Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis

Comprehensive body fluid identification and contributor assignment by combining targeted sequencing of mRNA and coding region SNPs

Forensic genetic analyses aim to retrieve as much information as possible from biological trace material recovered from crime scenes. While standard short tandem repeat (STR) profiling is essential to individualize biological traces, its significance is diminished in crime scenarios where the presence of a suspect's DNA is acknowledged by all parties. In such cases, forensic (m)RNA analysis can provide crucial contextualizing information on the source level about a trace's composition, i.e., body fluids/tissues, and has therefore emerged as a powerful tool for modern forensic investigations. However, the question which of several suspects contributed a specific component (body fluid) to a mixed trace cannot be answered by RNA analysis using conventional methods. This individualizing information is stored within the sequence of the mRNA transcripts. Massively parallel sequencing (MPS) represents a promising alternative, offering not only higher multiplex capacity, but also the typing of individual coding region SNPs (cSNPs) to enable the assignment of contributors to mixture components, thereby reducing the risk of association fallacies. Herein, we describe the development of an extensive mRNA/cSNP panel for targeted sequencing on the IonTorrent S5 platform. Our panel comprises 30 markers for the detection of six body fluids/tissues (blood, saliva, semen, skin, vaginal and menstrual secretion), along with 70 linkage-controlled cSNPs for contributor assignment. It exhibited high reliable detection sensitivity with RNA inputs down to 0.75 ng and a conservatively calculated probability of identity of 0.03 - 6 % for individual body fluid-specific cSNP profiles. Limitations and areas for future work include RNA-related allele imbalances, inclusion of markers to correctly identify rectal mucosa and the optimization of specific markers. In summary, our new panel is intended to be a major step forward to interpret biological evidence at sub-source and source level based on cSNP attribution of a body fluid component to a suspect and victim, respectively.

Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures

The evidentiary value of DNA profiles varies depending upon the context in which the DNA was found. Linking a DNA profile to a particular cellular phenotype in mixtures may aid in assessing its evidentiary relevance and value. We report the development of two dual-function high-resolution messenger RNA (mRNA) sequencing assays that can each identify the presence of 6 body fluids/tissues (blood, semen, saliva, vaginal secretions, menstrual blood, skin) and, via coding region SNPs (cSNPs) present in the body fluid-specific mRNA transcripts, directly associate particular body fluids with their specific DNA donors in mixtures. The original blood, semen, and saliva (BSS) assay contains 23 cSNPs for blood, semen, and saliva, while the expanded 6F (all 6 fluids/tissues) assay encompasses the BSS assay and also contains 23 additional cSNPs for vaginal secretions, menstrual blood, and skin. Software tools were developed to infer the identity of the body fluids present as well as providing the corresponding cSNP genotypes. Concomitant genomic DNA assays (BSS-d and 6F-d), required to genotype the same cSNPs from persons of interest/inferred contributors to the body fluid mixture, were also developed. Body fluid specificity was demonstrated by the ability to identify the body fluid origin of single-source and two-fluid admixtures. The discriminatory power (European Caucasians) for all body fluids is 0.957-0.997, with linkage disequilibrium considered. Reciprocal body fluid admixtures (mixture pairs with the same two donors but reversed body fluid types) were used to demonstrate the ability to identify the body fluid source of origin as well as associate the donor of each of the two fluids.

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime

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.

A data-driven, high-throughput methodology to determine tissue-specific differentially methylated regions able to discriminate body fluids

Tissue-specific differentially methylated regions (tDMRs) are regions of the genome with methylation patterns that modulate gene expression in those tissue types. The detection of tDMRs in forensic evidence can permit the identification of body fluids at trace levels. In this report, we have performed a bioinformatic analysis of an existing array dataset to determine if new tDMRs could be identified for use in body fluid identification from forensic evidence. Once these sites were identified, primers were designed and bisulfite modification was performed. The relative methylation level for each body fluid at a given locus was then determined using qPCR with high-resolution melt analysis (HRM). After screening 127 tDMR's in multiple body fluids, we were able to identify four new markers able to discriminate blood (2 markers), vaginal epithelia (1 marker) and buccal cells (1 marker). One marker for each target body fluid was also tested with pyrosequencing showing results consistent with those obtained by HRM. This work successfully demonstrates the ability of in silico analysis to develop a novel set of tDMRs capable of being differentiated by real time PCR/HRM. The method can rapidly determine the body fluids left at crime scenes, assisting the triers of fact in forensic casework.

