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.     

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.     

Fentanyl transdermal patches: Extraction and evaluation of a novel disposal method using NarcX®

Currently, there is no known commercially available product for disposing of used fentanyl transdermal patches. To eliminate the potential for harm and abuse, a proper disposal method is needed–one that neutralizes the dangerous amount of residual fentanyl that remains after therapeutic use of the fentanyl patch. The patent-pending liquid solution of activated carbon, known as NarcX^®, was investigated as a potential fentanyl adsorbing agent. In order to determine the amount of fentanyl remaining after a patch is treated with NarcX^®, here, we utilized hexanes to first dissolve the patch adhesive and then followed with liquid-liquid extraction with methanol to recover the fentanyl. Using liquid chromatography coupled to tandem mass spectrometry (LC/MS-MS), the extracts obtained with this method yielded between 85% and 117% recovery of fentanyl from new and unused patches. Further optimization of this method allowed for a quantitative evaluation of NarcX^®-treated fentanyl patches. 100 µg/h Apotex brand fentanyl patches were exposed to NarcX^® for 1, 24, 48, and 72 h. NarcX^® was shown to adsorb fentanyl from the patches with varying degrees of success, demonstrating an average of 66.98 ± 0.75% fentanyl adsorption after 72 h. These findings suggest that more work is needed to successfully neutralize the fentanyl patches in their entirety using NarcX^®; however, this work does demonstrate proof of concept.     

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.     

The Effect of Household Oxidizing Cleaners on Chemiluminescence of Blood Using Bluestar®

This study tests the effect of three common oxidizing cleaners on the ability of the Bluestar Forensic® presumptive test for blood to identify the presence of blood on ceramic tile after cleaning. The cleaners tested were Lysol®, OxiClean®, and Arm & Hammer®. This study also tested which cleaner was the most effective at removing blood, measured by the intensity of chemiluminescence, which was quantified using RGB values in ImageJ. A “hasty” 1‐min cleaning of a blood droplet was simulated using the three cleaners. The chemiluminescence of the Bluestar® reactions after cleaning the blood‐treated region was compared to an untreated region of the same tile for each cleaner, as well as to the treated regions of tiles between the three cleaners. Results indicate that none of the three cleaners removed all of the blood (all p < 0.001) and that Lysol® removed more blood compared to the OxiClean® and Arm & Hammer®.     

Internal Validation of RapidHIT®ID ACE Sample Cartridge and Assessment of the EXT Sample Cartridge*†

A new rapid DNA solution, the RapidHIT^®ID, can accommodate two different sample cartridges, ACE, for the analysis of a single swab and EXT, for the analysis of DNA extracts. An efficient internal validation designed for low‐throughput rapid DNA is described. An evaluation of the EXT sample cartridge is also described. Each cartridge generated profiles with sufficient data quality to meet CODIS eligibility in fewer than 120 min. The results exhibited 100% correlation when compared to conventional DNA typing methods. Precision, reproducibility, stochastic, mixture, and contamination experiments produced expected results. Sensitivity of the ACE sample cartridge was acceptable for buccal swab analysis. The sensitivity of the EXT sample cartridge is discussed. The ACE validation and the EXT evaluation utilized a minimalist, cost‐saving, efficient design to generate a validated RapidHIT^®ID instrument capable of producing genetic profiles from both extracted forensic DNA samples and buccal swab samples within 120 min.     

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.     

Differentiation of Twenty‐One Glitter Lip‐Glosses by Pyrolysis Gas Chromatography/Mass Spectroscopy*

Abstract: Differentiation of 21 glitter lip‐glosses from seven manufacturers was attempted by pyrolysis gas chromatography/mass spectroscopy. Samples were pyrolyzed on a ribbon probe at 800°C for 20 sec and analyzed with an Agilent^® 6890N Network GC System and Agilent^® 5973 Network Mass Selective Detector with MSD Productivity ChemStation^® Data Analysis software. The total ion chromatograms obtained were examined and differences in the presence or absence of certain chromatographic peaks corresponding to certain pyrolysis products (e.g., styrene, cyclohexane) noted. In cases where the total ion chromatograms between lip‐glosses were similar, select ion profiling was performed. Of the 21 lip‐glosses, 15 were differentiated by either the total ion chromatograms alone or through select ion profiling. Considering that lip‐glosses are typically worn by young women (who are disproportionately victims of sexual assault), this study offers the potential of being able to provide investigative leads in sexual assault investigations with evidentiary samples of this kind.     

