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.     

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.     

Comparison of Catalytic and Immunological Amylase Tests for Identifying of Saliva from Degraded Samples

The stability of salivary α‐amylase is a critical factor in both catalytic and immunological method‐based forensic saliva identification. This study aimed to assess the sensitivity of catalytic and immunological tests on degraded saliva samples. Degraded saliva stains were prepared by microbial decomposition using humid soil. Salivary α‐amylase activity was catalytically detected both qualitatively and quantitatively using the Phadebas^® amylase test. As immunological methods, we conducted qualitative and quantitative tests using the RSID?‐saliva test and ELISA, respectively. Salivary α‐amylase activity of degraded samples (incubated at 37°C for 12 h) was significantly lower than that of controls in the quantitative tests. All the degraded samples obtained by the humid soil produced negative results in the Phadebas^® tests, but showed positive results in the RSID?‐saliva test and ELISA. These results suggest that immunological tests are effective for testing degraded saliva samples that have lost their enzymatic activity.     

Developmental Validation of RSID™-Saliva: A Lateral Flow Immunochromatographic Strip Test for the Forensic Detection of Saliva

Abstract:  Current methods for forensic identification of saliva generally assay for the enzymatic activity of α-amylase, an enzyme long associated with human saliva. Here, we describe the R apid S tain ID entification (RSID™-Saliva), a lateral flow immunochromatographic strip test that uses two antisalivary amylase monoclonal antibodies to detect the presence of salivary amylase, rather than the activity of the enzyme. We demonstrate that RSID™-Saliva is accurate, reproducible, and highly sensitive for human saliva; RSID™-Saliva detects less than 1 μL of saliva. The sensitivity of RSID^TM-Saliva allows investigators to sample a fraction of a questioned stain while retaining the majority for DNA-STR analysis. We demonstrate that RSID™-Saliva identifies saliva from a variety of materials (e.g., cans, bottles, envelopes, and cigarette-butts) and it does not cross-react with blood, semen, urine, or vaginal fluid. RSID™-Saliva is a useful forensic test for determining which evidentiary items contain saliva and thus may yield a DNA profile.     

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.     

The use of Hemastix® severely reduces DNA recovery using the BioRobot® EZ1

Abstract: The choice of reagents for presumptive tests for blood, and subsequent extraction methodologies, can significantly affect both the quantity and quality of purified DNA. Blood samples directly tested with Hemastix^® yielded <1% of the DNA recovered from untested samples when purified using the Qiagen BioRobot^® EZ1 and EZ1^® DNA Investigator kit. Full short tandem repeat profiles were obtained from both tested and untested samples, suggesting that the Hemastix^® reagent(s) affect DNA binding, rather than produce DNA damage. The Hemastix^® inhibition of DNA yield could be overcome by the addition of MTL buffer to the sample prior to extraction. Laboratories may wish to modify current procedures for extracting blood samples, utilize other extraction/purification methodologies, or inform their submitting agencies to avoid direct exposure of questioned bloodstains to Hemastix^® reagents.     

The sensitivity and specificity of the RSID™-saliva kit for the detection of human salivary amylase in the Forensic Science Laboratory,Dublin, Ireland

We demonstrate here that the RSID?-saliva test can be used as a test for human salivary α-amylase on samples routinely examined in forensic casework. We show that the RSID?-saliva test detects salivary α-amylase at lower concentrations than the Phadebas^® Quantitative test, that the RSID?-saliva test does not cross-react with forensically important human fluids and that the RSID?-saliva test can be successfully integrated into the whole swab semen extraction method.     

Screening Biological Stains with qPCR versus Lateral Flow Immunochromatographic Test Strips: A Quantitative Comparison using Analytical Figures of Merit

Biological fluid identification is an important facet of evidence examination in forensic laboratories worldwide. While identifying bodily fluids may provide insight into which downstream DNA methods to employ, these screening techniques consume a vital portion of the available evidence, are usually qualitative, and rely on visual interpretation. In contrast, qPCR yields information regarding the amount and proportion of amplifiable genetic material. In this study, dilution series of either semen or male saliva were prepared in either buffer or female blood. The samples were subjected to both lateral flow immunochromatographic test strips and qPCR analysis. Analytical figures of merit—including sensitivity, minimum distinguishable signal (MDS) and limit of detection (LOD)—were calculated and compared between methods. By applying the theory of the propagation of random errors, LODs were determined to be 0.05 μL of saliva for the RSID? Saliva cards, 0.03 μL of saliva for Quantifiler^® Duo, and 0.001 μL of semen for Quantifiler^® Duo. In conclusion, quantitative PCR was deemed a viable and effective screening method for subsequent DNA profiling due to its stability in different matrices, sensitivity, and low limits of detection.     

