Development of a rapid, 96-well alkaline based differential DNA extraction method for sexual assault evidence

Toward Analysis at the Point of Need: A Digital Microfluidic Approach to Processing Multi-Source Sexual Assault Samples

Forensic case samples collected in sexual assaults typically contain DNA from multiple sources, which complicates short-tandem repeat (STR) profiling. These samples are typically sent to a laboratory to separate the DNA from sperm and non-sperm sources prior to analysis. Here, the automation and miniaturization of these steps using digital microfluidics (DMF) is reported, which may eventually enable processing sexual assault samples outside of the laboratory, at the point of need. When applied to vaginal swab samples collected up to 12 h post-coitus (PC), the new method identifies single-source (male) STR profiles. When applied to samples collected 24-72 h PC, the method identifies mixed STR profiles, suggesting room for improvement and/or potential for data deconvolution. In sum, an automated, miniaturized sample pre-processing method for separating the DNA contained in sexual assault samples is demonstrated. This type of automated processing using DMF, especially when combined with Rapid DNA Analysis, has the potential to be used for processing of sexual assault samples in hospitals, police offices, and other locations outside of the laboratory.

Advancements in differentiation between sperm cells and epithelial cells for efficient forensic DNA analysis in sexual assault cases

Most of the sexual assault casework samples are of mixed sources. Forensic DNA laboratories are always in the requirement of a precise technique for the efficient separation of sperm and non-sperm DNA from mixed samples. Since the introduction of the differential extraction technique in 1985, it has seen significant advancements in the form of either chemicals used or modification of incubation times. Several automated and semi-automated techniques have also adopted the fundamentals of conventional differential extraction techniques. However, lengthy incubation, several manual steps, and carryover over non-sperm material in sperm fraction are some of the major limitations of this technique. Advanced cell separation techniques have shown huge promise in separating sperm cells from a mixture based on their size, shape, composition, and membrane structure and antigens present on sperm membranes. Such advanced techniques such as DEParray, ADE, FACS, LCM, HOT and their respective pros and cons have been discussed in this article. As current-day forensic techniques should be as per the line of Olympic slogan i.e., faster, higher, stronger, the advanced cell separation techniques show a huge potential to be implemented in the casework samples.

Advantages of filtration method for sperm-DNA genotyping in sexual assault cases

Differential extraction (DE) is a conventional method to isolate sperms from forensic semen samples (e.g. vaginal swab containing semen) for sperm-DNA genotyping. Subsequent to selective digestion of somatic cells in a mixture sample, sperms are collected and purified as a pellet by repetitive centrifugation based on the specific gravity of sperm heads. However, the centrifugation operation requires a technical proficiency and an extensive time to prevent a loss of sperms from the pellet as much as possible. Therefore, we devised a "filtration method (FM)", in which a vacuum filtration operation based on the size of sperm heads is adapted, instead of DE, for isolation of sperms without any loss in principle. Sperms are collected and purified on a polycarbonate membrane filter. In this study, we have compared results of forensic assays by DE and FM for sperm-DNA genotyping from forensic semen samples. Consequently, FM had advantages of easy operation, timesaving, and high yield of sperms from semen samples compared with DE, although FM had a comparable ability to DE for a purification of sperms from mixture samples. Thus, we present that FM could simply lead to success of sperm-DNA genotyping and has a possibility to supersede DE as a gold-standard method.

Improved resolution of mixed STR profiles using a fully automated differential cell lysis/DNA extraction method

Sexual assault evidence often contains sperm cells, which are typically separated from nonsperm cells using manual differential lysis procedures. The goal of this study was to evaluate the automated QIAGEN QIAcube for this purpose and to compare it to manual QIAGEN and manual organic differential methods using DNA yields and STR profile data for assessment. DNA yields were determined by qPCR, followed by multiplex STR amplification, CE analysis, and mixture interpretation. The automated method was capable of effective cell separation, producing DNA yields sufficient for STR amplification. Further, sperm fraction human:male DNA ratios from the QIAcube samples were consistently closer to the desired 1:1 and STR profiles were less likely to result in mixtures, with 6-8× fewer female alleles detected (median 1.5 alleles). Ultimately, using the QIAcube for automated differential processing of semen-containing mixtures reduces the need for downstream mixture interpretation and improves STR profile quality with substantially less hands-on time.

