Assessing Methods for Enhanced Recovery of Touch DNA from Fingerprints: A Pilot Study

BACKGROUND Touch DNA samples are frequently discovered at crime scenes, including those found at the scene, on the victim, with the suspect, or on objects related to the incident. This study aimed to investigate 3 key factors affecting touch DNA samples: the characteristics person that shed the DNA, surfaces variants where the DNA was deposited, and different sampling methods effectiveness that influence DNA quantity, quality, and detection. METHODS 9 participants grouped into high, intermediate, and low shedder levels simultaneously tied 2 types of ropes, non-porous and porous. The first person will hold a rope for 5 min then pass it to the second person to hold on the same spot for another 5 min. DNA was collected from each rope using the double swab and tape-lift method, extracted, and quantified using real-time polymerase chain reaction (PCR). Touch DNA profile at 20 short tandem repeat loci was amplified in PCR system and detected on capillary electrophoresis. RESULTS Type of substrate (p = 0.97) or sampling method (p = 0.053) used for touch DNA collection did not significantly impact the DNA yield or profiling outcomes. A notable difference (p<0.001) was found in DNA quantity between high, intermediate, and low shedders, regardless of the substrate or method used. CONCLUSIONS Individual shedder level has a greater influence on the results of touch DNA analysis regarding the DNA quantity and profiling quality than substrate type and sample procedure.

Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Introducing the New Editorial Team

In unison, fingerprinting and DNA analysis have played a pivotal role in forensic investigations. Fingerprint powders that are available on the market can come in a range of colors and with specific properties. This study evaluated the efficiency of DNA extraction from samples coated with 3 brands of fingerprint powders: Lightning, Sirchie, and SupraNano, covering a range of colors and properties. A total of 23 fingerprint powders were tested using the Chelex, Promega DNA IQ™, and Applied Biosystems™ PrepFiler™ DNA extraction protocols. The DNA IQ™ and PrepFiler™ methods extracted higher yields of DNA in comparison to Chelex, which also accounted for better quality of PowerPlex x00AE; 21 DNA profiles recovered. There were no signs of degradation or inhibition in the quantification data, indicating that samples returning low DNA yield was due to interference during DNA extraction and not PCR inhibition. DNA profiles were recovered from the majority of fingerprint powders with only a single powder, Sirchie Magnetic Silver, failing to produce a profile using any of the methods tested. A link was observed between the DNA extraction chemistry, fingerprint powder property, that is, nonmagnetic, magnetic and aqueous, and the brand of fingerprint powder. Overall, the DNA IQ™ method was favorable for nonmagnetic fingerprint powders, while magnetic fingerprint powders produced more DNA profiles when extracted with the PrepFiler™ chemistry. This study highlights the importance of screening DNA extraction chemistries for the type of fingerprint powder used, as there is not a single DNA extraction method that suits all fingerprint powder brands and properties.

Typing DNA profiles from previously enhanced fingerprints using direct PCR

<h3>Abstract</h3> Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while SNP microarray data from compromised DNA typically obtainable from crime scene stains are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of deprecated DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 nanogram to 6.25 picogram led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 picogram for siblings and 1^st cousins, 1 nanogram for 2^nd cousins, while at 25 picogram and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800-200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones. <h3>Author Summary</h3> Investigative genetic genealogy (IGG), i.e., identifying unknown perpetrators of crime via genomic database-tracing of their relatives by means of microarray-based single nucleotide polymorphism (SNP) data, is a recently emerging field. However, SNP microarrays were developed for much higher DNA quantity and quality than typically available from crime scenes, while SNP microarray data on quality and quantity compromised DNA are largely missing. As first attempt to investigate how SNP microarray analysis of quantity and quality compromised DNA impacts kinship classification success in the context of IGG, we performed systematic SNP microarray analyses on DNA samples below the manufacturer-recommended quantity and quality as well as on mock casework samples and on skeletal remains. In addition to IGG, our results are also relevant for any SNP microarray analysis of compromised DNA, such as for the DNA prediction of appearance and biogeographic ancestry in forensics and anthropology and for other purposes.

Presently, Short Tandem Repeats (STRs) based forensic DNA typing technology is being globally used in solving a diverse range of forensic cases such as paternity, identification of unknown dead bodies/skeletal remains, or suspect in a case of rape or mass rape. The technology has invaded its tentacles in almost all areas of criminal investigation in the last few decades. The present forensic DNA technology is based on capillary electrophoresis and utilizes short tandem repeats(STRs).On one hand, the technology is extensively used in the investigation of crime in highly sensitive cases, but on the another hand, obtaining DNA profile from forensic samples are highly challenging many times. Advent of PCR has been a boon for handling the challenging samples in forensic DNA analysis. The quality DNA profiles from challenging samples rely on the yield and quality of DNA, which is mainly dependent upon the method used for DNA extraction. Any specific method can never be thought of to be useful for all variety of samples. Still, Phenol Chloroform Isoamyl Alcohol (PCIA) organic extraction method has been proven to be useful for a wide variety of samples from the simplest saliva/blood to complex teeth and bone samples. In the present study, we compared the yield of DNA from blood stains recovered from various surfaces using the PCIA extraction method and Chelex DNA extraction methods and their compatibility with present-day STR based capillary electrophoresis typing. The mean value of DNA yield was found 50.5 ng/ µl and 32.25 ng/ µl by PCIA and Chelex DNA extraction methods, respectively. Overall, the highest yield was observed from all the tested samples from the PCIA method.

