Alternative direct-to-amplification cell lysis techniques for forensically relevant non-sperm cells

While efforts have been made to reduce the pervasive backlog of sexual assault evidence collection kits, the actual laboratory process remains very time-consuming due to the requirement of a differential lysis step before DNA purification, as well as intricate mixture analysis towards the end of the DNA workflow. Recently, an alternative, direct-to-amplification sperm lysis method (using 1 M NaOH) was identified. However, a direct cell lysis method for non-sperm cells has not been identified yet. Thus, the primary objective of this work was to find an alternative method that is quick, inexpensive, and does not require multiple purification steps for the lysis of non-sperm cells in sexual assault samples. In this study, vaginal swab samples were lysed with the control method, prepGEM™, as well as six alternative reagents: alkaline buffer with 25–200 mM NaOH, high-salt stain extraction buffer, modified radioimmunoprecipitation assay (RIPA) buffer, mammalian protein extraction reagent (M-PER™), digitonin buffer, and urea/thiourea buffer. Quantification using Quantifiler® Trio of vaginal and semen lysates revealed that the alkaline (25 mM NaOH) and M-PER™ methods were efficient for the lysis of vaginal epithelial cells without substantial sperm cell lysis. Following quantification, analysis of STR profiles from vaginal lysates revealed that the M-PER™ method showed promising results across all metrics examined, including the percentage of detected STR alleles, mean peak heights, peak height ratio, and interlocus balance. Thus, this method was recommended as an alternative to the traditional differential lysis method for non-sperm cells given its ability to produce amplification-ready lysates without any DNA purification step.     

Evaluation of usefulness of further Y-STR analysis in sexual assault cases on PSA positive samples resulting in female autosomal STR profiling

Samples from male to female sexual assault cases that are positive for the presumptive prostate specific antigen (PSA) test often do not result in a male autosomal STR profile. Due to highly unequal proportions of female and male DNA in typical sexual assault samples, routine autosomal STR analysis often fails to detect the DNA of the assailant, even after differential extraction of the samples. Previous studies have already shown the value of Y-STR analysis in such cases [1]. In Belgium, forensic DNA laboratories are only allowed to perform Y-STR profiling on sexual assault samples by a specific requisition, after routine autosomal STR analysis has been performed. However, a request for additional Y-STR analysis is rather exceptional.In this study, we evaluated the usefulness of further Y-STR analysis. For 100 PSA positive rinses and swabs from male to female sexual assault cases resulting in female autosomal STR profiling, 7% resulted in a full or partial Y-STR profile useful for comparison, using the 23-loci Y-STR PowerPlex Y23 System (Promega). The success rate raised to 12.5% with a higher DNA input in the PCR mix. In conclusion, these results support the usefulness of performing Y-STRs analysis on the sperm DNA extracts to identify the alleged assailant in sexual assault cases.     

Developmental validation of the SPERM HY-LITER™ kit for the identification of human spermatozoa in forensic samples

Abstract: With sexual assault evidence, the visualization of spermatozoa confirms that ejaculation has occurred. However, microscopic examination of spermatozoa is a laborious process and can sometimes result in sperm cells being overlooked. Here, we present the developmental validation of the SPERM HY‐LITER? kit, which contains a human sperm–specific mouse monoclonal antibody coupled to a fluorescent Alexa 488 dye. The kit was tested using samples of human semen, saliva, blood, and urine, various animal semen extracts, sexual lubricants, and a commercially available spermicidal film. Postcoital vaginal swabs, degraded semen samples, and samples prepared with sample fixation techniques that deviated from the kit‐provided protocol were also tested. In each case, the SPERM HY‐LITER? kit was demonstrated to bind only to human sperm cell heads. Limitations to this fluorescent staining procedure include nonspecific staining and increased background fluorescence with extreme heat fixation in some samples.     

The Persistence of Sperm and the Development of Time Since Intercourse (TSI) Guidelines in Sexual Assault Cases at Forensic Science Ireland,Dublin, Ireland

The persistence of sperm using confirmatory microscopic analysis, the persistence of sperm with tails, time since intercourse (TSI) analysis, and results from the acid phosphatase (AP) reaction from approximately 5581 swabs taken from circa 1450 sexual assault cases are presented. The observed proportions of sperm in the vagina and anus declines significantly after 48 h TSI, and sperm on oral swabs were observed up to 15 h TSI. The AP reaction as a predictor of sperm on intimate swabs is questioned. All AP reaction times gave a low true positive rate; 23% of sperm‐positive swabs gave a negative AP reaction time. We show the AP reaction is an unsafe and an unreliable predictor of sperm on intimate swabs. We propose that TSI not AP informs precase assessment and the evaluative approach for sexual assault cases. To help inform an evaluative approach, TSI guidelines are presented.     

