Applicability of the ParaDNA® Screening System to Seminal Samples

Seminal fluid represents a common biological material recovered from sexual assault crime scenes. Such samples can be prescreened using different techniques to determine cell type and relative amount before submitting for full STR profiling. The ParaDNA^® Screening System is a novel forensic test which identifies the presence of DNA through amplification and detection of two common STR loci (D16S539 and TH01) and the Amelogenin marker. The detection of the Y allele in samples could provide a useful tool in the triage and submission of sexual assault samples by enforcement authorities. Male template material was detected on a range of common sexual assault evidence items including cotton pillow cases, condoms, swab heads and glass surfaces and shows a detection limit of 1 in 1000 dilution of neat semen. These data indicate this technology has the potential to be a useful tool for the detection of male donor DNA in sexual assault casework.     

A search for obligatory paternal alleles in a DNA database to find an alleged rapist in a fatherless paternity case

Abstract: A sexual assault case resulted in a pregnancy, which was subsequently aborted. The alleged father of the fetus was unknown. Maternal and fetal types were obtained using the 11‐locus AmpF?STR^® SGM Plus^® kit. The national DNA database was searched for the paternal obligatory alleles and detected two suspects who could not be excluded as father of the male fetus. Additional typing using the AmpF?STR^® Minifiler^? kit, containing three additional autosomal loci, was not sufficient to exclude either suspect. Subsequent typing using the PowerPlex^® 16, containing four additional loci, and Y‐Filer^? kits resulted in excluding one suspect. Searching a database for paternal obligatory alleles can be fruitful, but is fraught with possible false positive results so that finding a match must be taken as only preliminary evidence.     

A comparative study of two extraction methods routinely used for DNA recovery from simulated post coital samples

In sexual assault cases DNA profiling of spermatozoa can be of critical importance. Most methods use differential extraction of the spermatozoa to separate it from the female component. Here we have compared two commercially available differential extraction methods, the QIAamp^® DNA mini kit (Qiagen) and Differex™ with the DNA IQ^® System (Promega). Simulated postcoital samples were prepared using buccal cells from a female donor and spermatozoa from three male donors. A dilution series ranging from neat semen to a 1:1500 dilution (semen:dH₂O) was prepared and mixed with an equal volume of saliva from a female donor. Extraction efficiency was assessed using DNA concentration measured with NanoDrop 2000 and Quantifiler^® Human DNA Quantification Kit and the profile count of full, partial and mixed DNA profiles generated using SGM Plus and PowerPlex^® ESI 17. Statistical analysis was carried out using Randomisation in R, which is a robust model making no assumption of the distribution of data. Based on the amount of DNA extracted and the types of profiles no significant difference in the performance of the two extraction kits was seen. However, the processing time taken with the Differex™ System was about half than that of the QIAamp^® DNA mini kit and involved fewer liquid transfers.     

An Accelerated Analytical Process for the Development of STR Profiles for Casework Samples

Significant efforts are being devoted to the development of methods enabling rapid generation of short tandem repeat (STR) profiles in order to reduce turnaround times for the delivery of human identification results from biological evidence. Some of the proposed solutions are still costly and low throughput. This study describes the optimization of an analytical process enabling the generation of complete STR profiles (single‐source or mixed profiles) for human identification in approximately 5 h. This accelerated process uses currently available reagents and standard laboratory equipment. It includes a 30‐min lysis step, a 27‐min DNA extraction using the Promega Maxwell^®16 System, DNA quantification in <1 h using the Qiagen Investigator^® Quantiplex HYres kit, fast amplification (<26 min) of the loci included in AmpF?STR^® Identifiler^®, and analysis of the profiles on the 3500‐series Genetic Analyzer. This combination of fast individual steps produces high‐quality profiling results and offers a cost‐effective alternative approach to rapid DNA analysis.     