Forensic genetics

Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, an approach referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while DNA typically obtainable from crime scene stains is of low DNA quantity and quality, and SNP microarray data obtained from compromised DNA are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of compromised DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 ng to 6.25 pg led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 pg for siblings and 1st cousins, 1 ng for 2nd cousins, while at 25 pg and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800 to 200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones.

Short tandem repeat (STR) analysis of a perpetrator’s touch DNA on a victim’s skin is crucial in forensic science. This study evaluates the accuracy of male contributor assignment from skin-to-skin transferred touch DNA using STR profiling with and without whole-genome amplification (WGA). Each of 32 touch DNA samples was collected from a woman’s wrist after being grasped by a man, with each sample divided into three aliquots: one left as a non-WGA sample, another subjected to WGA via multiple displacement amplification (MDA), and the third amplified using modified T oligo-primed PCR (TOP-PCR). Ninety-six (32 × 3) STR profiles were analysed via capillary electrophoresis (CE) and massively parallel sequencing (MPS), with male contributors assigned using EuroForMix. Among the 10 Qubit-detectable samples of the 32 touch DNA samples, the accuracy rates of male contributor assignment using CE were 50% (non-WGA), 40% (MDA) and 70% (TOP-PCR) and using MPS were 100.0% (non-WGA), 50.0% (MDA), and 80.0% (TOP-PCR). For the 22 Qubit-undetectable samples, the accuracy rates using CE were 13.6% (non-WG3A), 4.5% (MDA) and 59.1% (TOP-PCR) and using MPS were 68.2% (non-WGA), 0% (MDA-) and 77.3% (TOP-PCR). In conclusion, TOP-PCR may improve the accuracy of male contributor assignment for Qubit-undetectable samples.

Forensic analysis.

Specific and sensitive mRNA biomarkers for the identification of skin in ‘touch DNA’ evidence

Objective To apply multiple displacement amplification (MDA)to improve primer extension preamplification (IPEP) for whole genome amplification (WGA) and to compare their effects on forensic DNA analysis. Methods DNA samples of varying amounts were for WGA based on MDA and IPEP.WGA products yield was evaluated by real-time quantitative PCR and STR genotyping performance was determined with AmpFLSTR? Identifiler(R) Kit. Results The DNA quantity was increased about 103～106 folds by MDA and 25～310 folds by IPEP. The least genome DNA amount is 1ng for MDA and 0.05ng for IPEP to obtain accurate genotypes of all loci. IPEP products and MDA products of 0.01 ng～0.1 ng DNA exhibited more loci observed than original DNA that was not for WGA,and IPEP products exhibited more loci observed than MDA products. Conclusion Both MDA and IPEP can improve STR genotyping of forensic minute DNA. The yield of MDA is higher than IPEP but the sensitivity of IPEP is higher than MDA and the STR genotyping effect of IPEP products is better than MDA products so IPEP is better for forensic trace DNA analysis. Key words: Multiple displacement amplification; Improved primer extension preamplification; Whole genome amplification; STR genotyping

The majority of crime scenes contain DNA that is either present in small amounts or degraded, making it difficult to obtain usable DNA profiles using conventional technologies. The current standard for analyzing casework samples is the specific amplification of short tandem repeats (STR), which is limited by DNA quality and quantity. Since the goal of forensic science is to identify a suspect or victim regardless of trace quality, we evaluated three technological approaches to better characterize and exploit these traces: (i) ultra-sensitive pulse-field electrophoresis on a Femto Pulse System (FPS) to visualize DNA content, (ii) real-time quantitative PCR based on Alu repeats to quantify human DNA and analyze its integrity, and (iii) 16S ribosomal RNA gene (16S rRNA) amplicon sequencing to identify microbiota. We optimized FPS analysis using DNA from model traces (blood, saliva, semen, touch DNA, and vaginal swabs) and applied the protocol to 100 casework samples. We found differences between the FPS profiles of model and casework samples, showing a variation in fragment size and distribution, suggesting the presence of non-human DNA. Using Alu-qPCR and 16S rRNA amplicon sequencing, we determined the amount and proportion of human and non-human DNA. Human DNA was detected in 84% of traces with an average of 70 pg per trace, while 16S rRNA revealed microbial DNA as the most abundant DNA in traces. These analyses provide new insights into forensic trace composition, allowing better sorting and profiling of traces.

Advancements in the sensitivity of commercial kits have enabled the genotyping of trace samples, establishing touch DNA as a valuable tool in forensic genetics, especially when fingerprints are absent or lack detail. However, analysis remains challenging due to various factors, including sex, age, surface type, and DNA source. This study investigated whether touching the face before depositing touch DNA on cell phone screens improves the quality and quantity of DNA recovered and assessed the effects of sex, age, and their interaction. Samples from 30 volunteers were collected with and without prior facial contact. DNA was genotyped with the PowerPlex® ESI17 System. Likelihood ratios were calculated via LRmix Studio. Although the DNA quantity was low, the cell phone screens yielded good-quality profiles. Facial contact significantly increased DNA quantity and allelic match percentages. No significant differences were observed for sex or age, but a statistically significant sex-age interaction was found for allelic match percentages. Males aged 18-29 years exhibited better results than females did in that group for finger-derived DNA; for face-derived DNA, this occurred in those aged 30-49 years. Face-derived DNA provided higher allelic match percentages for both sexes, individuals aged ≥ 50 years, younger females and males aged 30-49 years. Despite the limited sample size, the study illustrates how self-touching behavior can impact forensic DNA recovery. These insights can contribute to a better understanding of touch DNA and highlight the potential for improved identification and misinterpretation depending on the DNA source.