Automation of the Differential Digestion Process of Sexual Assault Evidence,

Sexual assault evidence samples require the use of a specific process known as a differential digestion to separate sperm from nonsperm cells prior to DNA extraction. An automated differential digestion process was developed using a selective degradation technique, which uses DNase I to digest the remaining nonsperm DNA in the sperm fraction. The use of DNase on pristine samples, as well as aged and degraded samples, was assessed to ensure that the quantity and quality of the sperm DNA were not compromised or adversely affected. Samples processed using the selective degradation technique yielded comparable DNA yield and DNA typing data to the conventional differential digestion process. The automated process utilized 96‐well plates for high throughput and incorporated microscope slide preparations for confirmation of sperm. It reduced processing time by about sixfold and was paramount in the elimination of the Oakland Police Department Criminalistics Laboratory's sexual assault kit backlog.     

Electrospray and MALDI mass spectrometry in the identification of spermicides in criminal investigations.

Electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have been used to examine evidence in a sexual assault investigation. Because condoms are being used increasingly by sexual assailants and some condom brands include the spermicide nonoxynol-9 (nonylphenoxy polyethoxyethanol) in the lubricant formulation, the recovery, and identification of nonoxynol-9 from evidence items may assist in proving corpus delicti. A method was developed for the recovery of nonoxynol-9 from internal vaginal swabs and for its identification by reverse phase liquid chromatography/electrospray ionization mass spectrometry (LC ESI-MS), nanoelectrospray ionization (nanoESI) mass spectrometry, and high resolution MALDI Fourier transform mass spectrometry (MALDI-FTMS). The method was tested on extracts from precoitus, immediate postcoitus, and four-hours postcoitus vaginal swabs provided by a volunteer whose partner does not normally use condoms, but for this trial used a condom having a water-soluble gel-type lubricant that includes 5% nonoxynol-9 in its formulation. Subsequently, LC ESI-MS was used to identify traces of nonoxynol-9 from the internal vaginal swab of a victim of a sexual assault.     

Y-STR profiling in extended interval (> or = 3 days) postcoital cervicovaginal samples

Depending upon specific situations, some victims of sexual assault provide vaginal samples more than 36-48 h after the incident. We have tested the ability of commercial and in-house Y-STR systems to provide DNA profiles from extended interval (> or =3 days) postcoital samples. The commercial Y-STR systems tested included the AmpFlSTR Yfiler (Applied Biosystems), PowerPlex Y (Promega) and Y-PLEX 12 (Reliagene) products whereas the in-house systems comprised Multiplex I (MPI) and Multiplex B (MPB). Three donor couples were recruited for the study. Postcoital cervicovaginal swabs (x2) were recovered by each of the three females at specified intervals after sexual intercourse (3-7 days). Each time point sample was collected after a separate act of sexual intercourse and was preceded by a 7-day abstention period. As a negative control, a precoital swab was also recovered prior to coitus for each sampling and only data from postcoital samples that demonstrated a lack of male DNA in the associated precoital sample was used. A number of DNA profile enhancement strategies were employed including sampling by cervical brushing, nondifferential DNA extraction methodology, and post-PCR purification. Full Y-STR profiles from cervicovaginal samples recovered 3-4 days after intercourse were routinely obtained. Profiles were also obtainable 5-6 days postcoitus although by this stage partial profiles rather than full profiles were a more likely outcome. The DNA profiles from the sperm fraction of a differential lysis were superior to that obtained when a nondifferential method was employed in that the allelic signal intensities were generally higher and more balanced and exhibited less baseline noise. The incorporation of a simple post-PCR purification process significantly increased the ability to obtain Y-STR profiles, particularly from 5- to 6-day postcoital samples. Remarkably an 8 locus Y-STR profile was obtained from a 7-day postcoital sample, which is approaching the reported time limit for sperm detection in the cervix.     

Isolation and identification of female DNA on postcoital penile swabs

After sexual assault, cells originating from the assailant may be recovered from the victim. Through polymerase chain reaction (PCR)-based technology, positive scientific identification of the assailant may be made from these cells. Described is a prospective study describing a method for positively identifying cells from a female sex partner obtained from postcoital swabs of the penis of the male sex partner. Swabs were taken from the penis of a man at 1- to 24-hour intervals after coitus. DNA was isolated from each swab through standard organic extraction methods. The presence of female DNA was detected using the gender-specific amelogenin marker. Extracted DNA was amplified for eight different genetic loci using the Promega PowerPlex kit (Promega) and Amplitaq Gold (Perkin Elmer). Amplified samples were electrophoresed on precast sequencing gels (Hitachi) and were analyzed fluorescently using Hitachi's FMBIO 2 fluorescent scanner and software. Each sample obtained from a penile swab or condom was compared to male and female buccal controls. Female DNA was isolated from all postcoital penile swabs as determined by exclusive amplification of the X-chromosome specific 212 base pair amelogenin marker. In all cases, scientific identification of the female DNA from the swabs was determined by coamplification of eight STR loci (PowerPlex) and was compared to female and male control profiles. Cells shed from a female victim during sexual intercourse can be retrieved from the penis of a male offender after sexual intercourse during a 1- to 24-hour postcoital interval. DNA can be extracted from these cells and can be used to scientifically identify the female sexual participant through PCR-based technology. It is suggested that penile swabs be taken from alleged perpetrators of sexual assaults to associate them with a female victim.     