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.     

Manual and Automated Cardiopulmonary Resuscitation (CPR): A Comparison of Associated Injury Patterns,

The purpose of this study was to identify and compare patterns of trauma associated with AutoPulse^® CPR and manual CPR. Finalized autopsy records from 175 decedents brought to the Harris County Institute of Forensic Sciences were reviewed, 87 received manual‐only CPR, and 88 received AutoPulse^® CPR (in combination with manual CPR as per standard protocol). The characteristic pattern observed in manual‐only CPR use included a high frequency of anterior rib fractures, sternal fractures, and midline chest abrasions along the sternum. The characteristic pattern observed in AutoPulse^® CPR use included a high frequency of posterior rib fractures, skin abrasions located along the anterolateral chest and shoulder, vertebral fractures, and a few cases of visceral injuries including liver lacerations, splenic lacerations, and hemoperitoneum. Knowledge of the AutoPulse^® CPR injury pattern can help forensic pathologists differentiate therapeutic from inflicted injuries and therefore avoid an erroneous assessment of cause and manner of death.     

Validation of a DNA Quantitation Method on the Biomek® 3000

Abstract: Laboratory automation has the ability to increase the throughput and efficiency of laboratory processes to keep pace with current backlogs and requests for analysis. This paper addresses the specific studies employed to properly evaluate an automated method for DNA quantitation setup using Applied Biosystems Quantifiler? Human DNA Quantification kit on a Biomek^® 3000. The calibration of robotic pipetting as well as comparison with manually performed steps confirmed the accuracy of the automated methods used. Reproducibility studies evaluated differences between robotic and manually prepared human DNA standard curves. Additional studies examined DNA samples of known quantities, extract storage formats, sensitivity, and an assessment of contamination. The Biomek^® 3000 not only demonstrated reproducibility and accuracy that equaled or surpassed the manual method but also revealed a contamination‐free method to replace the multiple pipetting steps required during quantitation setup.     

Analysis of Δ-tetrahydrocannabinol in oral fluid samples using solid-phase extraction and high-performance liquid chromatography–electrospray ionization mass spectrometry

An analytical method using solid-phase extraction (SPE) and high-performance liquid chromatography–mass spectrometry (LC–MS) has been developed and validated for the confirmation of Δ⁹-tetrahydrocannabinol (THC) in oral fluid samples. Oral fluid was extracted using Bond Elut LRC-Certify solid-phase extraction columns (10 cm³, 300 mg) and elution performed with n-hexane/ethyl acetate. Quantitation made use of the selected ion-recording mode (SIR) using the most abundant characteristic ion [THC + H⁺], m/z 315.31 and the fragment ion, m/z 193.13 for confirmation, and m/z 318.00 for the protonated internal standard, [d₃-THC + H⁺]. The method proved to be precise for THC, in terms of both intra-day and inter-day analyses, with coefficients of variation less than 10%, and the calculated extraction efficiencies for THC ranged from 76 to 83%. Calibration standards spiked with THC between 2 and 100 ng/mL showed a linear relationship (r² = 0.999). The method presented was applied to the oral fluid samples taken from the volunteers during the largest music event in Portugal, named Rock in Rio-Lisboa. Oral fluid was collected from 40 persons by expectoration and with Salivette^®. In 55% of the samples obtained by expectorating, THC was detected with concentration ranges from 1033 to 6552 ng/mL and in 45% of cases THC was detected at concentrations between 51 and 937 ng/mL. However, using Salivette^® collection, 26 of the 40 cases had an undetectable THC.     

