A method to estimate the age of bloodstains using quantitative PCR

RNA quality score evaluation: A preliminary study of RNA integrity number (RIN) and RNA integrity and quality number (RNA IQ)

In the past several years, with the in-depth development of RNA-related research, exploring the application of transcriptome and corresponding RNA biomarkers has become one of the research hotspots in the field of forensic science. High-quality RNA is essential for successful downstream workflows, especially in the steps of screening biomarkers by microarray or RNA sequencing (RNA-seq). Thus, accurately evaluating the quality of RNA samples is a critical step in obtaining meaningful expression data. The RNA integrity number (RIN) generated from the Agilent Bioanalyzer system has been widely used for RNA quality control in the past two decades. Recently, Thermo Fisher Scientific launched a ratiometric fluorescence-based method to quickly check whether an RNA sample has degraded, and the results are presented as RNA integrity and quality number (RNA IQ). Both quality score systems determine RNA quality using a numerical system based on a scale of 1-10, with 1 denoting significantly degraded specimens and 10 representing high-quality, intact RNA samples. In this preliminary study, we evaluated the consistency, reproducibility and linearity of two quality scores in RNA quality determination by analyzing heat- and RNase- artificially degraded samples. Meanwhile, the expression levels of three microRNAs (hsa-let-7 g-5p, hsa-miR-93-5p and hsa-miR-191-5p) in intact and severely degraded RNA samples were estimated by TaqMan-qPCR and droplet digital PCR. Overall, both quality scores showed good repeatability and reproducibility in their respective tests. In the samples subjected to thermal degradation, RIN showed a trend corresponding to heating time, while RNA IQ value showed almost no change on the time gradient. However, in RNase A mediated degradation, RNA IQ value observed better linearity. Furthermore, the expression levels of three microRNAs in the severely degraded samples did not show significant changes compared to the intact RNA samples. RNA degradation is a very complex and highly variable process, which is difficult to comprehensively evaluate through any one index and cannot directly compare these two parameters. Nevertheless, combined with previous research results and the expression levels of three microRNAs in this study, analyzing RNA biomarkers with stable regions or small sizes in challenged samples may be a conservative and reliable approach.

Transcriptomic changes and prediction of time since deposition of blood stains

In forensics, it is important to determine the time since deposition (TSD) of bloodstains, one of the most common types of biological evidence in criminal cases. However, no effective TSD inference methods have been established despite extensive attempts in forensic science. Our study investigated the changes in the blood transcriptome over time, and we found that degradation could be divided into four stages (days 0-2, 4-14, 21-56, and 84-168) at 4 °C. A random forest prediction model based on these transcriptional changes was trained on experimental samples and tested in separate test samples. This model was able to successfully predict TSD (area under the curve [AUC] = 0.995, precision = 1, and recall = 1). Thus, this proof-of-concept pilot study has practical significance for assessing physical evidence. Meanwhile, 11 upregulated and 13 downregulated transcripts were identified as potential time-marker transcripts, laying a foundation for further development of TSD analysis methods in forensic science and crime scene investigation.

Quantitative PCR analysis of bloodstains of different ages

An accurate method to estimate the age of a stain or the time since deposition (TsD) would represent an important tool in police investigations for evaluating the true relevance of a stain. In this study, two laboratories reproduced an mRNA-based method for TsD estimation published by another group. The qPCR-based assay includes four transcripts (B2M, LGALS2, CLC, and S100A12) and showed preferential degradation of the 5' end over the 3' end. In this study, the blood-specific marker ALAS2 was added to examine whether it would show the same degradation pattern. Based on our qPCR data several elastic net models with different penalty combinations were created, using training data from the two laboratories separately and combined. Each model was then used to estimate the age of bloodstains from two independent test sets each laboratory had prepared. The elastic net model built on both datasets with training samples up to 320 days old displayed the best prediction performance across all test samples (MAD=18.9 days). There was a substantial difference in the prediction performance for the two laboratories: Restricting TsD to up to 100 days for test data, one laboratory obtained an MAD of 2.0 days when trained on its own data, whereas the other laboratory obtained an MAD of 15 days.