Detection and Identification of Kratom (Mitragyna speciosa) and Marijuana (Cannabis sativa) by a Real-Time Polymerase Chain Reaction High-Resolution Melt Duplex Assay,

Mitragyna speciosa (MS), a plant commonly known as kratom, is a widely used “legal high” opiate alternative for pain relief. DNA extracted from MS and 26 additional plant species was amplified by PCR using primers targeting the strictosidine beta-D-glucosidase (SGD) and secologanin synthase 2 (SLS2) genes and detected by high-resolution melt curves using three intercalating dyes. Amplicon sizes were confirmed using agarose gel electrophoresis. The observed melt temperatures for SGD and SLS2 were 77.08 ± 0.38°C and 77.61 ± 0.46°C, respectively, using SYBR^® Green I; 80.18 ± 0.27°C and 80.59 ± 0.08°C, respectively, using Radiant^™ Green; and 82.19 ± 0.04°C and 82.62 ± 0.13°C, respectively, using the LCGreen^® PLUS dye. The SLS2 primers demonstrated higher specificity and identified MS DNA at 0.05 ng/μL. In a duplex reaction, SLS2 and tetrahydrocannabinoic acid synthase gene primers detected and differentiated MS and Cannabis sativa (CS) by melt peaks at 82.63 ± 0.35°C and 85.58 ± 0.23°C, respectively, using LCGreen^® PLUS.     

PCR-based detection of salivary bacteria as a marker of expirated blood

Distinguishing between bloodstains caused by a spatter pattern or by expirated blood may be crucial to a forensic investigation. Expirated blood is likely to be contaminated with saliva but current techniques have limited sensitivity, especially with small bloodstains. We report that a PCR assay, designed to detect salivary bacteria, can amplify streptococcal DNA from saliva stains applied to fabrics for at least 62 days after seeding. Bacterial DNA was detected when 0.01 µl of saliva was present in the stain and the amplification was not affected by contamination with blood. These findings indicate that PCR amplification of salivary microbial DNA may have application in the identification of expirated bloodstains in forensic case-work.     

Post mortem markers of chronic alcoholism

We compared the post mortem diagnostic value of γ-glutamyltransferase (GGT), carbohydrate-deficient transferrin (CDT), alcoholic liver disease (ALD), blood alcohol concentration (BAC), the presence of multiple bruises and poor hygiene of the feet as markers of chronic alcoholism (heavy continuous drinking) in 32 alcoholics with 32 age-sex matched controls drawn from a forensic autopsy population. Alcoholics and controls were selected on the basis of positive and negative medical history but controls were excluded if BAC exceeded 70 mg%. Femoral venous blood, urine and vitreous humour alcohol concentrations were determined by headspace gas chromatography (GC). BAC was positive in 19 alcoholics (mean 234 mg%, range 2–570 mg%) and six controls (mean 32 mg%, range 2–52 mg%). Serum GGT was measured by a kinetic photometric method, and CDT by both isoelectric focusing/laser densitometry and by a commercial radioimmunoassay kit (CDTect^™). Features of alcoholic liver disease were graded histologically using two weighted scoring systems. Eleven alcoholics tested positive for GGT, CDTq and ALD, nine were positive for two tests, five for one test and three were negative for all three tests. No controls were positive for all three tests but six were positive for two tests and nine for only one test; 17 were negative for all three tests. Using the normal clinical cut-off values GGT, CDTq and CDTect^™ gave poor specificity which was improved at moderate cost to sensitivity by raising cut off values for each test. Comparison of receiver operating characteristic curves, likelihood ratios and post-test odds showed CDT to be the best individual test, followed by ALD and GGT. Quantitation of CDT by IEF/laser densitometry performed slightly better than MAEC/RIA by CDTect^™. CDT shows considerable promise as a post mortem marker of chronic alcoholism.     

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.     

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.     

Autosomal short tandem repeat analysis of ancient DNA by coupled use of mini- and conventional STR kits

Abstract: Multiplex autosomal short tandem repeat (STR) genotyping enables researchers to obtain genetic information from ancient human samples. In this study, we tested newly developed AmpF?STR^® MiniFiler? kit for autosomal STR analysis of ancient DNA (aDNA), using human femurs (n = 8) collected from medieval Korean tombs. After extracting aDNA from the bones, autosomal STR analyses were repeated for each sample using the AmpF?STR^® MiniFiler? and Identifiler? kits. Whereas only 21.87% of larger‐sized loci profiles could be obtained with the Identifiler? kit, 75% of the same loci profiles were determined by MiniFiler? kit analysis. This very successful amplification of large‐sized STR markers from highly degraded aDNA suggests that the MiniFiler? kit could be a useful complement to conventional STR kit analysis of ancient samples.     

Development and validation of the AmpFℓSTR® Identifiler® Direct PCR Amplification Kit: a multiplex assay for the direct amplification of single-source samples

Abstract: The AmpF?STR^® Identifiler^® Direct PCR Amplification Kit is a new short tandem repeat multiplex assay optimized to allow the direct amplification of single‐source blood and buccal samples on FTA^® card without the need for sample purification and quantification. This multiplex assay has been validated according to the FBI/National Standards and SWGDAM guidelines. Validation results revealed that slight variations in primer concentration, master mix component concentration, and thermal cycling parameters did not affect the performance of the chemistry. The assay’s sensitivity was demonstrated by amplifying known amounts of white blood cells spotted onto FTA^® cards, and the assay’s specificity was verified by establishing minimal cross‐reactivity with nonhuman DNA. No effect on the age of the sample stored on the FTA^® substrate was observed and full concordance was established in the population study. These findings of the validation study support the use of the Identifiler^® Direct Kit for forensic standards and database samples genotyping.     

Assessing the background levels of body fluids on hands

Forensic scientists are often asked to assist the court by evaluating the significance of finding body fluids on the hands of an individual; however, there is an absence of published data regarding the background levels of body fluids on hands. Whilst the scientist can use casework experience to inform the courts on the significance of the results, it would be advantageous to have data which could assist with this interpretation. This study was designed to ascertain the background levels of blood, semen, saliva, hairs/fibres and staining/debris on hands in the general population by sampling from delegates attending a scientific conference.The findings suggest that approximately one third of the population would be expected to have hairs or fibres on their hands and that females are more likely to have visible staining on their hands than males. Presumptive tests for blood and semen yielded negative results in all samples; however, almost 2 % of the samples were found to contain a very low number of sperm heads. In contrast, the majority of samples tested positive for the presence of saliva using the presumptive Phadebas® amylase test. The data supports the caution applied by forensic practitioners when evaluating the presence of saliva detected using the presumptive Phadebas® amylase test based on the lack of specificity and indicates that the RSID™-Saliva test would be more suitable to use.     

Developmental Validation of the PrepFiler™ Forensic DNA Extraction Kit for Extraction of Genomic DNA from Biological Samples*

Abstract: The PrepFiler? Forensic DNA Extraction Kit enables isolation of genomic DNA from a variety of biological samples. The kit facilitates reversible binding of DNA with magnetic particles resulting in high DNA recovery from samples with very low and high quantities of biological materials: 0.1 and 40 μL of human blood (donor 2) provided 14 and 2883 ng of DNA, respectively. Following the revised SWGDAM guidelines, performance of the developed method was investigated using different sample types including saliva on swabs, semen stains on cotton fabric, samples exposed to environment, samples with polymerase chain reaction (PCR) inhibitors, blood stains (on denim, cotton cloth, and FTA^® paper), and touch evidence‐type samples. DNA yields for all samples tested were equal or better than those obtained by both phenol–chloroform extraction and commercial kits tested. DNA obtained from these samples was free of detectable PCR inhibitors. Short tandem repeat profiles were complete, conclusive, and devoid of PCR artifacts.     

Assessment of PowerPlex® Fusion 5C’s ability to type degraded DNA

DNA samples collected at crime scenes are often degraded so this research focused on the ability of the Promega PowerPlex® Fusion 5C amplification kit to type both naturally and artificially degraded DNA.DNA was degraded naturally by placing equal volumes of blood on white fabric that was stored either inside, outside in a shaded area, or outside in direct sunlight. Samples were then collected every 10 days for 60 days and the DNA extracted (QIAamp® DNA Investigator). Artificially degraded samples were created by exposing extracted DNA to either UV light or 95 °C heat for varying times. DNA was also degraded artificially by placing blood samples into a 50% bleach solution for varying times prior to extraction.Following sample treatment, standard forensic DNA analysis was performed including quantification (Investigator® Quantiplex) and amplification (PowerPlex® Fusion 5C). Separation and detection were performed on an ABI 3130xl capillary electrophoresis unit and analysis was performed using GeneMapper ID v3.2.1.While the time and shade samples showed similar amounts of degradation, the samples exposed to direct sun showed more degradation. The artificially degraded samples showed more signs of degradation such as reduced overall peak height and peak height imbalance at heterozygous loci. There were also some cases where an allele that was known to be in the profile exhibited total dropout. Although there were some instances of both allelic dropout and heterozygote peak imbalance, PowerPlex® Fusion was able to reliably type degraded DNA as all alleles detected were consistent with the known donor profile. The results show that PowerPlex® Fusion is a robust kit capable of handling forensically challenged samples.     

Mucosal Cell Isolation and Analysis from Cellular Mixtures of Three Contributors

In forensic genetic analyses, mixtures of various biological materials are common samples. Micromanipulation, which is performed based on differences in cellular morphology, is an effective method for the isolation of cells from mixtures. In this study, mucosal cell was isolated from somatic cellular mixtures (blood and saliva) based on micromanipulation and a low volume‐PCR (LV‐PCR) platform. One hundred and twenty‐six parallel LV‐PCR processes were performed using an Identifiler^® kit, with 107 reactions yielding single‐source DNA profiles. Among them, 54 full profiles (50%) and 37 partial profiles (13–15 loci) were obtained. Based on the above method, we obtained a single‐source DNA profile from a cigarette butt contaminated by two victims’ blood in a murder case. The generated genotype was used to query a DNA database, and a perfect match was found.