Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation

Genealogically bewildered individuals and forensic identification: a review of current and emerging solutions

The increasing use of assisted reproductive technologies (ART) with donor gametes is driven by rising infertility rates, delayed parenthood, and the need to prevent hereditary diseases. Greater social acceptance of diverse family structures, advancements in reproductive medicine, and improving success rates also contribute. Accessibility, affordability, and cross-border reproductive care further expand ART's reach, making donor gametes a preferred option for many individuals and couples worldwide. The widespread application of ART has led to an increasing number of donor-conceived individuals, many of whom are now reaching reproductive maturity. This demographic shift introduces significant challenges for traditional forensic genetic identification methods, which rely on biological reference samples from genetically related individuals. The absence of such samples complicates the identification process, particularly for individuals conceived via gamete donation or adoption, where biological and legal parentage are incongruent. Conventional forensic genetic analyses, including short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling of autosomal, Y-chromosome, X-chromosome, and mitochondrial DNA, exhibit limited efficacy in these scenarios. While these methods can sometimes identify individuals conceived using a single donor gamete, they are insufficient for cases involving dual donor gametes or mitochondrial replacement therapy. Emerging methodologies such as forensic genetic genealogy, DNA methylation profiling, and human microbiome analysis offer innovative approaches but necessitate further clinical validation and standardization.

Past, Present and Future Perspectives of Forensic Genetics

Forensic genetics has experienced remarkable advancements over the past decades, evolving from the analysis of a limited number of DNA segments to comprehensive genome-wide investigations. This progression has significantly improved the ability to establish genetic profiles under diverse conditions and scenarios. Beyond individual identification, forensic genetics now enables the inference of physical traits (e.g., eye, hair, and skin color, as well as body composition), biogeographic ancestry, lifestyle habits such as alcohol and tobacco use, and even the transfer of genital microbiomes post-coitus, among other characteristics. Emerging trends point to a future shaped by the integration of cutting-edge technologies, including CRISPR-Cas systems, artificial intelligence, and machine learning, which promise to further revolutionize the field. This review provides a thorough exploration of forensic genetics, tracing its evolution from its foundational methods (past) to its diverse modern applications (present) and offering insights into its potential future directions.

Development of a novel latent deoxyribonucleic acid detection technique for crime scene investigation using quartz tuning fork-based biosensor technology

The forensic Deoxyribonucleic Acid (DNA) fingerprinting is a tool for investigating crime scenes by identifying/tracing criminals and linking crime scenes. However, in cases where experts are unable to detect and identify any biological traces or human-derived cells at the crime scene or while testing the samples in the laboratories, all the advantages offered by forensic laboratories lose their significance. It becomes a waste of time, effort, and resources allocated to these laboratories. Therefore, there is an urgent need for technology that enables crime scene experts to detect latent and concealed human traces before they leave the scene. This work aims to provide a novel qualitative and quantitative approach to tackle the challenges faced by crime scene experts in identifying challenging traces using instant, low-cost, uncomplicated, portable, sensitive detection technology by introducing the Quartz Tuning Fork (QTF)-based biosensor technology as an initial screening technique. A probe layer functionalized the QTF-based biosensor to capture DNA fragments. The response of the functionalized QTF sensor to different concentrations of DNA was measured as a resonance frequency shift, which increased as the concentration of DNA increased. The QTF response for DNA was also confirmed by measuring the resonance frequency of the functionalized QTF after capturing DNA and after washing with DNA removal solution (DNAZap). The resonance frequency of the QTF immersed in DNA was increased after immersion in the DNA removal solution. Finally, functionalized QTF showed a high sensitivity for the DNA fragments with a limit of detection of 140 pg/µl.

The development of two fast genotyping assays for the differentiation of hemp from marijuana

The legalization of hemp cultivation in the United States has raised the need for reliable methods to distinguish between legal hemp and illegal marijuana. Genetic analysis has emerged as a powerful tool, surpassing traditional chemical methods in specific aspects, such as analyzing trace amounts, aged samples, and different parts of the sample. Genetic differences in cannabinoid synthase genes offer promise for precise crop type determination, particularly focusing on genes like tetrahydrocannabinolic acid synthase (THCAS), cannabidiolic acid synthase (CBDAS), and cannabichromenic acid synthase (CBCAS). However, previous research faced several challenges in developing discriminatory genetic markers, including limited sample sizes, high similarity between the synthase genes, and the presence of pseudo synthase genes. A comprehensive study using Next-Generation Sequencing (NGS) introduced a differentiation flowchart based on THCAS, CBDAS, and THCAS pseudogenes. To bridge the gap between NGS and the practical requirements of crime laboratories, two rapid genotyping assays were developed: a CE-based SNaPshot™ assay and a TaqMan™ real-time PCR assay. While the SNaPshot™ assay effectively differentiated various hemp and marijuana types, differentiation was limited with marijuana samples containing THC% close to the 0.3% legal threshold (0.3%-1%). The TaqMan™ qPCR SNP genotyping assay provided quicker results, making it an efficient choice for crime laboratories. However, this method had the same limitations as the SNaPshot™ assay with addtional challenges in differentiating edible hemp seed samples, and it did not provide additional CBD information. The study also highlighted the influence of two variants of one THCAS pseudogene on chemotype determination, emphasizing the necessity for precise genetic analysis for accurate categorization of cannabis varieties.

Human complex mixture analysis by "FD Multi-SNP Mixture Kit"

Introduction

Multiple linked single nucleotide polymorphisms (SNPs) have shown potential in personal identification and mixture detection. However, the limited number of marker and sequencing errors have obstructed accurate DNA typing.

Methods

To develop more candidate loci, the diversity value (D-value) was introduced as a new parameter for screening the novel polymorphic multiple linked-SNP markers, referred to as multi-SNP. In this study, a "FD Multi-SNP Mixture Kit" comprising 567 multi-SNPs was developed for mixture detection. Additionally, a new computational error correction method was applied as a quality control approach for sequencing data.

Results

The results demonstrated higher typing success rates than the conventional CE typing method. For single-source DNA, approximately 70-80 loci were detected with a DNA input of 0.009765625 ng. More than 65% of the minor alleles were distinguishable at 1 ng DNA with a frequency of 0.5% in 2- to 4-person mixtures.

Conclusion

This study offers a polymorphic and high-resolution detection method for DNA genotyping and complex mixture detection, providing an alternative strategy for addressing challenging mixed DNA traces.

Genetic Polymorphisms and Forensic Parameters of Thirteen X-Chromosome Markers in the Iraqi Kurdish Population

X-chromosome short tandem repeat (X-STR) tools are crucial in forensic genetics and human population fields. This study presents the development and validation of a multiplex STR system consisting of thirteen X-STR loci and amelogenin specific to the human X chromosome. The system was optimized and tested for species specificity, sensitivity, stability, and DNA mixture using 9947A female and 9948 male control genomic DNA. The amplified products of nine loci were sequenced to determine the correct amplicon length. Allele frequencies, forensic parameters, mean exclusion chance (MEC), linkage disequilibrium (LD), and allelic patterns were investigated using DNA samples from 225 (159 male, 66 female) unrelated Kurdish individuals who live in Sulaymaniyah province in the Kurdistan region of Iraq. The most informative locus in the Kurdish population was GATA172D05, while the least informative locus was DXS10164. The results demonstrated that the 13 X-STR system is highly polymorphic and sensitive for forensic DNA identification. Genetic distance-based clustering, metric multidimensional scaling (MDS), and correlation matrix were analyzed for 19 ethnic groups and populations. The phylogenetic tree showed that populations clustered according to their ethnogeographic relationships. The findings revealed genetic links between the Iraqi Kurds, Caucasians, Iraqi Arabs, United States (U.S.) ethnic groups, and Chinese populations.

Genetic characteristics of spouse selection based on short tandem repeats in DNA and lunula count on fingertip

OBJECTIVE

The aim of this study was to assess the correlation of spouse selection with short tandem repeats (STRs) in DNA and with the number of fingertip lunulae to investigate the role of heredity in spouse selection.

METHODS

We randomly selected a total of 286 couples (husband and wife) as a couple group while 200 paired subjects (a man randomly matched with a woman as a pair of subjects) were selected as a non-spouse group for DNA typing, and to investigate lunulae in spouse selection, a total of 554 couples were selected as a couple group and 500 pairs of subjects were selected as a control group.

RESULTS

A significant difference of STR matching number (a large value implies a higher genetic similarity) between spouse group and non-spouse group were observed (12.3 ± 2.7 vs. 11.8 ± 2.6; p < 0.05). A significant difference of the lunula matching number (difference of lunula counts between a paired subjects, a lower value implies a higher genetic similarity) between two groups were also observed for the lunula counts (1.55 ± 1.88 vs. 3.53 ± 2.40; p < 0.01).

CONCLUSION

Significant and unprecedented relationships were found between the couples and polymorphic STRs, and between spouse selection and lunula counts. Polymorphic STRs and fingertip lunulae counts provide an initial insight into the potentially important contributions that genetic characteristics may play a key role in spouse selection.

Discrimination of monozygotic twins using mtDNA heteroplasmy through probe capture enrichment and massively parallel sequencing

Differentiating between monozygotic (MZ) twins remains difficult because they have the same genetic makeup. Applying the traditional STR genotyping approach cannot differentiate one from the other. Heteroplasmy refers to the presence of two or more different mtDNA copies within a single cell and this phenomenon is common in humans. The levels of heteroplasmy cannot change dramatically during transmission in the female germ line but increase or decrease during germ-line transmission and in somatic tissues during life. As massively parallel sequencing (MPS) technology has advanced, it has shown the extraordinary quantity of mtDNA heteroplasmy in humans. In this study, a probe hybridization technique was used to obtain mtDNA and then MPS was performed with an average sequencing depth of above 4000. The results showed us that all ten pairs of MZ twins were clearly differentiated with the minor heteroplasmy threshold at 1.0%, 0.5%, and 0.1%, respectively. Finally, we used a probe that targeted mtDNA to boost sequencing depth without interfering with nuclear DNA and this technique can be used in forensic genetics to differentiate the MZ twins.