Background Levels of Salivary-α-amylase Plus Foreign DNA in Cases of Oral Intercourse: a Female Perspective

Saliva plus DNA from a suspect is commonly encountered in sexual assault cases on bodily swabs. However, without background knowledge, the weight of this evidence is unknown. It may indicate the presence of saliva resulting from cunnilingus, or it may represent indirect transfer. In this study, females who refrained from cunnilingus donated 43 items of underwear and 19 vaginal swabs. The samples were subjected to Phadebas^®, RSID^™-Saliva and mRNA profiling and were subsequently DNA-profiled to determine the prevalence of background saliva in the female population. The results report that 15.8% of females who refrained from cunnilingus were positive for saliva and a further 10.5% also had DNA from unknown source(s). These findings of the rate of indirect transfer were evaluated with the Bayesian approach, and it was found that the evidence of saliva plus a high foreign DNA source adds moderately strong support to the allegation of cunnilingus.     

Discriminating Hodgdon Pyrodex® and Triple Seven® Using Gas Chromatography–Mass Spectrometry

Abstract: Pyrodex ^® and Triple Seven ^® are black powder substitutes that often find use as fillers in improvised explosive devices, such as pipe bombs. These propellants have essentially the same overall appearance and oxidizers, but different fuels. For example, Pyrodex ^® contains sulfur, sodium benzoate, and dicyandiamide (DCDA), whereas Triple Seven ^® lacks sulfur but also contains 3‐nitrobenzoic acid. In this method, intact particles and postblast solid residues were reacted with bis(trimethylsilyl)trifluoroacetamide + 1% trimethylchlorosilane in acetonitrile for 30 min at 60°C. The resultant trimethylsilyl derivatives of the organic fuels were then analyzed by gas chromatography–mass spectrometry. Each derivative was clearly resolved from other components, and high‐quality mass spectra were obtained. In addition, characteristic fragments resulting from loss of a methyl radical from the molecular ion (m/z 163 for sulfur, m/z 171 for DCDA, m/z 179 for benzoic acid, and m/z 224 for nitrobenzoic acid) were able to be monitored.     

Qiagen's Investigator™ Quantiplex Kit as a Predictor of STR Amplification Success from Low‐Yield DNA Samples,

Qiagen's Investigator? Quantiplex kit, a total human DNA quantitation kit, has a 200‐base pair internal control, fast cycling time, and scorpion molecules containing a covalently linked primer, probe, fluorophore, and quencher. The Investigator? Quantiplex kit was evaluated to investigate a value under which complete short tandem repeat (STR) failure was consistently obtained. Buccal swabs were extracted using the Qiagen QIAamp^® DNA Blood Mini Kit, quantified with the Investigator? Quantiplex kit using a tested half‐volume reaction, amplified with the ABI AmpFlSTR^® Identifiler kit, separated on the 3100Avant Genetic Analyzer, and data analyzed with GeneMapper^® ID v.3.2. While undetected samples were unlikely to produce sufficient data for statistical calculations or CODIS upload (2.00 alleles and 0.82 complete loci on average), data may be useful for exclusionary purposes. Thus, the Investigator? Quantiplex kit may be useful for predicting STR success. These findings are comparable with previously reported data from the Quantifiler? Human kit.     

Enhancing the Visibility of Injuries with Narrow‐Banded Beams of Light within the Visible Light Spectrum

The use of narrow‐banded visible light sources in improving the visibility of injuries has been hardly investigated, and studies examining the extent of this improvement are lacking. In this study, narrow‐banded beams of light within the visible light spectrum were used to explore their ability in improving the visibility of external injuries. The beams of light were induced by four crime‐lites^® providing narrow‐banded beams of light between 400 and 550 nm. The visibility of the injuries was assessed through specific long‐pass filters supplied with the set of crime‐lites^®. Forty‐three percent of the examined injuries improved in visibility by using the narrow‐banded visible light. In addition, injuries were visualized that were not visible or just barely visible to the naked eye. The improvements in visibility were particularly marked with the use of crime‐lites^® “violet” and “blue” covering the spectrum between 400–430 and 430–470 nm. The simple noninvasive method showed a great potential contribution in injury examination.     

