within an hour. The lowest concentration that amplified of this microfluidic PCR detection system was as low as 1 copies/μL. The results showed that the high specificity of this chip system in disease detection played an important role in customs inspection and quarantine during customs clearance.

CONCLUSION

The microfluidic PCR detection system established in this study could meet the requirement for rapid detection of samples at the customs port. This chip could avoid the risky process of transporting the samples from the sampling site to the testing lab, and drastically reduce the inspection cycle. Moreover, it would enable parallel inspections on one chip, which greatly raised the efficiency of inspection.

Use of Molecular Methods to Authenticate Animal Species and Tissue in Bovine Liver Dietary Supplements

Dietary supplements containing bovine (subfamily Bovinae) liver are susceptible to fraud due to their high value and the lack of modern detection methods available for processed animal tissues. The objective of this research was to use molecular methods to authenticate dietary supplements claiming to contain bovine liver or beef liver through the verification of animal species and tissue type. A total of 53 bovine/beef liver dietary supplements were purchased from online sources. The presence of liver was verified with reverse transcription and real-time PCR testing for microRNA-122 (miR-122), which is highly expressed in liver tissue. Multiplex real-time PCR targeting domestic cattle (Bos taurus), horse (Equus caballus), sheep (Ovis aries), and pork (Sus scrofa) was used to verify species. Samples that failed species identification with multiplex real-time PCR underwent DNA mini-barcoding. Overall, bovine species were detected in 48/53 liver supplements: 35 samples were confirmed as domestic cattle with multiplex real-time PCR and an additional 13 samples were confirmed as domestic cattle or Bos spp. with DNA mini-barcoding. One of these samples was also positive for sheep/lamb, which was declared on the label. One product contained undeclared pork in addition to beef. MiR-122 was detected in 51 out of 53 supplements, suggesting the presence of liver. While this study demonstrates the potential use of tissue-specific microRNAs in verifying tissues in dietary supplements, more research is needed to evaluate the specificity of these markers.

MicroRNAs: An Update of Applications in Forensic Science

MicroRNAs (miRNAs) are a class of non-coding RNAs containing 18–24 nucleotides that are involved in the regulation of many biochemical mechanisms in the human body. The level of miRNAs in body fluids and tissues increases because of altered pathophysiological mechanisms, thus they are employed as biomarkers for various diseases and conditions. In recent years, miRNAs obtained a great interest in many fields of forensic medicine given their stability and specificity. Several specific miRNAs have been studied in body fluid identification, in wound vitality in time of death determination, in drowning, in the anti-doping field, and other forensic fields. However, the major problems are (1) lack of universal protocols for diagnostic expression testing and (2) low reproducibility of independent studies. This review is an update on the application of these molecular markers in forensic biology.

A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification

Identifying the types of body fluids left at the crime scene can be essential to reconstructing the crime scene and inferring criminal behavior. MicroRNA (miRNA) molecule extracted from the trace of body fluids is one of the most promising biomarkers for the identification due to its high expression, extreme stability and tissue specificity. However, the detection of miRNA markers is not the answer to a yes-no question but the probability of an assumption. Therefore, it is a crucial task to develop complicated methods combining multi-miRNAs as well as computational algorithms to achieve the goal. In this study, we systematically analyzed the expression of 10 most probable body fluid-specific miRNA markers (miR-451a, miR-205-5p, miR-203a-3p, miR-214-3p, miR-144-3p, miR-144-5p, miR-654-5p, miR-888-5p, miR-891a-5p and miR-124-3p) in 605 body fluids-related samples, including peripheral blood, menstrual blood, saliva, semen and vaginal secretion. We introduced the kernel density estimation (KDE) method and six well-established methods to classify the body fluids in order to find the most optimal combinations of miRNA markers as well as the corresponding classifying method. The results show that the combination of miR-451a, miR-891a-5p, miR-144-5p and miR-203a-3p together with KDE can achieve the most accurate and robust performance according to the cross-validation, independent tests and random perturbation tests. This systematic analysis suggests a reference scheme for the identification of body fluids in an accurate and stable manner.

