Effect of swabbing technique and duration on forensic DNA recovery

Potential for DNA loss during collection and packaging of fired cartridge cases at a crime scene

DNA recovery from fired cartridge cases (FCCs) found at a crime scene is complicated by the limited DNA amounts typically available for collection. While this challenge is unavoidable, recovery rates may be improved by optimizing handling and packaging processes to better preserve the available DNA. Here we compared existing methods of collecting and packaging FCCs at a crime scene and assessed the utility of a novel cartridge collection device to determine which combination best preserves DNA integrity and amounts. FCCs loaded with touch DNA or blood and some DNA-free FCCs were collected and placed into paper or plastic packaging by one of 12 methods. Packages were handled in a manner that mimicked handling during casework, after which the location of DNA within the packaging was assessed to determine where transfer/loss had occurred. We observed that DNA can be lost from FCCs to an examiner's glove during collection, to the inside of packaging after handling and transport, and between FCCs in the same packaging. The novel cartridge collection device mitigated this transfer in many cases and could be considered a means of preserving DNA on FCCs. The results demonstrate the potential for preserving DNA by avoiding direct contact between the FCC and other items.

Enhancing trace DNA profile recovery in forensic casework using the amplicon RX post-PCR clean-up kit

This study evaluated the effectiveness of the amplicon RX post-PCR clean-up kit in enhancing trace DNA profile recovery from forensic casework samples amplified using the GlobalFiler PCR amplification kit. The impact of post-PCR clean-up on allele recovery and signal intensity was assessed in both trace casework samples and control samples across a range of DNA concentrations. The results showed that the amplicon RX method significantly improved allele recovery compared to the 29-cycle protocol (p = 8.30 × 10-12) and achieved slightly better results than the 30-cycle protocol (p = 0.019). Additionally, the Amplicon RX method demonstrated a significant increase in signal intensity (p = 2.70 × 10-4), reflecting improved sensitivity in detecting trace DNA profiles compared to the 30-cycle protocol. In the evaluation of control samples, the amplicon RX method consistently outperformed both the 29- and 30-cycle protocols, especially at lower DNA concentrations (D3: 0.001 ng/µL). While the performance of all methods declined at the lowest concentration (D4: 0.0001 ng/µL), the Amplicon RX method still demonstrated superior allele recovery (p = 0.014 compared to 29 cycles; p = 0.011 compared to 30 cycles). Therefore, the Amplicon RX method should be widely adopted in forensic laboratories to enhance the analysis of extremely low-template and compromised samples. These findings highlight the potential of the amplicon RX post-PCR clean-up kit to improve trace DNA analysis in forensic casework. Further research is recommended to validate these results and explore its broader application in forensic DNA analysis, particularly in complex DNA mixtures and extremely low-template samples.

Trace DNA and its persistence on various surfaces: A long term study investigating the influence of surface type and environmental conditions - Part two, non-metals

The work presented herein is the second part of a large-scale persistence project aimed at identifying trends in trace DNA persistence. This study aims to show how different environmental storage conditions and target surface characteristics influence the persistence of cellular and cell free DNA (cfDNA) over time. To eliminate variation within the experiment, we used a proxy DNA deposit consisting of a synthetic fingerprint solution, cellular DNA, and/or cfDNA. Samples were collected and analysed from eight non-metal surfaces over the course of 1 year (27 time points) under three different environmental storage conditions. The results of this experiment show that surface characteristics in conjunction with DNA type greatly influence DNA persistence. Variation in the amount of DNA recovered over time was greatly influenced by surface porosity. CfDNA persisted at significantly higher levels on non-porous surfaces, and cellular DNA persisted at higher levels on porous items. Furthermore, statistically significant differences in DNA persistence were found among the items classified as non-porous surfaces and among the items classified as porous surfaces. Additionally, this study showed that the sample storage environment had a larger impact on DNA persistence than previously observed for metal surfaces [1]. When considering DNA type, cellular DNA was shown to persist for longer than cfDNA and persistence as a whole appears to be better when DNA is deposited alone rather than in mixtures. Unsurprisingly, it was found that the amount of DNA recovered from trace deposits decreased over time. However, DNA decay is highly dependent on the surface type and exhibits higher variability at short time points and on porous surfaces. For each of the surfaces tested, DNA persisted 1 year past deposition (in some combination of DNA type and environmental condition), except for wood, on which DNA did not persist in any capacity past four months. This data is intended to add to our understanding of DNA persistence and the factors which affect it.