Analyzing the Dynamics and Morphology of Cast‐off Pattern at Different Speed Levels Using High‐speed Digital Video Imaging

During a bloodstain pattern analysis, one of the essential tasks is to distinguish between different kinds of applied forces as well as to estimate their level of intensity. In this study, high‐speed digital imaging has been used to analyze the formation of cast‐off patterns generated by a simulated backswing with a blood‐bearing object. For this purpose, 0.5 mL blood was applied evenly over the last 5 cm of a blade simulant. Bloodstains were created through the controlled acceleration of a backswing at different speed levels between 1.1 m/sec and 3.8 m/sec. The flight dynamics of blood droplets were captured with an Olympus^® i‐Speed 3 high‐speed digital camera with a Nikon^® AF Nikkor 50 mm f/1.8 D lens and analyzed using the Olympus i‐Speed 3 Viewer software. The video analysis showed that, during the backswing, blood droplets would move toward the lower end of the knifepoint and would be tangentially thrown off. These droplets impacted on the horizontal surface according to the arc of the swing. An increase in velocity led to longer cast‐off patterns with distinct morphological characteristics. Under laboratory conditions, bloodstain pattern analysis allows certain conclusions about the intensity of a backswing and provides instructions on the position of the offender. However, due to the number of unknown variables at a crime scene, such interpretation of cast‐off patterns is extremely limited and should be performed with extreme caution.     

Effects of histological staining on the analysis of human DNA from archived slides

Abstract: Archived slides of cell smears treated with histological stains for sperm detection are often the only source of DNA available when cold cases are reopened. There have been conflicting reports as to the negative effects of particular histological stains on DNA recovery and quality from human cells, making stain selection an important consideration for forensic laboratories. This study investigates the effect of several staining systems on DNA recovery from histological slide samples stored from 0 to 10 weeks. DNA profiles obtained after analysis of these samples with AmpFlSTR^® Identifiler? and increased cycle AmpFlSTR^® SGM Plus? short tandem repeat (STR) profiling systems and the effects that these stains have on DNA quantity and quality over time are described. Results indicate that Christmas Tree and Hematoxylin and Eosin stains do not have significantly different effects on DNA quality after 10‐week storage of slides. This research will assist scientists to select staining systems that have minimal deleterious effects on the DNA recovered.     

STR Genotyping from a Dry‐Cleaned Skirt in a Sexual Assault Case

In this sexual assault case, the standard preliminary semen examinations could not confirm physically or biochemically whether the accused's semen had stained the victim's skirt because the skirt had been dry‐cleaned for stain removal and had been worn for more than a year after the assault. Fortunately, however, a photograph taken just after the assault was found in the court records that showed white stains on the checkered skirt. The locations of the stains were estimated based on the checkered pattern of the fabric, and microscopic examination using Baecchi's staining revealed the presence of spermatozoa. Further analysis indicated the male DNA profile generated from the sperm cells was consistent with the suspect's DNA using three multiplex STR typing systems for a total of 21 autosomal and 17 Y chromosomal short tandem repeats (STRs). Ultimately, the result of the DNA profile played a very useful role as additional evidence.     

Gender Determination of Adult Individuals by Three‐Dimensional Modeling of Canines

Gender determination is a fundamental issue in forensic anthropology. Many techniques based on bone and dental remains have been proposed. It is not always possible to implement the techniques using bones, but teeth are often perfectly preserved. It has been demonstrated that the canine has the greatest sexual dimorphism, and the aim of this work was to provide an easy and accurate dental technique for determining the gender in the absence of other skeletal elements. The sample was composed of 210 CT scans with four healthy canines. The 840 canines were modeled using MIMICS^® 10.01 software. The total volume of each tooth was determined. Seven mathematical models were determined by binary logistic regressions and ranked in order of relative performance. The seven proposed predictive models thus performed (0.910 ≤ AUC ≤ 0.938), with overall rates of correct predictions between 82.38 and 85.24%. The 4‐canine model is the most powerful for predicting the gender.     

Powdered Activated Carbon: An Alternative Approach to Genomic DNA Purification

Forensic evidence samples are routinely found as stains on various substrates, which may contain substances known to inhibit polymerase chain reaction (PCR). The goal of this study was to evaluate post‐Chelex^®100 purification using powdered activated carbon (PAC). Mock crime scene DNA extracts were analyzed using quantitative PCR and short tandem repeat (STR) profiling to test the DNA recovery and inhibitor removal using PAC with those of the Amicon^®Ultra 100K. For extracted bloodstains on soil and wood substrates, PAC and Amicon^®Ultra 100K generated similar DNA yield and quality. Moreover, the two methods significantly decreased the concentration of humic substances and tannins compared to nonpurified extracts (p < 0.001). In instances where extracts contained indigo dye (bloodstains on denim), Amicon^®Ultra 100K performed better than PAC due to improved amplifiability. Efficient adsorption of humic substances and tannins, which are common inhibitors, indicates PAC's potential application in the purification of high‐template DNA extracts.     

Detection and Identification of Psilocybe cubensis DNA Using a Real‐Time Polymerase Chain Reaction High Resolution Melt Assay,

Psilocybe cubensis, or “magic mushroom,” is the most common species of fungus with psychedelic characteristics. Two primer sets were designed to target Psilocybe DNA using web‐based software and NBCI gene sequences. DNA was extracted from eighteen samples, including twelve mushroom species, using the Qiagen DNeasy^® Plant Mini Kit. The DNA was amplified by the polymerase chain reaction (PCR) using the primers and a master mix containing either a SYBR^® Green I, Radiant? Green, or LCGreen Plus^® intercalating dye; amplicon size was determined using agarose gel electrophoresis. The PCR assays were tested for amplifiability, specificity, reproducibility, robustness, sensitivity, and multiplexing with primers that target marijuana. The observed high resolution melt (HRM) temperatures for primer sets 1 and 7 were 78.85 ± 0.31°C and 73.22 ± 0.61°C, respectively, using SYBR^® Green I dye and 81.67 ± 0.06°C and 76.04 ± 0.11°C, respectively, using Radiant? Green dye.     

A rapid wire-based sampling method for DNA profiling

Abstract: This paper reports the results of a commission to develop a field deployable rapid short tandem repeat (STR)‐based DNA profiling system to enable discrimination between tissues derived from a small number of individuals. Speed was achieved by truncation of sample preparation and field deployability by use of an Agilent 2100 Bioanalyser^TM. Human blood and tissues were stabbed with heated stainless steel wire and the resulting sample dehydrated with isopropanol prior to direct addition to a PCR. Choice of a polymerase tolerant of tissue residues and cycles of amplification appropriate for the amount of template expected yielded useful profiles with a custom‐designed quintuplex primer set suitable for use with the Bioanalyser^TM. Samples stored on wires remained amplifiable for months, allowing their transportation unrefrigerated from remote locations to a laboratory for analysis using AmpFlSTR^® Profiler Plus^® without further processing. The field system meets the requirements for discrimination of samples from small sets and retains access to full STR profiling when required.     

The Use of Forensic Tests to Distinguish Blowfly Artifacts from Human Blood,Semen, and Saliva

This study investigated whether routinely used forensic tests can distinguish 3‐day‐old or 2‐week‐old fly artifacts, produced after feeding on human blood, semen, or saliva, from the biological fluid. Hemastix^®, Hemident^?, and Hemascein^? were unable to distinguish blood from artifacts. Hemastix^® returned false positives from negative controls. ABAcard^® Hematrace^® and Hexagon OBTI could distinguish blood from 3‐day‐old artifacts, but not 2‐week‐old artifacts. Phadebas^® and SALIgAE^® were unable to distinguish saliva from artifacts. RSID^?‐Saliva was able to distinguish saliva from 3‐day‐old artifacts, but not 2‐week‐old artifacts. Semen tests Seminal Acid Phosphatase, RSID^?‐Semen, and ABAcard^® p30 were all able to distinguish semen from 3‐day‐old artifacts, but not 2‐week‐old artifacts. The tests investigated cannot be relied upon to distinguish artifacts from biological fluids. However, if an artifact is identified by its morphology, a positive result may indicate which biological fluid the fly consumed, and this knowledge may prove useful for investigators searching for DNA.     