Accurate quantification of DNA using on-site PCR (osPCR) by characterizing DNA amplification at single-molecule resolution

Despite the need in various applications, accurate quantification of nucleic acids still remains a challenge. The widely-used qPCR has reduced accuracy at ultralow template concentration and is susceptible to nonspecific amplifications. The more recently developed dPCR is costly and cannot handle high-concentration samples. We combine the strengths of qPCR and dPCR by performing PCR in silicon-based microfluidic chips and demonstrate high quantification accuracy in a large concentration range. Importantly, at low template concentration, we observe on-site PCR (osPCR), where only certain sites of the channel show amplification. The sites have almost identical ct values, showing osPCR is a quasi-single molecule phenomenon. Using osPCR, we can measure both the ct values and the absolute concentration of templates in the same reaction. Additionally, osPCR enables identification of each template molecule, allowing removal of nonspecific amplification during quantification and greatly improving quantification accuracy. We develop sectioning algorithm that improves the signal amplitude and demonstrate improved detection of COVID in patient samples.

Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines

In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r² ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.

The estimation of bloodstain age utilizing circRNAs and mRNAs biomarkers

Determining the time since deposition (TsD) of bloodstains can provide forensic investigators with additional clues, as it can corroborate eyewitness accounts, limit the number of suspects, and help confirm alibis. Bloodstains are the most common bodily fluid stains at crime scenes. In this study, we examined the relative expression levels (REs) of circRNAs and mRNAs data in bloodstains over ten time points by Real-time quantitative polymerase chain reaction (qPCR), to determine the utility of the relative expression levels of RNA markers for TsD estimation. Forensic samples more than just appear in indoor settings, we also evaluated the use of RNA degradation rate to indicate the age of bloodstains in different environments including indoor and outdoor conditions. The expression levels of six blood-specific mRNA markers (GYPA, CD93, ALAS2, SPTB, HBB, HBA), three highly expressed circRNAs in human peripheral blood (hsa_circ_0001445, hsa_circ_0000972, hsa_circ_0000095) and three reference genes (18 S, ACTB and U6) were analyzed across numerous ageing time points. Analysis of the degradation rates of individual RNAs under indoor and outdoor conditions showed that they exhibited a unique degradation profile during the four-month storage interval, with both circRNAs and mRNAs linearly showing continuous degradation, while U6 is more stable than other reference gene markers. In the current study, we firstly used circRNAs as additional novel biomarkers for bloodstain age estimation, and at the same time proved that different environments had a significant impact on the REs of certain blood biomarkers, and sex differences did not affect the age estimation of bloodstains. The REs of the selected RNA molecules in this study showed a non-linear relationship with bloodstain age and the mathematical formula for estimating the bloodstain age based on the relative expression levels of hsa_circ_0001445, ALAS2 and HBB can be used to estimate the TsD of bloodstains from the REs of bloodstains of unknown age, which represent a potentially effective approach to looking for time-dependent changes and TsD estimation.

Using total RNA quality metrics for time since deposition estimates in degrading bloodstains

The physicochemical changes occurring in biomolecules in degrading bloodstains can be used to approximate the time since deposition (TSD) of bloodstains. This would provide forensic scientists with critical information regarding the timeline of the events involving bloodshed. Our study aims to quantify the timewise degradation trends and temperature dependence found in total RNA from bloodstains without the use of amplification, expanding the scope of the RNA TSD research which has traditionally targeted mRNA and miRNA. Bovine blood with ACD-A anticoagulant was deposited and stored in plastic microcentrifuge tubes at 21 or 4°C and tested over different timepoints spanning 1 week. Total RNA was extracted from each sample and analyzed using automated high sensitivity gel electrophoresis. Nine RNA metrics were visually assessed and quantified using linear and mixed models. The RNA Integrity Number equivalent (RINe) and DV200 were not influenced by the addition of anticoagulant and demonstrated strong negative trends over time. The RINe model fit was high (R²  = 0.60), and while including the biological replicate as a random effect increased the fit for all RNA metrics, no significant differences were found between biological replicates stored at the same temperature for the RINe and DV200. This suggests that these standardized metrics can be directly compared between scenarios and individuals, with DV200 having an inflection point at approximately 28 h. This study provides a novel approach for blood TSD research, revealing metrics that are not affected by inter-individual variation, and improving our understanding of the rapid RNA degradation occurring in bloodstains.