Contribution to the Development of Guidelines in the Analysis of Biological Evidence in Sexual Assault Investigations

This investigation intends to study materials and techniques used for biological evidence collection in sexual assault cases and is divided into two stages: in stage one, methods for biological evidence collection (the single swab (including three variants) and the “double swab technique”) were compared; in stage two, swabs’ component material was compared. The sampling was composed of 42 heterosexual couples who provided mock samples. The collection methods in which the whole swab is covered by evidence presented significantly better outcomes (p < 0.001), such as the “double swab technique.” Additionally, nylon swabs proved to present significantly better features regarding the capacity of sample elution, providing significantly higher amounts of DNA (p ≤ 0.034). This study provides guidelines for better collection of biological evidence regarding the collection method using a swab and the proper swab material to utilize.     

Single sperm cell isolation by micromanipulation for human identification in sexual assault

This study proposes a new alternative solution in preferential extraction methods or microdissection to isolate and analyse single sperm cells in case of sexual assault. After the transfer of swabs in liquid culture medium, perpetrator's spermatozoas can be physically separated from victim's epithelial cells by using classical techniques of micromanipulation as ICSI (IntraCytoplasmic Spermatozoa Injection), usually applied for IVF (In vitro Fertilization).     

Identification and isolation of male cells using fluorescence in situ hybridisation and laser microdissection, for use in the investigation of sexual assault

In cases of sexual assault involving an azoospermic assailant, vaginal swabs taken from the victim may fail to provide an autosomal DNA profile with which to search a suspect database, as the signal from any male cells present would be masked by that from the overwhelming number of female cells collected on the swab. Here, we describe a method of visually identifying diploid male cells in such samples using fluorescence in situ hybridisation, and selectively harvesting them by means of laser microdissection. This combination of techniques was tested on 26 post-coital vaginal swabs taken at a range of times after intercourse; the collected cells were then subjected to a simple lysis procedure and DNA was amplified using the AmpFlSTR^® SGMPlus^® multiplex under low copy number conditions. Useful DNA profiles were generated from samples taken up to 24 h after intercourse.     

A novel approach to condom lubricant analysis: In-situ analysis of swabs by FT-Raman Spectroscopy and its effects on DNA analysis

Current methods for the analysis of swabs for condom lubricants require a portion of the swab to be extracted. This requirement causes issues for those who require the swab for DNA extraction. A novel method is presented that facilitates analysis of the swab without the need for extraction. The method was shown to be equivalent to the traditional methods in terms of its sensitivity and discriminating power.The impact of the method on subsequent DNA extraction of swabs was assessed and no detrimental effects were observed.The method was used to conduct a survey of the current market for the supply of condoms in the UK. 90% of the UK condom market consists of condoms lubricated with PDMS.     

Filtration based DNA preparation for sexual assault cases

Police departments in the United States currently have as many as 500,000 unprocessed swabs taken from rape victims. The standard method for purifying sperm from these swabs is to resuspend first all cells and to digest selectively the excess of the victim's epithelial cells. The intact sperm are then separated from the contaminating solubilized DNA by centrifugation, careful removal of supernatant, and extensive washing of the sperm pellet, all steps that are difficult to automate. Vacuum driven filtration is an alternative method for separating sperm from digested epithelial cells that requires only pipetting steps and can be readily automated in a 96 well format. Sperm DNA is enriched 45-fold using this process and the yield of PCR ready DNA is roughly 20% of the amount originally present on the swab.     

A Comparison of Common Swabbing Materials for the Recovery of Organic and Inorganic Explosive Residues

The efficiency of solvent based extraction methods used to remove explosive residues from four different swab types was investigated. Known amounts of organic and inorganic residues were spiked onto a swab surface with acetonitrile or ethanol:water combined with ultrasonication or physical manipulation used to extract the residues from each swab. The efficiency of each procedure was then calculated using liquid chromatography‐ultraviolet detection for organic residues and ion chromatography for inorganic residues. Results indicated that acetonitrile combined with physical agitation proved to be the most efficient method; returning analyte recoveries c. 95% for both alcohol based swabs and cotton balls. Inorganic residues were efficiently extracted using ethanol:water, while the use of acetonitrile followed by water significantly reduced the recovery of inorganic residues. Swab storage conditions were then investigated with results indicating decreased storage temperatures are required to retain the more volatile explosives.     

