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

Identification of menstrual blood and vaginal fluid using a 4-plex MSRE-PCR system applicable to alleged sexual assault cases

Menstrual blood and vaginal fluid are frequently encountered in conjunction with semen in alleged sexual assault cases. There are few tests with high specificity for these two body fluids and here we report on a 4-plex MSRE-PCR system for the detection of menstrual blood and vaginal fluid. The assay uses four markers in a multiplex PCR: a positive control (PC), digestive control (DC), menstrual blood-specific (MB) marker and vaginal fluid-specific (VF) marker. Menstrual blood and vaginal fluid samples were identified by the MB and VF markers as expected. Additionally, the results using samples from saliva, semen and blood were also correctly identified, with an absence of both the MB and VF markers as expected, even though MB and VF signals can occur within a few non-target body fluids (urine, nasal fluid and skin). It was found that the methylation levels at the markers for both menstrual blood and vaginal fluid have differences between individuals. The methylation level of the marker for menstrual blood was affected by the day during the menstruation cycle, which also affected the sensitivity of the test. DNA required for correct identification of menstrual blood increased from 1 ng at day 1 to 1.5 ng for day 5. The sensitivity of the assay using samples from vaginal fluid was at least 0.5 ng of DNA for confident identification. Menstrual blood samples deposited on seven types of materials frequently encountered in forensic investigations were all correctly assigned. Also, samples of simulated mixed menstrual blood and vaginal fluid were tested and the results were all concordant as expected. These data help to verify the applicability of the 4-plex MSRE-PCR system in forensic casework.

Identification of body fluid sources based on microbiome antibiotic resistance genes using high-throughput qPCR

Identifying the origin of body fluids is a critical step in forensic investigation. Recently, the development of high-throughput sequencing technology has led to the use of microbiomes for body fluid identification in forensic studies. However, high-throughput sequencing data are difficult to analyze, the sequencing protocol is complicated. An increasing number of studies have focused on antibiotic resistance genes (ARGs) in the human microbiome. The abundance and diversity of ARGs in different parts of the human body can be detected using quantitative polymerase chain reaction (qPCR). To date, no studies have inferred the sources of body fluids based on ARGs. Therefore, we attempted to use ARGs as a tool to infer the origin of body fluids. We assessed the abundance and diversity of 64 ARGs in blood, semen, saliva, vaginal secretions (VS), nasal secretions (NS), and fecal samples using high-throughput qPCR. The results showed that ARGs were more diverse in fecal samples, which was significantly higher than those of other sample types (P < 0.05). Principal coordinate analysis (PCoA) showed that the samples clustered mainly according to their type. We constructed a random forest classification model based on 64 ARGs with a prediction accuracy of 92.68 %. Next, we evaluated the importance of the features in the random forest model (mean decrease accuracy, MDA). Subsequently, we constructed prediction models for the top 40 and 20 ARGs after sorting genes with the highest MDA, and their prediction accuracies were both 92.68 %. The accuracy of the top 10 ARGs was 87.80 %. Notably, when only the top 10 characterized ARGs were used to construct models for saliva, semen, and VS samples, the prediction accuracy reached was 95.24 %. This shows that blood, semen, saliva, NS, VS, and fecal samples can be accurately identified using ARGs. Our results suggest that ARGs are promising markers for forensic body fluid identification.

Discovery of specific protein markers in multiple body fluids and their application in forensic science

Identification of multiple body fluids is crucial for the reconstruction and corroboration of crime event. However, for the body fluids with high component similarities, such as peripheral blood and menstrual blood, reliable distinguishing markers are still lacking. Furthermore, a comprehensive protein marker assay for multiple body fluids is urgently necessary for complex crime events. Herein, we established a highly specific and detectable method for discovering protein markers in peripheral blood, menstrual blood, saliva, semen and vaginal fluid through integrating in-depth discovery proteomics and a two-step targeted screening approach. Four menstrual blood markers with high endometrial specificities were identified for differentiation from peripheral blood and exhibited moderate protein concentrations for reproducible analysis with a protein quantitation CV value of 8.66%. Finally, a targeted discrimination method with 16 protein markers was established. We successfully identified 47 blind samples with 100% specificity and detection rate, sourced from five types of body fluids and presented on matrices such as cotton, tissues, slides or fluid. Overall, this work developed an effective method for discovering body fluid biomarkers, obtained specific protein markers to identify five kinds of body fluids and their targeted monitoring will show great significance for forensic science.