Synthesis, Characterization, and Application of Poly(4,4'-Cyclohexylidene Bisphenol Oxalate) for Solid-Phase Extraction of DNA

The present study has synthesized poly(4,4'-cyclohexylidene bisphenol oxalate) by the condensation of oxalyl chloride with 4,4'-cyclohexylidene bisphenol, where its efficacy was tested for the solid-phase extraction of DNA. The synthesized polymer in the form of a white powder was characterized by FTIR, TGA-DTG, SEM, and BET analysis. The study utilized solid-phase application of the resulting polymer to extract DNA. The analysis of results provided the information that the extraction efficiency is a strong dependent of polymer amount and binding buffer type. Among the three types of buffers tested, the GuHCl buffer produced the most satisfactory results in terms of yield and efficiency of extraction. Moreover, the absorbance ratio of A260/A280 in all of the samples varied from 1.682 to 1.491, thereby confirming the capability of poly(4,4'-cyclohexylidene bisphenol oxalate) to elute pure DNA. The results demonstrated an increased DNA binding capacity with respect to increased percentage of the polymer. The study has concluded that poly(bisphenol Z oxalate) can be applied as one of the potential candidates for the high efficiency extraction of DNA by means of a simple, cost-effective, and environmentally friendly approach compared to the other traditional solid-phase methods.

Improving the efficacy of the standard DNA differential extraction method for sexual assault evidence

The efficacy of a DNA differential extraction procedure relies on reducing the amount of non-sperm female DNA carryover into the sperm fraction, while providing a sufficient recovery of male DNA from the sperm cell component. A standard approach to this extraction is to use a mild initial lysis step to digest the female (epithelial cell) component in the mixture, followed by a series of centrifugation and wash steps to further purify the resulting sperm-pellet fraction. This sperm fraction is then digested in the presence of a chemical reducing agent in preparation for DNA extraction. This method has been employed with relatively few changes since its introduction in the mid-1980s, despite numerous attempts to develop new or improved procedures. In this report, we demonstrate that it is possible to improve the efficacy of the standard differential extraction by applying simple modifications that can reduce the amount of female DNA carryover into the sperm fraction, with no adverse effects on the recovery of male DNA. In one modification, the addition of a second mild lysis step at the beginning of the differential extraction procedure improved the average male-to-female DNA ratio in the sperm fraction by 3- to 6-fold. In another modification, a "tube transfer" step was added to move the re-suspended sperm pellet to a new tube for the second mild lysis and subsequent wash steps. With this modification, the average male-to-female DNA ratio in the sperm fraction was improved by 4- to 90-fold, relative to results obtained for the non-modified differential extraction method. These modifications may be accomplished using tools and reagents that are already present in most forensic DNA laboratories, so that implementation should be relatively low-cost and practical.

NucleoSpin(®) XS Columns for DNA Concentration and Clean-Up

The phenol-chloroform (organic) extraction method continues to be a preferred method for extraction of DNA from forensic evidence samples that may contain low quantities of DNA and polymerase chain reaction (PCR) inhibitors. The aqueous extracts from the organic extraction of DNA require subsequent concentration and cleanup, which has traditionally been performed with microdialysis filter units, including the Centricon(®) and Microcon(®) centrifugal filter devices. Here, we describe the use of the NucleoSpin(®) XS silica columns as an alternative for the concentration and purification of the aqueous extracts from the organic extraction and for the removal of PCR inhibitors from existing DNA extracts.

Current developments in forensic interpretation of mixed DNA samples (Review)

A number of recent improvements have provided contemporary forensic investigations with a variety of tools to improve the analysis of mixed DNA samples in criminal investigations, producing notable improvements in the analysis of complex trace samples in cases of sexual assult and homicide. Mixed DNA contains DNA from two or more contributors, compounding DNA analysis by combining DNA from one or more major contributors with small amounts of DNA from potentially numerous minor contributors. These samples are characterized by a high probability of drop-out or drop-in combined with elevated stutter, significantly increasing analysis complexity. At some loci, minor contributor alleles may be completely obscured due to amplification bias or over-amplification, creating the illusion of additional contributors. Thus, estimating the number of contributors and separating contributor genotypes at a given locus is significantly more difficult in mixed DNA samples, requiring the application of specialized protocols that have only recently been widely commercialized and standardized. Over the last decade, the accuracy and repeatability of mixed DNA analyses available to conventional forensic laboratories has greatly advanced in terms of laboratory technology, mathematical models and biostatistical software, generating more accurate, rapid and readily available data for legal proceedings and criminal cases.

Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach

Background

Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim’s epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim’s DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim’s fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim’s fraction, and then digest the residual victim’s DNA with a nuclease.

Methods

The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases.

Results

For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles.

Conclusions

In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods.