Evaluation of Forensic Genetic Parameters of 24 STR Loci and Y indel in a Southern Region Saudi Population Sample Using GlobalFiler™ PCR Amplification Kit

The last three decades have seen rapid advances in the field of short tandem repeats (STRs) genotyping technology. Autosomal STRs have emerged as a powerful tool in forensic identification and paternity investigations. The indigenous population of Saudi Arabia is irregularly distributed and has historically been organized into geographically distinct groups or tribes of patrilineal descent. So far, there has been no detailed investigation of the southern region Saudi population to assist in the interpretation of DNA-based forensic evidence and in the construction of DNA database. The objective of this study is to investigate the genetic structure in 154 unrelated healthy Saudi subjects within three generations from the southern Saudi regions using a GlobalFiler™ PCR Amplification kit. Intra- and Inter-population genetic diversity as well as the forensic genetics parameters were analyzed. Our results showed that SE33 and TPOX loci were the most and the least polymorphic loci, respectively. The PIC, PE, TPI, Ho and He varied from 0.56116 (TPOX) to 0.94393 (SE33), 0.26638 (TPOX) to 0.83859 (SE33), 1.1875 (TPOX) to 6.33333 (SE33), 0.57894 (TPOX) to 0.92105 (SE33) and 0.6169 (TPOX) to 0.952 (SE33), respectively. The highest PM was observed for D22S1045 (0.223944) and the highest PD for SE33 (0.98935). The combined PD was 99.99999999% and the combined PM was equal to 3.19021E-25. Phylogenetic parameters showed that the southern region Saudi population had the closest genetic relationship with the Saudi, Emirati, Kuwaiti, and Bahraini populations. The study offers some important insights into the southern region Saudi population structure using GlobalFiler™ PCR Amplification kit.

Efficient DNA Sampling in Burglary Investigations

In terms of crime scene investigations by means of forensic DNA-analyses, burglaries are the number one mass crime in Switzerland. Around one third of the DNA trace profiles registered in the Swiss DNA database are related to burglaries. However, during the collection of potential DNA traces within someone’s residence after a burglary, it is not known whether the sampled DNA originated from the perpetrator or from an inhabitant of said home. Because of the high incidence of burglaries, crime scene investigators usually do not collect reference samples from all the residents for economical and administrative reasons. Therefore, the presumably high probability that a DNA profile belonging to a person authorized to be at the crime scene ends up being sent to a DNA database for comparison, has to be taken into account. To our knowledge, no investigation has been made to evaluate the percentage of these non-perpetrator profiles straying into DNA databases. To shed light on this question, we collected reference samples from residents who had been victims of recent burglaries in their private homes. By comparing the profiles established from these reference samples with the profiles generated from trace DNA, we can show that the majority of the DNA samples collected in burglary investigations belong to the residents. Despite the limited number of cases included in the study, presumably due to a crime decline caused by the pandemic, we further show that trace DNA collection in the vicinity of the break and entry area, in particular window and door glasses, is most promising for sampling perpetrator instead of inhabitant DNA.

Development of novel PCR primer sets for DNA metabarcoding of aquatic insects, and the discovery of some cryptic species

DNA barcoding is a powerful tool that provides rapid, accurate, and automatable species identification by using standardized genetic region(s). It can be a powerful tool in various fields of biology such as for revealing the existence of cryptic species and/or rare species and in environmental science such as when monitoring river biota. Biodiversity reduction in recent times has become one of the most serious environmental issues on a worldwide scale. DNA barcoding techniques require the development of sets of universal PCR primers for DNA metabarcoding. We tried to develop universal primer sets for the DNA barcoding of all insect groups. In this study, we succeeded in designing not only universal primer sets for DNA barcoding regions of almost all insects, which were designed to include a hypervariable site between highly conserved sites, but also primer sets for longer fragment sequences for registration in a database. We confirmed successful amplification for 14 orders, 43 families, and 68 species with DNA barcoding in the mtDNA 16S rRNA region, and for 13 orders, 42 families, and 66 species with DNA barcoding in the mtDNA 12S rRNA region. A key feature is that the DNA fragments of the DNA barcoding regions amplified by these primer sets are both short at about 200-bp, and longer fragment sequences will increase the level of data registration in the DNA database. Such resulting database enhancements will serve as a powerful tool for increasingly accurate assessment of biodiversity and genetic diversity.

Precision DNA Mixture Interpretation with Single-Cell Profiling

Wet-lab based studies have exploited emerging single-cell technologies to address the challenges of interpreting forensic mixture evidence. However, little effort has been dedicated to developing a systematic approach to interpreting the single-cell profiles derived from the mixtures. This study is the first attempt to develop a comprehensive interpretation workflow in which single-cell profiles from mixtures are interpreted individually and holistically. In this approach, the genotypes from each cell are assessed, the number of contributors (NOC) of the single-cell profiles is estimated, followed by developing a consensus profile of each contributor, and finally the consensus profile(s) can be used for a DNA database search or comparing with known profiles to determine their potential sources. The potential of this single-cell interpretation workflow was assessed by simulation with various mixture scenarios and empirical allele drop-out and drop-in rates, the accuracies of estimating the NOC, the accuracies of recovering the true alleles by consensus, and the capabilities of deconvolving mixtures with related contributors. The results support that the single-cell based mixture interpretation can provide a precision that cannot beachieved with current standard CE-STR analyses. A new paradigm for mixture interpretation is available to enhance the interpretation of forensic genetic casework.

The Effects of DNA Databases on the Deterrence and Detection of Offenders

This paper studies the effects of adding criminal offenders to a DNA database. Using a large expansion of Denmark’s DNA database, we find that DNA registration reduces recidivism within the following year by up to 42 percent. It also increases the probability that offenders are identified if they recidivate, which we use to estimate the elasticity of crime with respect to the detection probability and find that a 1 percent higher detection probability reduces crime by more than 2 percent. We also find that DNA registration increases the likelihood that offenders find employment, enroll in education, and live in a more stable family environment. (JEL J22, J24, K42)

Exploring STR sequencing for forensic DNA intelligence databasing using the Austrian National DNA Database as an example

Here, we present the results from a population study that evaluated the performance of massively parallel sequencing (MPS) of short tandem repeats (STRs) with a particular focus on DNA intelligence databasing purposes. To meet this objective, 247 randomly selected reference samples, earlier being processed with conventional capillary electrophoretic (CE) STR sizing from the Austrian National DNA Database, were reanalyzed with the PowerSeq 46Y kit (Promega). This sample set provides MPS-based population data valid for the Austrian population to increase the body of sequence-based STR variation. The study addressed forensically relevant parameters, such as concordance and backward compatibility to extant amplicon-based genotypes, sequence-based stutter ratios, and relative marker performance. Of the 22 autosomal STR loci included in the PowerSeq 46GY panel, 99.98% of the allele calls were concordant between MPS and CE. Moreover, 25 new sequence variants from 15 markers were found in the Austrian dataset that are yet undescribed in the STRSeq online catalogue and were submitted for inclusion. Despite the high degree of concordance between MPS and CE derived genotypes, our results demonstrate the need for a harmonized allele nomenclature system that is equally applicable to both technologies, but at the same time can take advantage of the increased information content of MPS. This appears to be particularly important with regard to database applications in order to prevent false exclusions due to varying allele naming based on different analysis platforms and ensures backward compatibility.