Developmental validation of an mRNA-cSNP profiling panel for body fluids identification and individualization

Forensic analysis of body fluid stains is extremely important, which helps reconstruct crime scenes. It involves two main challenges: body fluid identification (BFID) and individualization. The former aims to ascertain the type/origin of the body fluid stain, while the latter tries to assign the stain to a specific donor. Generally, they are addressed through RNA and DNA analyses, respectively, but this can be time-consuming, laborious, and sometimes yield suboptimal results, especially mixed body fluid stains. To overcome these limitations, we developed an innovative mRNA-based sequencing panel with a dual function. This system comprises 34 body fluid-specific mRNA genes and 39 cSNP markers (amplicon length: 50 ~ 90 bp), enabling a direct link between specific body fluids and their donors. We thoroughly validated the integrated system according to the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM) on the MGI massively parallel sequencing (MPS) platform. As a result, this panel showed robust identification efficiency for body fluids at 20 ng RNA input, and the range of cumulative discrimination power (CDP) value was 0.802445047 ~ 0.999310789 in five types of body fluid. Furthermore, it had been employed in actual cases and provided the guidance. In conclusion, this system can efficiently, rapidly, and accurately perform body fluid identification and individualization for single-source and mixed samples, meeting the daily investigative demands in forensic genetics.

Differentiation of five forensically relevant body fluids using a small set of microRNA markers

In forensic investigations, identifying the type of body fluid allows for the interpretation of biological evidence at the activity level. Over the past two decades, significant research efforts have focused on developing molecular methods for this purpose. MicroRNAs (miRNAs) hold great promise due to their tissue-specific expression, abundance, lack of splice variants, and relative stability. Although initial findings are promising, achieving consistent results across studies is still challenging, underscoring the necessity for both original and replication studies. To address this, we selected 18 miRNA candidates and tested them on 6 body fluids commonly encountered in forensic cases: peripheral blood, menstrual blood, saliva, semen, vaginal secretion, and skin. Using reverse transcription quantitative PCR analysis, we confirmed eight miRNA candidates (miR-144-3p, miR-451a, miR-205-5p, miR-214-3p, miR-888-5p, miR-891a-5p, miR-193b-3p, miR-1260b) with high tissue specificity and four (miR-203a-3p, miR-141-3p, miR-200b-3p, miR-4286) with lesser discrimination ability but still contributing to body fluid differentiation. Through principal component analysis and hierarchical clustering, the set of 12 miRNAs successfully distinguished all body fluids, including the challenging discrimination of blood from menstrual blood and saliva from vaginal secretion. In conclusion, our results provide additional data supporting the use of a small set of miRNAs for predicting common body fluids in forensic contexts. Large population data need to be gathered to develop a body fluid prediction model and assess its accuracy.

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.

Mass spectrometry-based proteomic analysis of biological stains identifies body fluids specific markers

The identification of biological stains and their tissue resource is an important part of forensic research. Current methods suffer from several limitations including poor sensitivity and specificity, trace samples, and sample destruction. In this study, we profiled the proteomes of menstrual blood, peripheral blood, saliva, semen, and vaginal fluid with mass spectrometry technology. Tissue-enhanced and tissue-specific proteins of each group have been proposed as potential biomarkers. These candidate proteins were further annotated and screened through the combination with the Human Protein Atlas database. Our data not only validates the protein biomarkers reported in previous studies but also identifies novel candidate biomarkers for human body fluids. These candidates lay the foundation for the development of rapid and specific forensic examination methods.