The persistence and stability of miRNA in bloodstained samples under different environmental conditions

miRNA markers have been an area of forensic interest to identify body fluid sources in recent years. In this study, reverse transcription and quantitative real time polymerase chain reaction (RT-qPCR) were performed to detect the existence of blood-specific miRNA markers in bloodstained samples under different environmental conditions, Blood samples from 6 individuals were deposited onto glass plates and exposed to different temperature, humidity, ultraviolet light intensity, and natural condition. When samples were stored to a series of estimated test times, total RNA was extracted and the Ct values of the target RNAs were detected, targets included two miRNA markers (hsa-miR-16-5p, hsa-miR-451a) and one reference gene (U6 snRNA). Analysis results showed that miR-451a represented strong stability and could be detected at all detection points. Meanwhile, each RNAs exhibited unique degradation characteristics, compared to U6, miRNAs showed stronger stability. Additionally, rain had an adverse effect on RNAs stability and accelerates its degradation rate.

mRNA profiling of mock casework samples: Results of a FoRNAP collaborative exercise

In recent years, forensic mRNA profiling has increasingly been used to identify the origin of human body fluids. By now, several laboratories have implemented mRNA profiling and also use it in criminal casework. In 2018 the FoRNAP (Forensic RNA Profiling) group was established among a number of these laboratories with the aim of sharing experiences, discussing optimization potential, identifying challenges and suggesting solutions with regards to mRNA profiling and casework. To compare mRNA profiling methods and results a collaborative exercise was organized within the FoRNAP group. Seven laboratories from four countries received 16 stains, comprising six pure body fluid / tissue stains and ten mock casework samples. The laboratories were asked to analyze the provided stains with their in-house method (PCR/CE or MPS) and markers of choice. Five laboratories used a DNA/RNA co-extraction strategy. Overall, up to 11 mRNA markers per body fluid were analyzed. We found that mRNA profiling using different extraction and analysis methods as well as different multiplexes can be applied to casework-like samples. In general, high input samples were typed with high accuracy by all laboratories, regardless of the method used. Irrespective of the analysis strategy, samples of low input or mixed stains were more challenging to analyze and interpret since, alike to DNA profiling, a higher number of markers dropped out and/or additional unexpected markers not consistent with the cell type in question were detected. It could be shown that a plethora of different but valid analysis and interpretation strategies exist and are successfully applied in the Forensic Genetics community. Nevertheless, efforts aiming at optimizing and harmonizing interpretation approaches in order to achieve a higher consistency between laboratories might be desirable in the future. The simultaneous extraction of DNA alongside RNA showed to be an effective approach to identify not only the body fluid present but also to identify the donor(s) of the stain. This allows investigators to gain valuable information about the origin of crime scene samples and the course of events in a crime case.

Evaluating the use of hypoxia sensitive markers for body fluid stain age prediction

To augment DNA profiling and body fluid identification techniques efforts are being made to increase the amount of information available from a crime scene stain, which includes efforts to identify externally visible characteristics through phenotypic analysis. A key question surrounding crime scene stains is the length of time between deposition of the stain and its subsequent recovery, in that is the stain recovered related to the incident in question or from a previously deposited stain number of weeks earlier? The inability to answer this fundamental question has a detrimental effect upon the successful completion of a criminal investigation. Once a body fluid leaves the body, the oxygen concentration in the environment changes; therefore, it may be that this change could cause a change in the expression of hypoxia-sensitive biomarkers. Here, a range of bloodstains, liquid saliva and liquid semen samples were collected at 0 days, 7 days, 14 days, 21 days and 28 days of degrading at room temperature (19-22 °C), before undergoing total RNA extraction and cDNA synthesis. Blood was recovered from filter paper with 3 mm², with saliva and semen being left in their tubes and swabbed at the appropriate times. All samples then underwent quantitative PCR targeting Vascular Endothelial Growth Factor A (VEGFA) and Hypoxia-Inducible Factor 1 Alpha (HIF1A), with B-Actin (ACTB) as a reference gene. A range of linear and quadratic correlation values was obtained from the qPCR data and used to develop a predictive model with a mean absolute deviation (MAD) of 4.2, 2.1, and 5 days for blood, saliva, and semen respectively. Blind testing indicated that a stain age prediction model based upon VEGFA with ACTB as a reference gene could be used on samples up to four weeks old with a margin of error ranging from 2 days through to 5 days. While a sizeable potential time frame exists using this model; this represents a significant step towards the target of having an accurate stain age prediction model.