Sperm elution: An improved two phase recovery method for sexual assault samples

This report describes the validation of a two phase cell recovery technique for the elution of two common cell types, epithelia and spermatozoa, from frequently examined items submitted as part of sexual assault casework. Furthermore, separation of cell types prior to microscopic examination of cell pellets improves the scientist's confidence in observing and scoring spermatozoa that may be present. During the validation, Orchid Cellmark's Sperm Elution© method consistently recovered a greater number of spermatozoa from simulated sexual assault items and swabs taken following consensual sexual intercourse compared to a water extraction technique. On average the Sperm Elution method recovered over twice the number of spermatozoa compared to the water method. The ability to separate the cell types present allows a rapid microscope slide search for spermatozoa and faster DNA extraction protocol in comparison to Cellmark's previous preferential method.     

Microchip-based cell lysis and DNA extraction from sperm cells for application to forensic analysis

The current backlog of casework is among the most significant challenges facing crime laboratories at this time. While the development of next-generation microchip-based technology for expedited forensic casework analysis offers one solution to this problem, this will require the adaptation of manual, large-volume, benchtop chemistry to small volume microfluidic devices. Analysis of evidentiary materials from rape kits where semen or sperm cells are commonly found represents a unique set of challenges for on-chip cell lysis and DNA extraction that must be addressed for successful application. The work presented here details the development of a microdevice capable of DNA extraction directly from sperm cells for application to the analysis of sexual assault evidence. A variety of chemical lysing agents are assessed for inclusion in the extraction protocol and a method for DNA purification from sperm cells is described. Suitability of the extracted DNA for short tandem repeat (STR) analysis is assessed and genetic profiles shown. Finally, on-chip cell lysis methods are evaluated, with results from fluorescence visualization of cell rupture and DNA extraction from an integrated cell lysis and purification with subsequent STR amplification presented. A method for on-chip cell lysis and DNA purification is described, with considerations toward inclusion in an integrated microdevice capable of both differential cell sorting and DNA extraction. The results of this work demonstrate the feasibility of incorporating microchip-based cell lysis and DNA extraction into forensic casework analysis.     

Enhanced elution of sperm from cotton swabs via enzymatic digestion for rape kit analysis

This report describes development of a method for enhanced cell elution from cotton swabs. The method exploits an enzyme mixture for digestion of the cotton to remove intact cells, and can be utilized in conjunction with or to circumvent conventional differential extraction (DE). Samples digested with Aspergillus niger cellulase yielded sperm cell recoveries (18+/-3.5%) similar to conventional DE buffer (23+/-7.8%) while providing intact epithelial cells. Storage time affected the concentration of enzyme required for optimal sperm cell recovery, with longer times requiring increased cellulase concentrations. Cellulase from A. niger yielded a twofold enhancement in sperm cell elution over buffer alone, and preliminary testing of higher activity cellulases from Trichoderma reesei and Trichoderma viride showed even greater enhancement. These results indicate that cellulose-digesting enzymes enhance the release of sperm and epithelial cells from a cotton swab over buffer alone, providing for efficient DNA analysis.     

Comparison of enzyme assay and radioimmunoassay for the measurement of human acid phosphatase in cases of sexual assault

We investigated whether a radioimmunoassay for prostatic acid phosphatase might be used as a more specific test for the identification of semen in samples from cases of sexual assault than the measurement of total acid phosphatase enzyme activity. The results of the measurement of acid phosphatase by enzyme assay in semen and vaginal swab extracts were compared with the results of the radioimmunoassay. It was found that the radioimmunoassay is a sensitive and more specific method than the enzymic determination of acid phosphatase. Incidentally we have found that a low concentration of an immunological cross reacting acid phosphatase is present in semen free vaginal swab extracts.     

A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods

The Metropolitan Police Service currently uses cotton swabs to retrieve DNA for forensic profiling. Recently, a new nylon flocked swab type has become available from Copan (MicroRheologics, Brescia, Italy) that it is claimed, offers increased sample recovery and release yields. If true, the flocked swab may have important applications in DNA evidence retrieval. This study examines the DNA retrieval capability of cotton and nylon flocked swabs when extracted using three common extraction platforms (QIAcube, BioRobot EZ1 and manually processed QIAamp DNA investigator kit). Results indicate that both swab types are capable of recovering high percentages of DNA (>50%); however, the extraction platform selected was shown to have a significant effect upon DNA retrieval. Across all experiments, the cotton swab combined with the spin-column extractions was shown to be most effective, with the nylon swab and BioRobot EZ1 combination being the least effective. These findings illustrate the importance of extraction method selection.