Body Fluid Identification Research Articles

Evaluation of a blood-specific DNA methylated region and trial for allele-specific blood identification from mixed body fluid DNA.

The identification of blood samples obtained from crime scenes has been an important step in forensic investigation. Recently, a novel approach using the blood-specific methylated CpG site cg06379435 has been reported. In this study, we developed a real-time polymerase-chain-reaction-based method that can simply and rapidly quantitate the methylation ratio of cg06379435 and its neighboring CpGs and set the threshold ratios for blood identification by analyzing various body fluid samples. Blood identification using the thresholds was successfully performed in the analysis of a small amount (1ng) of DNA from blood and various aged blood samples, including 29-year-old stains. We also demonstrated a test for allele-specific blood identification from a mixed DNA sample by bisulfite sequencing analysis of these CpG sites and their neighboring single nucleotide polymorphism, rs7359943 (A/G), which is of relevance in cases where mixed samples are obtained from crime scenes. The stability of DNA methylation in aged samples and the usefulness of neighboring genetic information shown in this study suggest that DNA-methylation-based body fluid identification will play a major role in future forensic investigations.

Forensic DNA methylation profiling from evidence material for investigative leads.

DNA methylation is emerging as an attractive marker providing investigative leads to solve crimes in forensic genetics. The identification of body fluids that utilizes tissue-specific DNA methylation can contribute to solving crimes by predicting activity related to the evidence material. The age estimation based on DNA methylation is expected to reduce the number of potential suspects, when the DNA profile from the evidence does not match with any known person, including those stored in the forensic database. Moreover, the variation in DNA implicates environmental exposure, such as cigarette smoking and alcohol consumption, thereby suggesting the possibility to be used as a marker for predicting the lifestyle of potential suspect. In this review, we describe recent advances in our understanding of DNA methylation variations and the utility of DNA methylation as a forensic marker for advanced investigative leads from evidence materials. [BMB Reports 2016; 49(7): 359-369]

Forensic body fluid identification and differentiation by Raman spectroscopy

The ability to identify body fluid traces at crime scenes, and preserve any DNA present, is critically important in forensic science. Identification can be difficult because many of the current techniques are specific to one body fluid, and typical biochemical methods are destructive – preventing any further analysis. To develop a universal, confirmatory, nondestructive, approach that can be used to differentiate and identify body fluids, we combined the specificity of Raman spectroscopy with the analytical power of statistical modeling. Raman spectra were collected from 75 body fluid samples, including peripheral blood, saliva, semen, sweat, and vaginal fluid. After preprocessing, samples were split into calibration and validation datasets. Several chemometric analysis techniques were trained and tested to find the best model. Combining classification modeling with variable selection resulted in a single, robust, technique. This enhanced model accurately predicted the identity of 99.9% of the spectra from the calibration dataset, after cross-validation. More importantly, it correctly predicted the identity of 100% of the spectra in the external validation dataset. All five body fluids were successfully discriminated by coupling Raman spectroscopy and chemometrics. This technique is both reliable and nondestructive, offering substantial advantages over the current techniques used to identify body fluids.

Forensic discrimination of vaginal epithelia by DNA methylation analysis through pyrosequencing.

The accurate identification of body fluids from crime scenes can aid in the discrimination between criminal and innocent intent. This research aimed to determine if the levels of DNA methylation in the locus PFN3A could be used to discriminate vaginal epithelia from other body fluids. In this work we bisulfite-modified and amplified DNA samples from blood, saliva, semen, and vaginal epithelia using primers for PFN3A. Through pyrosequencing we were able to show that vaginal epithelia present distinct methylation levels when compared to other body fluids. Mixtures of different body fluids present methylation values that correlate with single-source body fluid samples and the primers for PFN3A are specific for primates. This report successfully demonstrated that the analysis of methylation in the PFN3A locus can be used for vaginal epithelia discrimination in forensic samples.

Novel identification of biofluids using a multiplex methylation-specific PCR combined with single-base extension system.