Discrimination of menstrual and peripheral blood traces using attenuated total reflection Fourier transform-infrared (ATR FT-IR) spectroscopy and chemometrics for forensic purposes

Body fluid traces can provide highly valuable clues in forensic investigations. In particular, bloodstains are a common occurrence in criminal investigation, and the discrimination of menstrual and peripheral blood is a crucial step for casework involving rape and sexual assault. Most of the current protocols require the detection of characteristic menstrual blood components using sophisticated procedures that need to be performed in a laboratory. The present study uses attenuated total reflection Fourier transform-infrared (ATR FT-IR) spectroscopy as a nondestructive technique for discriminating menstrual and peripheral blood traces. This method incorporates statistical analysis and was evaluated by internal and external validation testing. A partial least squares discriminant analysis (PLSDA) classification model was created for differentiating the two types of blood in a binary manner. Excellent separation between menstrual and peripheral blood samples was achieved during internal validation. External validation resulted in 100% accuracy for predicting a sample as peripheral or menstrual blood. This study demonstrates that ATR FT-IR spectroscopy combined with chemometrics is a reliable approach for rapid and nondestructive discrimination of menstrual and peripheral bloodstains. It offers a significant advantage to forensic science due to the availability of portable instruments and the potential for bloodstain analysis at a crime scene. Graphical abstract.

Development of a multiplex RT-PCR assay and statistical evaluation of its use in forensic identification of vaginal fluid

The identification of vaginal fluid from casework samples of sexual assaults provides important probative evidence of vaginal intercourse. The aim of this study was to establish a more specific procedure for identifying vaginal fluids for forensic purposes. Vaginal fluid marker candidates have been evaluated quantitatively and five of these markers (ESR1, SERPINB13, KLK13, CYP2B7P1, MUC4) have been amplified simultaneously by a multiplex reverse transcription-polymerase chain reaction (RT-PCR) procedure. Each amplicon has been separated and quantified automatically using chip electrophoresis. Subsequently, in the present study, detectability and cross-reactivity of the developed multiplex procedure were assessed in detail using various forensically relevant body fluids. Then, a cutoff value for the positive detection of vaginal fluids was set for each marker by Youden index. The ability of the multiplex RT-PCR assay to distinguish between vaginal and other body fluids was evaluated statistically using a likelihood ratio (LR) that was estimated using a Bayesian estimation approach to consider the infrequency of detection. A high LR was obtained when all five markers showed positive results (LR = 4.33 × 109; 95% credible interval, 3.95 × 107 -2.87 × 1012). The developed procedure was validated using vaginal fluid samples under various conditions. High LRs were found for aged vaginal fluid stains, although each amplicon peak was low. It was also able to identify vaginal stains mixed with other body fluids. In conclusion, the multiplex RT-PCR-based procedure followed by the statistical evaluation using LR could be a powerful tool for the objective identification of vaginal fluids.

Forensic discrimination of menstrual blood and peripheral blood using attenuated total reflectance (ATR)-Fourier transform infrared (FT-IR) spectroscopy and chemometrics

Body fluids are one of the most important pieces of evidence encountered in forensic cases especially in cases of sexual assault. Analysis of such evidence can help to establish a link between the perpetrator, the victim, and the crime scene and thereby assist in crime reconstruction. However, one of the biggest challenges faced by the investigators in sexual assault cases is that of ascertaining the issue of consent of the victim. In this matter, differentiation of menstrual blood (either in dried or stained form) from traumatic peripheral blood can give a potential solution on this particular aspect. A number of studies have been attempted to differentiate these two body fluids using various biochemical and serological methods. However, the methods employed are limited by factors such as sample destructivity and non-specificity, and the methods are susceptible to false positive results. In the present study, the scope of attenuated total reflectance (ATR)-Fourier transform infrared (FT-IR) spectroscopy in discriminating samples of menstrual blood and peripheral blood has been investigated, in combination with chemometric tools such as principal component analysis (PCA), partial least square regression (PLSR), and linear discriminant analysis (LDA). PCA resulted in 93.3% accuracy, whereas PLSR and LDA resulted in 100% accuracy for the discrimination of peripheral blood from menstrual blood. Application of PCA for the discrimination of menstrual blood from vaginal fluid and seminal fluid delivered 100% classification. Similarly, 100% classification was achieved while differentiating between menstrual blood and blood look-alike substances. Furthermore, in the current study, the effect of substrates on the analysis of menstrual blood has also been studied and described. Graphical Abstract.

