Collaborative swab performance comparison and the impact of sampling solution volumes on DNA recovery

DNA typing of cyanoacrylate fumed latent fingerprints using GlobalFiler™ and ForenSeq™ Signature Prep kits

DNA typing of latent fingerprints is highly desirable to increase chances of individualization. We recovered DNA from Cyanoacrylate (CA) fumed fingerprints and used both GlobalFiler™ and ForenSeq™ DNA Signature Prep kits for DNA typing. For GlobalFiler™, samples were processed using a protocol modified for Low Template (LT)-DNA samples (half-volume reactions, 30 cycles) while for ForenSeq™ DNA Signature Prep, samples were processed using a standard protocol and fluorometer-based library quantitation. We evaluated genotyping success and quality of profiles in terms of completeness, Peak Height Ratio/Allele Coverage Ratio, presence of PCR artifacts and drop-in alleles. With GlobalFiler™, average autosomal STR (aSTR) profile completeness was 44.4% with 2-20 pg, 54.3% with 22-60 pg, and 95% with 64-250 pg DNA input. CODIS uploadable profiles were obtained in 2/10, 3/11, and 11/12 samples in these ranges. With ForenSeq™ DNA Signature Prep, average aSTR profile completeness was 19.7% with 1-20 pg and 45.2% with 22-47 pg but increased to 78.3% with 68-122 pg and 86.7% with 618-1000 pg DNA input. Uploadable profiles were obtained in 0/12, 4/11, 4/7, and 3/3 samples for these ranges. Results show very high sensitivity using both kits. Half-volume reactions and 30 cycles had minimal negative effect on Globalfiler™ profile quality, providing support for wider use after validation experiments to routinely improve results from LT samples. A standard protocol for the ForenSeq™ DNA Signature Prep kit was also highly successful with LT DNA obtained from CA-fumed fingerprints with additional information from isometric STR alleles and other markers.

Shedding more light on shedders

We report on testing 100 individuals for their shedder status with the aim of demonstrating whether the process of cell staining is reproducible when testing a large number of people. A previous report using the same method was based on 11 donors and indicated that there may be a continuum of shedder types within this small sample set. In this report we also expand the time points post-handwashing to 0, 15, 30, 60, and 180 min. Triplicate samples were collected from both the right and left thumbs. Samples were collected by donors placing a thumb on a clean glass slide and then adding a DNA binding dye. The number of cells were recorded within three separate square millimetre areas (cells/mm2) at 220x magnification. The experiments were conducted in triplicate on three different days, giving a total of 72 thumbprints per individual. Finally, there were 3438 observed frames in the entire dataset. Of the 100 donors, 98 gave consistent and reproducible cell number deposition. There was no difference between the cells deposited by the left and right thumbs in 13 of 15 tested. Males tended to deposit more cells than females. If applying arbitrary boundary to a cell count to definitively determine shedder status, then many of the donors fell within two categories. This study based on 100 individuals strongly suggests that shedder status is a continuum phenomenon.

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.

DEPArray™ single-cell technology: A validation study for forensic applications

In forensics investigations, it is common to encounter biological mixtures consisting of homogeneous or heterogeneous components from multiple individuals and with different genetic contributions. One promising mixture deconvolution strategy is the DEPArray™ technology, which enables the separation of cell populations before genetic analysis. While technological advances are fundamental, their reliable validation is crucial for successful implementation and use for casework. Thus, this study aimed to 1) systematically validate the DEPArray™ system concerning specificity, sensitivity, repeatability, and contamination occurrences for blood, epithelial, and sperm cells, and 2) evaluate its potential for single-cell analysis in the field of forensic science. Our findings confirmed the effective identification of different cell types and the correct assignment of successfully genotyped single cells to their respective donor(s). Using the NGM Detect™ Amplification Kit, the average profile completeness for diploid cells was approximately 80%, with ∼ 290 RFUs. In contrast, haploid sperm analysis yielded an average completeness of 51% referring to the haploid reference profile, accompanied by mean peak heights of ∼ 176 RFUs. Although certain alleles of heterozygous loci in diploid cells showed strong imbalances, the overall peak balances yielded acceptable values above ≥ 60% with a mean value of 72% ± 0.21, a median of 77%, but with a maximum imbalance of 9% between heterozygous peaks. Locus dropouts were considered stochastic events, exhibiting variations among donors and cell types, with a notable failure incidence observed for TH01. Within the wet-lab experimentation with >500 single cells for the validation, profiling was performed using the consensus approach, where profiles were selected randomly from all data to better mirror real casework results. Nevertheless, complete profiles could be achieved with as few as three diploid cells, while the average success rate increased to 100% when using profiles of 6-10 cells. For sperms, however, a consensus profile with completeness >90% of the autosomal diploid genotype could be attained using ≥15 cells. In addition, the robustness of the consensus approach was evaluated in the absence of the respective reference profile without severe deterioration. Here, increased stutter peaks (≥ 15%) were found as the main artifact in single-cell profiles, while contamination and drop-ins were ascertained as rare events. Lastly, the technique's potential and limitations are discussed, and practical guidance is provided, particularly valuable for cold cases, multiple perpetrator rapes, and analyses of homogeneous mixed evidence.