Knowledge of the composition of complex body fluid mixtures may aid forensic investigations greatly. However, many of the traditional tests are presumptive in nature and can lead to ambiguous results. The aim of this study is to establish a reliable method to identify various biofluids via analysis of their DNA methylation profiles. A total of eight biofluid-specific methylated markers for saliva, venous blood, vaginal fluids, and semen were isolated from the open database of Infinium HumanMethylation450 BeadChip. These biofluid-specific markers, a control marker to confirm bisulfite conversion, and a gender marker, were combined into a 10-plex methylation-specific PCR single-base-extension (MSP-SBE) system. Analysis of 65 DNA samples isolated from venous blood, semen, vaginal fluid, saliva, and menstrual blood that had been treated with bisulfite, resulted in all eight markers detecting the body fluid to which they were designed. Unambiguous body fluid identification occurred from both single sources of body fluids and complex mixtures. A threshold was devised for each marker to minimize the chance of a false inclusion. The efficacy of the assay and application to forensic practice was demonstrated using five non-probative samples from real alleged sexual assault cases. The system unambiguously determined the biofluid types for the non-probative forensic samples that previously resulted in inconclusive or conflicting results using traditional tests. The results demonstrated the 10-plex MSP-SBE system established in this study is both sensitive and specific when applied to body fluid identification and can be readily adopted into forensic practice.

Direct identification of forensic body fluids using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The examination of body fluids such as blood, seminal fluid, urine or saliva is a key aspect of forensic science in regards to investigation of crimes against the person such as murder and rape. This article describes a streamlined and simplified approach for the identification of body fluids using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS) that avoids fractionation or isolation of proteins. It is applicable to the examination of microliter quantities (or less) of neat fluids, extracts or suspensions of dried fluids or deposits of fluids in situ on tufts of fibers plucked from fabrics, which has practical application in the examination of crime-related items such as underwear or face masks. Hemoglobin was used as a marker for blood, α-amylase for saliva, semenogelins, prostate-specific antigen and acid phosphatase for seminal fluid and uromodulin for urine. Aged stains were successfully analyzed; blood proteins were easily detected in an 11-year-old blood stain.

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

Applying molecular genetic approaches for the identification of forensically relevant body fluids, which often yield crucial information for the reconstruction of a potential crime, is a current topic of forensic research. Due to their body fluid specific expression patterns and stability against degradation, microRNAs (miRNA) emerged as a promising molecular species, with a range of candidate markers published. The analysis of miRNA via quantitative Real-Time PCR, however, should be based on a relevant strategy of normalization of non-biological variances to deliver reliable and biologically meaningful results. The herein presented work is the as yet most comprehensive study of forensic body fluid identification via miRNA expression analysis based on a thoroughly validated qPCR procedure and unbiased statistical decision making to identify single source samples.

Forensic body fluid identification: state of the art

Body fluid identification is a key component in the forensic scientists' tool box and has been carried out both at the crime scene and in the laboratory for many years. Historically, methods relied on (bio) chemical-based tests, many of which lacked specificity. In this review, current technologies for identifying body fluids are described including the use of RNA (mRNA and miRNA), epigenetics, spectroscopic techniques such as Raman spectroscopy and micro-spectrophotometry, biosensors, and immunochromatographic methods which are outlined alongside their strengths and weaknesses. The potential for new insights into the identification of cells from new technologies such as massively parallel sequencing is explored. forensic science, body fluid identification

Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence

The identification of body fluids is an essential tool for clarifying the course of events at a criminal site. The analytical problem is the fact that the biological material has been very often exposed to detrimental exogenous influences. Thereby, the molecular substrates used for the identification of the traces may become degraded. So far, most protocols utilize cell specific proteins or RNAs. Instead of measuring these more sensitive compounds this paper describes the application of the differential DNA-methylation. As a result of two genome wide screenings with the Illumina HumanMethylation BeadChips 27 and 450k we identified 150 candidate loci revealing differential methylation with regard to the body fluids venous blood, menstrual blood, vaginal fluid, saliva and sperm. Among them we selected 9 loci as the most promising markers. For the final determination of the methylation degree we applied the SNuPE-method. Because the degree of methylation might be modified by various endogenous and exogenous factors, we tested each marker with approximately 100 samples of each target fluid in a validation study. The stability of the detection procedure is proved in various simulated forensic surroundings according to standardized conditions. We studied the potential influence of 12 relatively common tumors on the methylation of the 9 markers. For this purpose the target fluids of 34 patients have been analysed. Only the cervix carcinoma might have an remarkable effect because impairing the signal of both vaginal markers. Using the Illumina MiSeq device we tested the potential influence of cis acting sequence variants on the methylation degree of the 9 markers in the specific body fluid DNA of 50 individuals. For 4 marker loci we observed such an influence either by sole SNPs or haplotypes. The identification of each target fluid is possible in arbitrary mixtures with the remaining four body fluids. The sensitivity of the individual body fluid tests is in the same range as for the forensic STR-analysis. It is the first forensic body fluid protocol which considers the exogenic and endogenic parameters potentially interfering with the true results.

Developmental validation studies of epigenetic DNA methylation markers for the detection of blood, semen and saliva samples

Determining the type and origin of body fluids in a forensic investigation can provide important assistance in reconstructing crime scenes. A set of epigenetic markers, ZC3H12D, BCAS4 and cg06379435, have been developed to produce unique and specific patterns of DNA methylation that can be used to identify semen, saliva, and blood, respectively. To ensure the efficacy of these markers, developmental validation studies were performed to determine the conditions and limitations of this new tool for forensic analysis. DNA was extracted from human samples and bisulfite modified using commercial bisulfite modification kits. Specific primers were used to amplify the region of interest and the methylation profile of the CpG sites were determined by pyrosequencing. The percent methylation values at each CpG site were determined in multiple samples and averaged for each tissue type. The versatility of these new markers is presented by showing the results of validation studies on sensitivity, human specificity, stability and mixture resolution. When testing the markers using different organisms, we did obtain positive results for certain non-human primate samples, however, all other tested species were negative. The lowest concentration consistently detected varied from 0.1 to 10ng, depending on the locus, indicating the importance of primer design and sequence in the assay. The method also proved to be effective when inhibitors were present in the samples or when samples were degraded by heat. Simulated case- samples were also tested. In the case of mixtures of different cell types, the overall methylation values varied in a consistent and predictable manner when multiple cell types were present in the same sample. Overall, the validation studies demonstrate the robustness and effectiveness of this new tool for body fluid identification.

Body Fluids and Spectroscopic Techniques in Forensics: A Perfect Match?

Human body fluids are of great interest in forensics, due to the possibility to extract their genetic information. At the moment, there is the need to develop a non-destructive, rapid and user-friendly method for the detection and identification of the body fluids usually found at crime scenes: blood, semen, vaginal fluid, saliva, sweat and urine. In this review, the spectroscopic techniques used or being researched on this topic are discussed, taking into account their advantages, limitations and advances. Although, UV-Vis light sources are used worldwide in forensic laboratories for the location of body fluids, they are not selective enough to be confirmatory. HSI, FTIR and Raman spectroscopy seem to be suitable for the identification and discrimination of body fluids, though comprehensive research about some unsolved aspects must be performed first.

Whole blood and semen identification using mid-infrared and Raman spectrum analysis for forensic applications

The identification of body fluids is important in forensic science.

Body Fluid Identification Using mRNA Profiling.

RNA analysis is a valuable tool for the identification of the forensically relevant body fluids, saliva, blood, menstrual blood, cervicovaginal fluid, and semen. Multiple human mRNA and bacterial RNA markers have been identified for each of these body fluids. RNA and DNA can be coextracted from the same portion of a sample and RNA markers for different body fluids can be multiplexed in a single PCR, thereby maximizing the number of analyses that can be performed with limited sample material.