"The acid test"-validation of the ParaDNA® Body Fluid ID Test for routine forensic casework

The identification of the cellular origin and composition of crime scene-related traces can provide crucial insight into a crime scene reconstruction. In the last decade, especially mRNA-based body fluid and tissue identification (BFI) has been vigorously examined. Besides capillary electrophoretic (CE) and real-time quantitative PCR (RT-qPCR)-based approaches for mRNA detection, melt curve analysis bears potential as a simple-to-use method for BFI. The ParaDNA® Body Fluid ID Test relies on HyBeacon® probes and was developed as a rapid test for mRNA-based BFI of six different body fluids: vaginal fluid, seminal fluid, sperm cells, saliva, menstrual, and peripheral blood. The herein presented work was performed as an "acid test" of the system and should clarify whether the approach matches the requirements of forensic routine casework in German police departments. Tested samples consisted of single source as well as of mixed samples.

Human Organ Tissue Identification by Targeted RNA Deep Sequencing to Aid the Investigation of Traumatic Injury

Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers. The identifiable organs and tissues include brain, lung, liver, heart, kidney, intestine, stomach, skeletal muscle, adipose, and trachea. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific, with little cross-reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues. We also demonstrate the ability of the assay to successful identify the tissue source of origin using a single blind study.

Validation of an immunochromatographic D-dimer test to presumptively identify menstrual fluid in forensic exhibits

Identifying the biological source of a crime scene stain can be crucial for police investigations in many scenarios. Blood is one of the most common fluids found, and accurate differentiation between peripheral blood and menstrual fluid could provide valuable information regarding the issue of consent in sexual assault cases. For the detection of menstrual fluid, no easy-to-use presumptive test is available to date. Therefore, this study aimed to validate a simple immunochromatographic test for the indication of menstrual fluid, focusing on a D-dimer assay. The Clearview® rapid D-dimer test provides a diagnostic assay for the detection of fibrin degradation products. We validated the sensitivity and robustness of the assay using fresh and dried menstrual fluid samples, body fluid mixtures, diluted samples, and casework swabs. Cross reactivity was tested for saliva, semen, vaginal fluid, and blood. No false positive results were obtained; it was possible to successfully analyze mixtures, highly diluted samples, and casework swabs. The results of this study indicate that the D-dimer assay reliably detects menstrual fluid in forensic exhibits and is easy to implement into the current workflow of body fluid identification.

mRNA heptaplex protocol for distinguishing between menstrual and peripheral blood

The identification of menstrual blood is an important issue in forensic biology, but currently, there are no confirmatory methods for its detection. Here, we demonstrate a highly reliable simple heptaplex method that allows for the discrimination between menstrual and peripheral blood. The test has been used successfully in criminal casework, in which the origin of blood on a rape victim's underwear and trousers was questioned as being menstrual or traumatic peripheral blood. To solve this problem, transcripts of the following genes were used: mucin 4 (MUC4), human β-defensin 1 (HBD1), two matrix metalloproteinases (MMP7, MMP11), δ-aminolevulinate synthase 2 (ALAS2), hemoglobin alpha (HBA) and glucose 6-phosphate dehydrogenase (G6PDH). The sensitivity of the test is 0.3ng of RNA. The possibility of the detection and differentiation of menstrual and peripheral blood in mixtures that contain other body fluids was investigated. Reliable detection is possible for menstrual blood stains that are up to 1-2 years old if stored at room temperature. This easy approach, thanks to the amplification of 4 vaginal and 2 blood markers, minimizes the risk of false negative results.