A Comparison of Chemical Enhancements for the Detection of Latent Blood,,

Luminol, Bluestar^®, and Hemascein^® were tested to compare detection sensitivities to latent blood. Untreated, EDTA‐treated human blood, and a catalytically similar blood substitute were diluted (neat to 1:1,000,000) and pipetted onto a variety of substrates. Luminol and Bluestar^® performed similarly on all surfaces and fabrics. Hemascein^® yielded poor results on wood surfaces, but performed well in the detection of latent blood on fabrics. Results from untreated, EDTA‐treated, and synthetic blood results indicate that EDTA‐treated blood is similar or slightly less sensitive than untreated blood at all dilutions and on all substrates, and the synthetic blood is less sensitive than real blood, but consistent in detection threshold and thus is useful as a training aid. Additionally, some foods and household chemicals that have previously been shown to cross‐react were tested with Bluestar^®, Hemascein^®, and luminol. Hemascein^® cross‐reacted with many substances, while both luminol reagents were more discriminating.     

A Y‐Chromosomal Haplotype with Two Short Tandem Repeat Mutations*

Abstract:  The male‐specific Y‐chromosomal short tandem repeat (STR) is a useful tool in forensic casework. The Y haplotype comprised of 16 loci, which is amplified simultaneously by AmpFlSTR^® Yfiler^TM PCR kit and provides strong exculpatory evidence in individual identification. We reported a rare Y‐STR profile with a null allele at the DYS448 locus and an off‐ladder allele at the DYS456 locus, when genotyping material from a vaginal swab in an alleged rape case. Sequence analysis revealed that the DYS448 null allele was a true type of null allele because of a total deletion of 11 upstream repeats and 9 bp of the N₄₂ region, and there were numerous primer binding site mutations as well. The amplicon of the DYS456 locus was a small 92‐bp fragment that was off‐ladder, and sequencing analysis showed that there were only 10 repeats (AGAT)₁₀. This Y chromosome haplotype that was comprised of two variations provided helpful evidence for personal identification.     

Differential predictors of intimate partner sexual coercion versus physical assault perpetration

ABSTRACT

The current study attempted to strengthen existing literature regarding predictors of perpetrating intimate partner sexual violence to determine if there are unique predictors of sexual violence that differentiate it from physical abuse. It was hypothesised that men’s controlling, dominant and jealousy behaviours, and verbal aggression would significantly predict increased intimate partner sexual coercion and physical assault perpetration. These predictors were expected to be more predictive of sexual coercion than physical assault perpetration. Couples were recruited from the community (N?=?159) in a cross-sectional study recruiting couples with a violent male partner. Results demonstrated that men’s controlling behaviour was a significant predictor of sexual coercion and physical assault perpetration and behavioural jealousy was a significant predictor of sexual coercion perpetration. No predictors studied better predicted sexual coercion more than physical assault perpetration. These findings suggest that sexual coercion may be another type of physical assault without unique predictors.     

An Investigation of PCR Inhibition Using Plexor®‐Based Quantitative PCR and Short Tandem Repeat Amplification

A common problem in forensic DNA typing is PCR inhibition resulting in allele dropout and peak imbalance. In this paper, we have utilized the Plexor^® real‐time PCR quantification kit to evaluate PCR inhibition. This is performed by adding increasing concentrations of various inhibitors and evaluating changes in melt curves and PCR amplification efficiencies. Inhibitors examined included calcium, humic acid, collagen, phenol, tannic acid, hematin, melanin, urea, bile salts, EDTA, and guanidinium thiocyanate. Results were plotted and modeled using mathematical simulations. In general, we found that PCR inhibitors that bind DNA affect melt curves and C_T takeoff points while those that affect the Taq polymerase tend to affect the slope of the amplification curve. Mixed mode effects were also visible. Quantitative PCR results were then compared with subsequent STR amplification using the PowerPlex^® 16 HS System. The overall results demonstrate that real‐time PCR can be an effective method to evaluate PCR inhibition and predict its effects on subsequent STR amplifications.