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

Optimization and Validation of Candida auris Short Tandem Repeat Analysis

Candida auris is an easily transmissible yeast with resistance to different antifungal compounds. Outbreaks of C. auris are mostly observed in intensive care units. To take adequate measures during an outbreak, it is essential to understand the transmission route, which requires isolate genotyping. In 2019, a short tandem repeat (STR) genotyping analysis was developed for C. auris. To determine the discriminatory power of this method, we performed STR analysis of 171 isolates with known whole-genome sequencing (WGS) data using Illumina reads, and we compared their resolutions. We found that STR analysis separated the 171 isolates into four clades (clades I to IV), as was also seen with WGS analysis. Then, to improve the separation of isolates in clade IV, the STR assay was optimized by the addition of 2 STR markers. With this improved STR assay, a total of 32 different genotypes were identified, while all isolates with differences of >50 single-nucleotide polymorphisms (SNPs) were separated by at least 1 STR marker. Altogether, we optimized and validated the C. auris STR panel for clades I to IV and established its discriminatory power, compared to WGS SNP analysis using Illumina reads. IMPORTANCE The emerging fungal pathogen Candida auris poses a threat to public health, mainly causing outbreaks in intensive care units. Genotyping is essential for investigating potential outbreaks and preventing further spread. Previously, we developed a STR genotyping scheme for rapid and high-resolution genotyping, and WGS SNP outcomes for some isolates were compared to STR data. Here, we compared WGS SNP and STR outcomes for a larger sample cohort. Also, we optimized the resolution of this typing scheme with the addition of 2 STR markers. Altogether, we validated and optimized this rapid, reliable, and high-resolution typing scheme for C. auris.

Opportunity of Next-Generation Sequencing-Based Short Tandem Repeat System for Tumor Source Identification

Personal identification using the tumor DNA not only plays an important role in postoperative tissue management but also might be the only accessible source of biological material in forensic identification. Short tandem repeat (STR) is the worldwide accepted forensic marker; however, widespread loss of heterozygosity (L) in tumor tissues challenges the personal identification using the conventional capillary electrophoresis (CE)-based STR typing system (CE-STR). Because the tumors are mixtures of tumor cells and basal cells, we inferred that every germline-originated allele should be detected if the detection method was sensitive enough. Next-generation sequencing (NGS) is known as a highly sensitive application, which might be a promising tool for tumor source identification. In the study, we genotyped and compared the STR results between the platforms, and we found that the concordance was only 91.43%. Higher sensitivity did help identify more germline-originated alleles as expected, and 93.89% of them could be captured by using an NGS-based STR system (NGS-STR). The identity-by-state (IBS) scoring system was applied to generate a new tumor source identification method based on NGS-STR, and the number of loci with 2 identical alleles (A₂) proved to be an ideal criterion for the larger area under the receiver operating characteristic (ROC) curve (AUC). Both the sensitivity and specificity were above 98% in the cutoff of A₂ to distinguish the paired carcinoma (PC) sample group from the unrelated individual (UI) group, the simulated full sibling (FS) group, and the simulated parent–offspring (PO) group.

Evaluation and comparison of population genetics software in Rabari Tribe of Gujarat population

Background

Today, when forensic experts talk about quantifiable hereditary traits, they do not just depend on the assessment and examination of DNA profiles but also relate them to the population structures. The use of high-throughput molecular marker technologies and advanced statistical and software tools have improved the accuracy of human genetic diversity analysis in many populations with limited time and resources. The present study aimed to investigate the genomic diversity in Gujarat’s Rabari population, using 20 autosomal genetic markers.

Numerous bio-statistical software programs are available for the interpretation of population data in forensics. These statistics deal with the measurement of uncertainty and also provides a probability of a random match. The present paper aims to provide a practical guide to the analysis of population genetics data. Three statistical software packages named Cervus, Genepop, and Fstat are compared and contrasted. The comparison is performed on the profiles obtained from fifty unrelated blood samples of healthy male individuals. DNA was extracted using the organic extraction method, 20 autosomal STR loci were amplified using PowerPlex 21 kit (Promega, Madison, WI, USA) and detected on 3100 Genetic Analyser (Life Technologies Corporation, Carlsbad, CA, USA).

Results

A total of 170 alleles were observed in the Rabari Tribe of Gujarat population, and allele frequencies ranged from 0.010 to 0.480. The highest allele frequency detected was 0.480 for allele 9 at locus TH01. Based on heterozygosity and the polymorphism information content, FGA may be considered as the most informative markers. Both the combined power of discrimination (CPD) and the combined power of exclusion (CPE) for the 20 analyzed loci were higher than 0.999999. The combined match probability (CPM) for all 20 loci was 2.5 × 10−22.

Conclusions

With respect to the results, the 20 STR loci are highly polymorphic and discriminating in the Gujarat population and could be used for forensic practice and population genetics studies. However, Fstat demonstrated better genetic software for analysis of the demographic structure of a specific or set of populations.