Application of DNA Methylation in Forensic Science: A Review

DNA methylation is an epigenetic mechanism which plays a vital role in the control and regulation of gene expression. In the past few years DNA Methylation was widely investigated in Medical field to understand complex diseases, but of late there has been a surge in studies exploring its potential use in Forensic Science. The present review discusses the application of DNA methylation to decipher regularly encountered query faced by a criminalist which includes DNA authentication, Body fluid identification, paternity dispute, Ancestry, gender and age estimation and Identification of monozygotic twins. The review also gives an insight about DNA methylation limitations.

Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling

The forensic identification of human body fluids and tissues by means of messenger RNA (mRNA) profiling is a long studied methodology that is increasingly applied to casework samples. Previously, we have described an mRNA multiplex system that targets blood, saliva, semen, menstrual secretion, vaginal mucosa and skin (Lindenbergh et al. and van den Berge et al.) [1–2]. In this study we consider various topics to improve this mRNA profiling system or its use and adapt the method accordingly. Bodily secretions that may be encountered at a crime scene whilst not targeted by the multiplex—id est nasal mucosa, sweat, tears, faeces and urine-were examined for false positive signals. The results prompted us to identify a nasal mucosa marker that allows the discrimination of nasal mucosa from saliva or vaginal mucosa and nosebleed blood from peripheral blood. An updated version of the multiplex was prepared to which the nasal mucosa marker was added and in which markers for semen, vaginal mucosa and blood were replaced. Lactobacillus markers were regarded unsuitable as replacement for vaginal mucosa mRNA markers because of background signals on penile swabs that appeared devoid of female DNA. Furthermore, we provide approaches to deal with highly unbalanced mixtures. First, a differential extraction protocol was incorporated into a co-extraction protocol to allow DNA and RNA analysis of separated non-sperm and sperm fractions. In a second approach, besides the standard multiplex, a customized multiplex is used which excludes markers for prevailing cell types. This allows the use of lower cDNA inputs for the prevailing cell types and higher inputs for cell types that appear masked. Additionally, we assessed the relation between the percentage of alleles or markers detected in DNA or RNA profiles when decreasing sample amounts are analysed. While blood, saliva, semen and menstrual secretion show the trend that DNA profiling is more sensitive than RNA profiling, the reverse is seen for skin and variable results occur for vaginal and nasal mucosa. Lastly, we show that replicates are useful for interpretation of RNA data, as variations can be found even for true technical replicates. Increased numbers of replicates (over four) do, however, not cancel out the impact of this variation on data interpretation. Overall, the results of this study further forensic RNA profiling.

Reference gene study for forensic body fluid identification

Reference genes are used in forensic body fluid identification studies to normalise data generated during gene expression experiments. The use of reference genes improves the reliability of qRT-PCR. In this study, 10 most common reference genes UCE, TEF, GAPDH, 18S rRNA, ACTB, B2M, B-Actin, OAZ1, RPS 29 and S15 widely used in forensic body fluid identification studies were selected from relevant literature and qPCR efficiency and sensitivity of all the reference genes was tested using SYBR Green detection. Stability was also assayed using samples stored at room temperature for 6 months using Taqman assay probes. All the markers except TEF displayed high sensitivity and were detected down to 25pg of RNA input. Stability study demonstrates that B2M, ACTB, RPS29, and UCE are ideal markers for normalization in forensic body fluid identification studies. The study confirms that reference genes should be selected only upon adequate validation of their suitability.

Characterization of microRNA expression profiles in blood and saliva using the Ion Personal Genome Machine® System (Ion PGM™ System)

MicroRNA (miRNA) expression profiling is gaining interest in the forensic community because the intrinsically short fragment and tissue-specific expression pattern enable miRNAs as a useful biomarker for body fluid identification. Measuring the quantity of miRNAs in forensically relevant body fluids is an important step to screen specific miRNAs for body fluid identification. The recent introduction of massively parallel sequencing (MPS) has the potential for screening miRNA biomarkers at the genome-wide level, which allows both the detection of expression pattern and miRNA sequences. In this study, we employed the Ion Personal Genome Machine® System (Ion PGM™ System, Thermo Fisher) to characterize the distribution and expression of 2588 human mature miRNAs (miRBase v21) in 5 blood samples and 5 saliva samples. An average of 1,885,000 and 1,356,000 sequence reads were generated in blood and saliva respectively. Based on miRDong, a Perl-based tool developed for semi-automated miRNA distribution designations, and manually ascertained, 6 and 19 miRNAs were identified respectively as potentially blood and saliva-specific biomarkers. Herein, this study describes a complete and reliable miRNA workflow solution based on Ion PGM™ System, starting from efficient RNA extraction, followed by small RNA library construction and sequencing. With this workflow solution and miRDong analysis it will be possible to measure miRNA expression pattern at the genome-wide level in other forensically relevant body fluids.

MicroRNA markers for forensic body fluid identification obtained from miRCURY™ LNA array

MicroRNA is a promising marker for forensic body identification especially in compromised samples and mixtures because of its small size and tissue specific expression manner. Previously, five research groups have reported specific miRNAs screened from different arrays for body fluid identification. Our study aims to screen appropriate miRNAs for forensic body fluid identification through Exiqon’s miRCURY™ LNA Array. Five samples of six common body fluids were collected including peripheral blood, menstrual blood (six samples for menstrual blood), saliva, semen, vaginal secretion and skin swabs. Eight novel miRNAs and two reported markers were selected to identify five commom body fluids. Reliable miRNA markers for skin cells couldn’t be identified because relative expression ratios from array results were not large enough to identify target body fluid. Our result suggest that, maybe more markers should be combined together to identify the skin cells, and the strategy need to be refined. Our study first introduces skin cells into the microarray screening and enriches the candidates for forensic body fluid identification.

Characterization of cellular and extracellular DNA in saliva.

Although the presence of extracellular DNA in various body fluids was discovered long ago, only recently has it begun to attract attention for examining the genetic profiles of individuals in forensics studies. However, information on extracellular DNA is scarce. Among human body fluids, saliva is known to be rich in extracellular DNA. In this study, to analyze the possibility of identifying individuals and body fluids by using only extracellular DNA of saliva, we investigated the amount, size distribution, short tandem repeat (STR) profile, and methylation pattern of extracellular DNA from saliva and compared these with those of cellular DNA. The amount and size distribution of extracellular DNA was different from that of cellular DNA. However, their respective STR profiles were the same. The methylation patterns of the BCAS4 gene were different among donors, but no significant difference was observed between cellular and extracellular DNA. The results of our study suggest that identification of individuals and body fluids from saliva may be possible without the need for cells.

Degraded RNA transcript stable regions (StaRs) as targets for enhanced forensic RNA body fluid identification

The detection of messenger RNA (mRNA) using reverse transcriptase PCR (RT-PCR) is becoming common practice for forensic body fluid identification. However, the degraded and scarce nature of RNA from forensic samples mean that mRNA transcripts are not consistently detected or remain undetected in practice. Conventional primer design for RT-PCR (and quantitative RT-PCR) includes targeting primers to span exon–exon boundaries or by having the primers on two separate exons, and satisfying common primer thermodynamic criteria. We have found that the conventional placement of primers is not always optimal for obtaining reproducible results from degraded samples. Using massively parallel sequencing data from degraded body fluids, we designed primers to amplify transcript regions of high read coverage, hence, higher stability, and compared these with primers designed using conventional methodology. Our findings are that primers designed for transcript regions of higher read coverage resulted in vastly improved detection of mRNA transcripts that were not previously detected or were not consistently detected in the same samples using conventional primers. We developed a new concept whereby primers targeted to transcript stable regions (StaRs) are able to consistently and specifically amplify a wide range of RNA biomarkers in various body fluids of varying degradation levels.