Cell counting to monitor swab efficiency

Plastic bags, such as ziplock bags, have been used to transport illicit materials worldwide; however, very few studies have tried to optimize the recovery of DNA from these items. This study reports on the best combination of swabs and moistening solution for the greatest recovery of cellular material from ziplock bags. Five swabs, two different variations of Copan Diagnostics nylon 4N6FLOQSwabs, one Medical Wire rayon DRYSWAB, one IsoHelix rayon swab, and one Livingstone cotton swab, were evaluated with two moistening solutions, Triton X-100 in either distilled water or isopropanol. Fingermarks were deposited on ziplock bags and stained with Diamond™ Nucleic Acid Dye to allow visualization of the cells pre- and post-swabbing to determine the number of cells recovered. Based on cell counting data, swabs moistened with Triton X-100 in distilled water performed better than those moistened with isopropanol. Livingstone cotton swabs had the worst recovery of cellular material, while the other swabs tested had no significant difference in their respective solutions. A comparison of the best three swabs for cellular recovery yielded no differences in the DNA concentration extracted. A linear relationship was observed between the log number of cells recovered by swabbing and the DNA concentration following extraction and quantification. The process of monitoring cell collection using fluorescence microscopy on ziplock bags allowed evaluation of swabbing efficacy. Additionally, this study highlights the ability to evaluate cellular recovery independently of traditional extraction, quantification, or profiling techniques which may unequally affect samples.

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.

Effect of swabbing technique and duration on forensic DNA recovery

Various factors have been shown to affect performance of the conventional wet-dry double and single wet swabbing techniques to recover DNA, such as pressure and angle of application, volume and type of wetting agent, and swab type. However, casework laboratories in some jurisdictions have recently adopted different swabbing techniques that include wet-moist double swabbing and moist-dry single swabbing. Factors affecting the effectiveness of these recent techniques in maximising DNA recovery therefore need to be investigated. Here, the performance of traditional and recent swabbing techniques was compared and the impact of swabbing duration on DNA recovery was investigated. Ten µl aliquots of a known concentration of DNA extracted from human blood were deposited on pre-cleaned DNA-free cotton swatches (porous) and porcelain tiles (non-porous). Five swabbing techniques were used, of which three were double swabbing techniques: wet-moist, wet-wet and wet-dry, and two were single swabbing techniques: wet and moist-dry. For a 'wet' or 'moist' swab, 100 or 50 µL water was added, respectively. For a moist-dry swab, water was applied to one side of the swab, leaving the other side drier. Each swabbing technique was applied for two durations, 15 and 30 s per swab, with 5 reps of each combination (n = 100 plus controls). All samples were extracted and quantified, and a sub-set was profiled. The results showed that the wet-moist double swabbing technique with a swabbing duration of 30 s maximised DNA recovery from cotton. From tile, a single wet or moist-dry swab maximised DNA recovery, but increasing swabbing duration from 15 to 30 s had no impact. These data can be used to inform standardisation of DNA collection protocols across casework laboratories.

The DNA-Buster: The evaluation of an alternative DNA recovery approach

Touch DNA recovery techniques can have limitations, as their effectiveness depends on the substrate on which the DNA of a person of interest can be found. In this study, an in-house dry-vacuuming device, the DNA-Buster, was compared to traditional methods for its DNA recovery performance from items typically examined in forensic casework. The aim was to evaluate whether this dry-vacuuming approach can recover DNA efficiently, potentially complementing the well-established recovery strategies. For this, the performances of swabbing, taping, wet- (M-Vac®) and dry-vacuuming (DNA-Buster) were investigated quantitatively and qualitatively for touch DNA deposited on carpet, cotton sweater, stone, tile and wood. For the sweater, both vacuuming methods outperformed the other collection tools quantitatively. While the highest DNA amounts for the carpet were yielded by swabbing and taping, dry-vacuuming was equally good in reaching full DNA profiles, whereas less complete profiles were observed for the M-Vac®. For stone and tile, swabbing was optimal, whereas dry-vacuuming clearly underperformed for these substrates. Taping was the best recovery method for wood. Despite applying single donor DNA after thoroughly cleaning the items, undesired DNA mixtures were detected for all recovery techniques and all substrates. The overall research findings show first that the novel dry-vacuuming method is suited for DNA recovery from textiles. Secondly, they indicate that more attention should be paid to the substrate-collection dependency to ensure best practices in recovering genetic material in a precise, confident and targeted manner from the variety of forensic casework material.

The Perfect Match: Assessment of Sample Collection Efficiency for Immunological and Molecular Findings in Different Types of Fabrics

Body fluid identification at crime scenes can be crucial in retrieving the appropriate evidence that leads to the perpetrator and, in some cases, the victim. For this purpose, immunochromatographic tests are simple, fast and suitable for crime scenes. The potential sample is retrieved with a swab, normally a cotton swab, moistened in a specific buffer. Nonetheless, there are other swab types available, which have been proven to be efficient for DNA isolation and analysis. The aim of this study is to evaluate the efficiency of different swab types for body fluid identification as well as DNA isolation and characterization. Fifty microliters of human saliva were deposited in three different types of fabric (denim, cotton, and polyester). After 24 h at room temperature, samples were recovered by applying three different swab types, and the tests were performed. Subsequently, total DNA was recovered from the sample buffer. Cotton swabs performed worse in denim and cotton fabrics in both immunochromatography tests and DNA yield. No differences were observed for polyester. In contrast, and except for two replicates, it was possible to obtain a full DNA profile per fabric and swab type, and to identify the mtDNA haplogroup. In this paper, the impact of swab types on body fluid identification through the application of immunochromatographic tests is analyzed for the first time. This work corroborates previous research related to the influence of swab types in nuclear DNA isolation and characterization.