The life and death of RNA across temperatures

Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans. We illustrate the temperature dependence of RNA metabolism with examples from the synthesis to the degradation of mRNAs, and review recently emerged questions. Are cells exposed to greater temperature variations and gradients than previously surmised? How do cells reconcile the conflicting thermal stability requirements of primary and tertiary structures of RNAs? To what extent do enzymes contribute to the temperature compensation of the reaction rates in mRNA turnover by lowering the energy barrier of the catalyzed reactions? We conclude with the ecological, forensic applications of the temperature-dependence of RNA degradation and the biotechnological aspects of mRNA vaccine production.

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.

Evaluating the performance of five up-to-date DNA/RNA co-extraction methods for forensic application

The importance of RNA evidence is growing with new developments in RNA profiling methods and purposes. As forensic samples often can be of small quantity, extraction methods with high yields of both DNA and RNA are desirable. In order to identify the optimal DNA/RNA co-extraction workflow for forensic samples, we evaluated the performance of three frequently-used methods, two new approaches for DNA/RNA co-extraction and a manual phenol/chloroform RNA-only extraction method on blood and saliva samples. Based on a comprehensive analysis of the RNA and DNA quantities, as well as the STR genotyping and mRNA profiling results, we conclude that the two frequently-used co-extraction methods, combining commercially available DNA and RNA extraction kits, achieved the best performance. However, not any combination of commercially available DNA and RNA extraction kits works well and extensive optimization is necessary, as seen in the poor results of the two new approaches.

Post deposition aging of bloodstains probed by steady-state fluorescence spectroscopy

Blood is one of the most common body fluids discovered at crime scenes involving violent actions. It is one of the most important types of forensic evidence since it allows for the identification of the individual providing that there is a match with a known DNA profile. Determining the time since deposition (TSD) can assist investigators in establishing when the crime occurred or if a bloodstain present is actually related to the investigated event. To develop a forensically sound method for determining the TSD of a bloodstain, it is necessary to understand the underlying biochemical mechanisms occurring during aging. As biochemical processes occurring in blood are necessary for the continued survival of living organisms, they are important subjects of human biology and biomedicine and are well understood. However, the biochemistry of bloodstain aging ex vivo is primarily of interest to forensic scientists and has not yet been thoroughly researched. This preliminary study utilizes steady-state fluorescence spectroscopy to probe the changes in fluorescence properties of peripheral and menstrual blood up to 24-h post deposition. Peripheral and menstrual blood exhibited similar kinetic changes over time, assigned to the presence of the fluorophores: tryptophan, nicotinamide adenine dinucleotide (NADH), and flavins in both biological fluids. The biochemical mechanism of blood aging ex vivo is discussed.

Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study

Information on the time when a stain was deposited at a crime scene can be valuable in forensic investigations. It can link a DNA-identified stain donor with a crime or provide a post-mortem interval estimation in cases with cadavers. The available methods for estimating stain deposition time have limitations of different types and magnitudes. In this proof-of-principle study we investigated for the first time the use of microbial DNA for this purpose in human saliva stains. First, we identified the most abundant and frequent bacterial species in saliva using publicly available 16S rRNA gene next generation sequencing (NGS) data from 1,848 samples. Next, we assessed time-dependent changes in 15 identified species using de-novo 16S rRNA gene NGS in the saliva stains of two individuals exposed to indoor conditions for up to 1 year. We selected four bacterial species, i.e., Fusobacterium periodonticum, Haemophilus parainfluenzae, Veillonella dispar, and Veillonella parvula showing significant time-dependent changes and developed a 4-plex qPCR assay for their targeted analysis. Then, we analyzed the saliva stains of 15 individuals exposed to indoor conditions for up to 1 month. Bacterial counts generally increased with time and explained 54.9% of the variation (p = <2.2E–16). Time since deposition explained ≥86.5% and ≥88.9% of the variation in each individual and species, respectively (p = <2.2E–16). Finally, based on sample duplicates we built and tested multiple linear regression models for predicting the stain deposition time at an individual level, resulting in an average mean absolute error (MAE) of 5 days (ranging 3.3–7.8 days). Overall, the deposition time of 181 (81.5%) stains was correctly predicted within 1 week. Prediction models were also assessed in stains exposed to similar conditions up to 1 month 7 months later, resulting in an average MAE of 8.8 days (ranging 3.9–16.9 days). Our proof-of-principle study suggests the potential of the DNA profiling of human commensal bacteria as a method of estimating saliva stains time since deposition in the forensic scenario, which may be expanded to other forensically relevant tissues. The study considers practical applications of this novel approach, but various forensic developmental validation and implementation criteria will need to be met in more dedicated studies in the future.

Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers

Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples.

Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces

Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation.

Ten years of molecular ballistics-a review and a field guide

Molecular ballistics combines molecular biological, forensic ballistic, and wound ballistic insights and approaches in the description, collection, objective investigation, and contextualization of the complex patterns of biological evidence that are generated by gunshots at biological targets. Setting out in 2010 with two seminal publications proving the principle that DNA from backspatter collected from inside surfaces of firearms can be retreived and successfully be analyzed, molecular ballistics covered a lot of ground until today. In this review, 10 years later, we begin with a comprehensive description and brief history of the field and lay out its intersections with other forensic disciplines like wound ballistics, forensic molecular biology, blood pattern analysis, and crime scene investigation. In an application guide section, we aim to raise consciousness to backspatter traces and the inside surfaces of firearms as sources of forensic evidence. Covering crime scene practical as well as forensic genetic aspects, we introduce operational requirements and lay out possible procedures, including forensic RNA analysis, when searching for, collecting, analyzing, and contextualizing such trace material. We discuss the intricacies and rationales of ballistic model building, employing different tissue, skin, and bone simulants and the advantages of the “triple-contrast” method in molecular ballistics and give advice on how to stage experimental shootings in molecular ballistic research. Finally, we take a look at future applications and prospects of molecular ballistics.

Forensic transcriptome analysis using massively parallel sequencing

The application of transcriptome analyses in forensic genetics has experienced tremendous growth and development in the past decade. The earliest studies and main applications were body fluid and tissue identification, using targeted RNA transcripts and a reverse transcription endpoint PCR method. A number of markers have been identified for the forensically most relevant body fluids and tissues and the method has been successfully used in casework. The introduction of Massively Parallel Sequencing (MPS) opened up new perspectives and opportunities to advance the field. Contrary to genomic DNA where two copies of an autosomal DNA segment are present in a cell, abundant RNA species are expressed in high copy numbers. Even whole transcriptome sequencing (RNA-Seq) of forensically relevant body fluids and of postmortem material was shown to be possible. This review gives an overview on forensic transcriptome analyses and applications. The methods cover whole transcriptome as well as targeted MPS approaches. High resolution forensic transcriptome analyses using MPS are being applied to body fluid/ tissue identification, determination of the age of stains and the age of the donor, the estimation of the post-mortem interval and to post mortem death investigations.

The effect of environmental conditions on the rate of RNA degradation in dried blood stains

The relationship between RNA degradation and the age of a bloodstain has been suggested by the work of several investigators. A prior study from this laboratory described a qPCR assay that was effective at estimating the age of bloodstains stored in an environmentally controlled laboratory for periods of up to one year. In this study, the effect of the environmental conditions on the rate of RNA degradation during storage was analyzed. Bloodstains were prepared on stain cards and stored in one of 9 different environments for periods of up to 24 weeks. At selected times during the storage term, RNA was extracted, reverse transcribed, and the integrity of select transcripts analyzed. Three temperatures (37 °C, 20 °C, and 4 °C) and three relative humidities (rH) (75 %, 35 %, and 10 %) were combined pairwise. The rate of RNA degradation was found to increase 5-10 fold in stains stored at 37 °C versus those stored at 20 °C. The rate of RNA degradation was faster for stains stored at 20 °C compared to 4 °C but differed only 2-4 fold. Multivariate regression analysis suggests elevations in temperature or rH will accelerate RNA degradation and will do so to a similar extent. It is clear from the data that the integrity of the transcriptome in dried bloodstains is better preserved in a cold and dry environment. Investigations are ongoing to develop an approach for the estimation of sample age that incorporates the environmental conditions of a crime scene into the age estimate.