Impact of swabbing solutions on the recovery of biological material from non-porous surfaces

Cotton swabs are one of the most effective methods of retrieving biological evidence. The efficiency of swab-based DNA recovery is impacted by many factors, such as the swabbing technique, source of DNA and volume and type of wetting solution used to moisten the swab head. This study aimed to evaluate a series of different swab-moistening solutions. The types of swabbing solutions included buffers, detergent-based solutions, and chelating agents. The DNA deposits, including cell-free DNA, cellular DNA, blood, and saliva, were collected from three non-porous surfaces: plastic, glass, and metal. The difference in the performance of the swab-wetting solutions was heavily influenced by the type of biological fluid, with the chelating agents, EGTA and EDTA, being the most suitable for recovering DNA from saliva and blood samples. Conversely, water and detergent-based solutions were more appropriate for cell-free and cellular DNA material likely to be found in trace DNA deposits.

The detection of blood, semen and saliva through fabrics: A pilot study

This study aimed to identify if biological material could be detected on the opposite side to deposition on fabric by commonly used presumptive and/or secondary tests. Additionally, this study aimed to ascertain if there is a difference in the DNA quantity and quality from samples obtained from both sides of the same substrate: cotton, polyester, denim, or combined viscose and polyester swatches. Blood, semen, or saliva (25 μL) was deposited on one side of 5 replicates of each fabric type and left for 24 h. Blood swatches were tested using Hemastix® and the ABACard® HemaTrace® immunoassay, semen swatches were tested using acid phosphatase (AP) reagent, the ABACard® p30® immunoassay and hematoxylin and eosin staining, and saliva swatches were tested using Phadebas® paper and the RSID-Saliva™ immunoassay. Both sides of each swatch were separately wet/dry swabbed and subjected to DNA analysis. Blood was able to be detected on the underside of all fabrics using both tests. Semen was able to be detected on the underside of swatches using the presumptive AP test but not p30®, and sperm was rarely observed. Saliva was able to be detected by RSID-Saliva™ but not Phadebas® paper when the underside of swatches were tested. Across all biological materials, DNA was able to be recovered from the top side of all 60 swatches. For the underside, DNA was able to be recovered from 54 swatches. Of the 6 swatches that DNA was unable to be recovered from, one sample was from semen and the rest were from saliva. This study has demonstrated that DNA and components of interest in forensically relevant biological material can be recovered from the opposite side to where it was originally deposited, and that observing biological material and/or DNA on one side of fabric does not definitively indicate direct deposition on that side.

Comparison of swabbing and cutting-out DNA collection methods from cotton, paper, and cardboard surfaces

Choosing an inappropriate method of sample collection can often have a detrimental impact on DNA recovery. Multiple studies highlight the importance of selecting the recovery method based on the type of surface the DNA sample is located on. This study aimed to investigate the efficacy of sample collection via the single cotton swabbing method in comparison to recovery directly from the material cut from the surface. The three types of surfaces included cotton, paper, and cardboard. DNA sources comprised cell-free and cellular DNA, as well as blood and saliva as examples of body fluids commonly encountered at crime scenes. The data analysis revealed that the cutting-out method resulted in higher DNA recovery from all but cardboard surfaces, making it the more efficient collection method. Despite its limitations, the cutting-out method should be considered as the DNA recovery method of choice when suitable.

Determining the number and size of background samples derived from an area adjacent to the target sample that provide the greatest support for a POI in a target sample

When sampling an item or surface for DNA originating from an action of interest, one is likely to collect DNA unrelated to the action of interest (background DNA). While adding to the complexity of a generated DNA profile, background DNA has been shown to aid in resolving the genotypes of contributors in a targeted sample, and where references of donors to the background DNA are not available, strengthen the LR supporting a person of interest contributing to the targeted sample. This is possible thanks to advances in probabilistic genotyping, where forensic labs are able to deconvolute complex DNA profiles to obtain lists of genotypes and their associated weights. Coupled with DBLR™, one can then compare multiple evidentiary profiles to each other to determine the contribution of common, but unknown, contributors. Here, we consider factors associated with taking background samples and whether one should collect multiple background samples that all relate to a single target sample, or if one should collect larger background samples rather than smaller samples. Background samples consisted of DNA accumulated on the items primarily by one or both occupants of a single household, while targeted samples were generated from touch deposits, or saliva deposits that had been left to air dry. Samples were collected from areas of various sizes, consisting of only the background, the target and the background directly beneath it, and the target and additional surrounding background. A broad range of DNA quantities were recovered, with larger background samples (400 cm2) yielding significantly more DNA than smaller background samples (30 cm2). Significant differences in DNA quantities between target samples were not observed. Generated DNA profiles were interpreted using STRmix™ and DBLR™, and where there was support for a common donor between the background and target sample, pairwise comparisons were performed to observe the effect on the LR supporting the target DNA donor contributing to the targeted sample when conditioning on one (or two) common donor between the targeted sample and 1-8 background samples. Multiple background samples gave significantly higher LRs compared to a single background sample, the larger sampled background area resulted in larger LR gains than the smaller areas, and four or more background samples reduced LR variability considerably. Here we provide recommendations for the minimum and ideal number of additional background samples that should be collected, and that several smaller samples may be more beneficial than a single larger sample.