Current Methods for Body Fluid Identification Related to Sexual Crime: Focusing on Saliva, Semen, and Vaginal Fluid

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.

Expression profile analysis and stability evaluation of 18 small RNAs in the Chinese Han population

In recent years, differentially expressed small RNAs have been widely used to identify the compositions of forensically relevant biological samples, and a vast number of such RNA candidates have been proposed. Nevertheless, when assessing the expression levels of target small RNAs using relative quantitative analysis methods, credible internal controls are usually required for reliable data normalization. Therefore, the identification of optimal reference genes is an important task. In this study, the expression profile of 18 small RNA reference genes was characterized in the Chinese Han population using TaqMan real-time quantitative PCR. Systematic evaluations of these candidate genes were performed based on their expression levels and stability in several common types of body fluids (i.e., venous blood, menstrual blood, saliva, semen, and vaginal secretions). Analysis results from the ΔCq method, BestKeeper, NormFinder, and geNorm were integrated by RefFinder for ranking and comparing the candidates in each type of body fluid. Among all the candidates, miR-191 was identified as the most suitable reference gene because it had a favorable ranking value in all tested samples. In addition, miR-423, miR-93, miR-484, and let-7i were also shown to be applicable reference genes. Overall, this study provides detailed assessment results of these candidate genes in different body fluids; thus, it could be used as a guide for the selection of reference genes according to their performance in the sample of choice.

Identification of five types of forensic body fluids based on stepwise discriminant analysis

Peripheral blood, menstrual blood, semen, saliva and vaginal secretions are the five most common body fluids found at crime scenes, and the identification of these five body fluids is of great significance to the reconstruction of a crime scene and resolution of the case. However, accurate identification of these five body fluids is still a challenge. To address this problem, a mathematical model for differentiating five types of forensic body fluids based on the differential expression characteristics of multiple miRNAs in five body fluids (peripheral blood, menstrual blood, semen, saliva and vaginal secretions) was developed. A total of 350 forensic body fluids (70 of each type) were collected and tested, and relative expression of 10 miRNAs (miR-451a, miR-205-5p, miR-203-3p, miR-214-3p, miR-144-3p, miR-144-5p, miR-654-5p, miR-888-5p, miR-891a-5p, miR-124a-3p) in all samples was detected by SYBR Green real-time qPCR. Three hundred samples (60 samples of each body fluid) were used as the training set to screen meaningful identification markers by stepwise discriminant analysis, and a discriminant function was established. Fifty samples (10 samples of each body fluid) were used as a validation set to examine the accuracy of the model, and 25 samples (the types of samples were unknown to the experimenter) were used for a blind test. Except for miR-144-3p, the other miRNAs were selected to construct discriminant analysis models. The self-validation accuracy of the model was 99.7 %, cross-validation accuracy was 99.3 %, accuracy of the identification validation set was 100 %, and accuracy of the blind test result was 100 %. This study provides a reliable and accurate identification strategy for five common body fluids (peripheral blood, menstrual blood, semen, saliva, and vaginal secretions) in forensic medicine.

Development of a multiplex system for the identification of forensically relevant body fluids

Currently, mRNA profiling is widely investigated for forensic body fluid identification, while it is still required to advance the approach for those casework samples of limited quantity or low quality. The inclusion of circular RNAs (circRNAs) can facilitate the detection of mRNA markers in forensic body fluid identification. In this study, a multiplex assay for forensic body fluid identification (F18plex assay) was developed by incorporating 14 tissue-specific mRNA markers with circRNAs expression, 2 mRNA markers with high abundance and 2 housekeeping markers for the discrimination of the most common forensic body fluids, including blood, menstrual blood, saliva, vaginal secretion, semen and urine. The markers employed in the F18plex assay show similar specificity to previous reports. Additionally, even if all linear transcripts were completely erased, the expected markers in target biofluids could still be identified, which should help the discrimination of those aged biological stains. Results from sensitivity testing and the detection of mixtures demonstrate good sensitivity of the multiplex assay. Generally, full biomarker profiles could be obtained with ≥1 μl of blood, saliva, or semen, and ≥1 ng of total RNAs from menstrual blood, vaginal secretion, or urine samples, respectively, using this multiplex assay under the established conditions. Collectively, the newly established multiplex assay can assist in determining the biological origin of forensic stains.

Microbiome-based body site of origin classification of forensically relevant blood traces

Human blood traces are amongst the most commonly encountered biological stains collected at crime scenes. Identifying the body site of origin of a forensic blood trace can provide crucial information in many cases, such as in sexual and violent assaults. However, means for reliably and accurately identifying from which body site a forensic blood trace originated are missing, but would be highly valuable in crime scene investigations. With this study, we introduce a taxonomy-independent deep neural network approach based on massively parallel microbiome sequencing, which delivers accurate body site of origin classification of forensically-relevant blood samples, such as menstrual, nasal, fingerprick, and venous blood. A total of 50 deep neural networks were trained using a large 16S rRNA gene sequencing dataset from 773 reference samples, including 220 female urogenital tract, 190 nasal cavity, 213 skin, and 150 venous blood samples. Validation was performed with de-novo generated 16S rRNA gene massively parallel sequencing (MPS) data from 94 blood test samples of four different body sites, and achieved high classification accuracy with AUC values at 0.992 for menstrual blood (N = 23), 0.978 for nasal blood (N = 16), 0.978 for fingerprick blood (N = 30), and 0.990 for venous blood (N = 25). The obtained highly accurate classification of menstrual blood was independent of the day of the menses, as established in additional 86 menstrual blood test samples. Accurate body site of origin classification was also revealed for 45 fresh and aged mock casework blood samples from all four body sites. Our novel microbiome approach works based on the assumption that a sample is from blood, as can be obtained in forensic practise from prior presumptive blood testing, and provides accurate information on the specific body source of blood, with high potentials for future forensic applications.

Potential applications of microRNA profiling to forensic investigations

Within the forensic science community, there is a continued push to develop novel tools to aid in criminal investigations. microRNA (miRNA) analysis has been the focus of many researcher's attention in the biomedical field since its discovery in 1993; however, the forensic application of miRNA analysis has only been suggested within the last 10 years and has been gaining considerable traction recently. The primary focus of the forensic application of miRNA analysis has been on body fluid identification to provide confirmatory universal analysis of unknown biological stains obtained from crime scenes or evidence items. There are, however, other forensic applications of miRNA profiling that have shown potential, yet are largely understudied, and warrant further investigation such as organ tissue identification, donor age estimation, and more. This review paper aims to evaluate the current literature and future potential of miRNA analysis within the forensic science field.

Blood species identification based on deep learning analysis of Raman spectra

Blood analysis is an indispensable means of detection in criminal investigation, customs security and quarantine, anti-poaching of wildlife, and other incidents. Detecting the species of blood is one of the most important analyses. In order to classify species by analyzing Raman spectra of blood, a recognition method based on deep learning principle is proposed in this paper. This method can realize multi-identification blood species, by constructing a one-dimensional convolution neural network and establishing a Raman spectra database containing 20 kinds of blood. The network model is obtained through training, and then is employed to predict the testing set data. The average accuracy of blind detection is more than 97%. In this paper, we try to increase the diversity of data to improve the robustness of the model, optimize the network and adjust the hyperparameters to improve the recognition ability of the model. The evaluation results show that the deep learning model has high recognition performance to distinguish the species of blood.

A stepwise strategy to distinguish menstrual blood from peripheral blood by Fisher's discriminant function

Blood samples are the most common and important biological samples found at crime scenes, and distinguishing peripheral blood and menstrual blood samples is crucial for solving criminal cases. MicroRNAs (miRNAs) are important molecules with strong tissue specificity that can be used in forensic fields to identify the tissue properties of body fluid samples. In this study, the relative expression levels of four different miRNAs (miR-451, miR-205, miR-214 and miR-203) were analysed by real-time PCR, with 200 samples from 5 different body fluids, including two kinds of blood samples (peripheral blood and menstrual blood) and three kinds of non-blood samples (saliva, semen and vaginal secretion). Then, a strategy for identifying menstrual and peripheral blood based on Fisher's discriminant function and the relative expression of multiple miRNAs was established. Two sets of functions were used: Z1 and Z2 were used to distinguish blood samples from non-blood samples, and Y1 and Y2 were used to distinguish peripheral blood from menstrual blood. A 100% accuracy rate was achieved when 50 test samples were used. Ten samples were used to test the sensitivity of the method, and 10 ng or more of total RNA from peripheral blood samples and 10 pg or more of total RNA from menstrual blood samples were sufficient for this method. The results provide a scientific reference to address the difficult forensic problem of distinguishing menstrual blood from peripheral blood.

Evaluation of a co-extraction kit for mRNA, miRNA and DNA methylation-based body fluid identification

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.

Distinct spectrum of microRNA expression in forensically relevant body fluids and probabilistic discriminant approach

MicroRNA is attracting worldwide attention as a new marker for the identification of forensically relevant body fluids. A probabilistic discriminant model was constructed to identify venous blood, saliva, semen, and vaginal secretion, based on microRNA expression assessed via RT-qPCR. We quantified 15 candidate microRNAs in four types of body fluids by RT-qPCR and found that miR-144-3p, miR-451a-5p, miR-888-5p, miR-891a-5p, miR-203a-3p, miR-223-3p and miR-1260b were helpful to discriminate body fluids. Using the relative expression of seven candidate microRNAs in each body fluid, we implemented a partial least squares-discriminant analysis (PLS-DA) as a probabilistic discriminant model and distinguished four types of body fluids. Of 14 testing samples, 13 samples were correctly identified with >90% posterior probability. We also investigated the effects of microRNA expression in skin, semen infertility, and vaginal secretion during different menstrual phases. Semen infertility and menstrual phases did not affect our body fluid identification system. Therefore, the selected microRNAs were effective in identifying the four types of body fluids, indicating that probabilistic evaluation may be practical in forensic casework.

Detection of microRNAs in DNA Extractions for Forensic Biological Source Identification

Molecular-based approaches for biological source identification are of great interest in the forensic community because of a lack of sensitivity and specificity in current methods. MicroRNAs (miRNAs) have been considered due to their robust nature and tissue specificity; however, analysis requires a separate RNA extraction, requiring an additional step in the forensic analysis workflow. The purpose of this study was to evaluate miRNA detection in blood, semen, and saliva using DNA extraction methods commonly utilized for forensic casework. RT-qPCR analysis revealed that the tested miRNAs were consistently detectable across most tested DNA extraction methods, but detection was significantly reduced compared to RNA extracts in some biological fluids. DNase treatment was not necessary to achieve miRNA-specific results. A previously developed miRNA panel for forensic body fluid identification was evaluated using DNA extracts, and largely demonstrated concordance with results from samples deriving from RNA extracts of semen, blood, and saliva.

The expression of 10 candidate specific microRNA markers for human body fluid identification in animal buccal swabs

MicroRNAs (miRNAs) have been of interest in forensic science for body fluid identification with recent years. However, there is no study investigating the species specificity of miRNA markers by the SYBR Green method. Due to the conservation of miRNAs across species, miRNA markers maybe less species-specific than mRNA markers, and in forensic cases, animal buccal swabs are more likely to appear. Therefore, in this study we addressed the influence of 8 kinds of animal buccal swabs on human saliva, semen, vaginal secretion swabs and blood identification with 10 candidate specific miRNA markers by the SYBR Green quantitative PCR. Our data showed that the expression levels of the candidate specific miRNA markers miR-124a and 372 in the cat, dog, mouse and rabbit buccal swabs were in the same range as the human vaginal secretion swabs; buccal swabs from these animals also showed similar expression levels to human saliva for the candidate specific miRNA markers miR-200c, 205 and 658. These results indicated that biomaterials of buccal swabs from cats, dogs, mice and rabbits may be mistaken for human saliva or human vaginal secretion swabs, both of which could result in false positives for human body fluids. Thus, the interpretation of these miRNA profiles for human body fluid identification can be inaccurate in the presence of these animal buccal swabs. Therefore, we suggested performing species tests before human body identification with miRNA markers.