Genetic Identification of Communist Crimes’ Victims (1944–1956) Based on the Analysis of One of Many Mass Graves Discovered on the Powazki Military Cemetery in Warsaw,Poland

As the result of the communist terror in Poland, during years 1944–1956 more than 50,000 people died. Their bodies were buried secretly, and most places are still unknown. The research presents the results of identification of people buried in one of many mass graves, which were found at the cemetery Pow?zki Military in Warsaw, Poland. Exhumation revealed the remains of eight people, among which seven were identified genetically. Well‐preserved molars were used for the study. Reference material was collected from the closest living relatives. In one case, an exhumation of victim's parents had to be performed. DNA from swabs was extracted with a PrepFiler^® BTA Forensic DNA Extraction Kit and organic method. Autosomal, Y‐STR amplification, and mtDNA sequencing were performed. The biostatistical calculations resulted in LR values from 1608 to 928 × 10¹⁸. So far, remains of more than 50 victims were identified.     

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.     

SNP Miniplexes for Individual Identification of Random‐Bred Domestic Cats

Phenotypic and genotypic characteristics of the cat can be obtained from single nucleotide polymorphisms (SNPs) analyses of fur. This study developed miniplexes using SNPs with high discriminating power for random‐bred domestic cats, focusing on individual and phenotypic identification. Seventy‐eight SNPs were investigated using a multiplex PCR followed by a fluorescently labeled single base extension (SBE) technique (SNaPshot^®). The SNP miniplexes were evaluated for reliability, reproducibility, sensitivity, species specificity, detection limitations, and assignment accuracy. Six SNPplexes were developed containing 39 intergenic SNPs and 26 phenotypic SNPs, including a sex identification marker, ZFXY. The combined random match probability (cRMP) was 6.58 × 10^?19 across all Western cat populations and the likelihood ratio was 1.52 × 10¹⁸. These SNPplexes can distinguish individual cats and their phenotypic traits, which could provide insight into crime reconstructions. A SNP database of 237 cats from 13 worldwide populations is now available for forensic applications.     

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.     

Determining an Optimal Sequence for Chemical Development of Latent Prints on Cartridge Casings and Shotgun Shells*,†

Abstract: In developing latent prints on cartridge casings and shotgun shells, multiple chemical processes should be used in order to obtain the best results. In Phase I, this study established an optimal chemical sequence for both Brass and Nickel cartridge casings based on six sequences involving four chemicals: Cyanoacrylate, Black Powder, Rhodamine 6G and Acidified Hydrogen Peroxide. Phase II was a validation study of Phase I involving a random sample of both Brass and Nickel cartridge casings, which were processed according to the determined optimal sequences. In addition, ribbed shotgun shells were processed under Phase I results and determined to be dependent upon the utilization of a CrimeScope at 515 nm. Consideration should be given to the type of cartridge case being examined. Although limitations exist, some chemical sequences undeniably work better than others. All photographs were manipulated with Adobe^® Photoshop^®. All results were verified by a senior latent print examiner.     

Embutramide,a Component of Tanax®(T‐61) as a New Drug of Abuse?

Tanax^®(T‐61) is a euthanasia solution commonly used in veterinary medicine in Europe. It consists of three active components: embutramide, mebezonium iodide, and tetracaine hydrochloride. Human consumption of Tanax^®(T‐61) is usually associated with suicide attempts. In our 15‐year‐long practice, embutramide was detected only three times but within a short period. First, it was found in the urine of a 42‐year‐old veterinarian, and the other two observations were made in a 16‐year‐old young man. Urine samples were analyzed using Shimadzu Prominence TOX.I.S.II. HPLC–DAD system with online SPE extraction system. Both of the two patients denied any intention to die. These cases show that this veterinary drug may also be considered as potential drugs of abuse.     

False Positives Observed on the Seratec® PSA SemiQuant Cassette Test with Condom Lubricants

Abstract: In the course of the validation of a new component of the prostate‐specific antigen (PSA) SemiQuant Cassette Test marketed by Seratec^®, a false‐positive reaction was observed when testing samples collected from the surface of unused, lubricated condoms. A variety of personal lubricants and condoms were tested to determine the frequency of the false positive, as well as its potential source. Samples were extracted in both water and the manufacturer‐provided buffer, and the test was performed according to the manufacturer’s suggested protocol. The false positive was observed intermittently, but occurred consistently with samples containing nonoxynol‐9, a strong detergent utilized as a spermicide. The reaction may be attributable to the combination of latex and nonoxynol‐9. Because of the unreliability of the test to confirm the presence of PSA in samples collected from condoms, the PSA cassette is an unsuitable method for confirming the presence of seminal fluid in condoms.     

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.