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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (25 February 2026) | Viewed by 12557

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Dr. Mauro Pesaresi

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Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto, 60126 Ancona, Italy
Interests: legal medicine; forensic pathology; sudden death; sudden unexpected death in epilepsy (SUDEP); sudden cardiac death (SCD); forensic genetics; nuclear and mitochondrial DNA polymorphisms; DNA persistence; DNA phenotyping; individual identification; activity level and probabilistic genotyping
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Dear Colleagues,

There have been significant advances in forensic science in the last several years, and the development and application of genetics have revolutionized approaches to this field.

For the first time, in 1984, the term “DNA fingerprint” was mentioned by Alec Jeffreys, who analyzed polymorphic regions of DNA. Even though the gold-standard method for forensic genotyping is still the analysis of STR polymorphisms through capillary electrophoresis, forensic laboratories are gradually introducing complementary assays based on more advanced technological platforms. Both the scope and scale of DNA analysis in forensic science are set to continue expanding in the foreseeable future. Current research in advanced forensic genetics is aiming to enhance the accuracy, speed, and effectiveness of DNA analysis in legal contexts. Key objectives include improving identification precision, even with degraded, mixed, or limited samples, through advanced technologies such as next-generation sequencing (NGS) and new individual biomarkers such as microhaplotypes. The NGS technique is also applicable to phenotyping, which comprises the prediction of a person's externally visible characteristics regarding appearance, biogeographic ancestry, and age using DNA from crime scene samples, to provide investigative leads to help find unknown perpetrators that cannot be identified through forensic STR profiling. Forensic genetics has become an important field in forensic science, helping in cause-of-death investigations and post-mortem interval estimation and introducing promising biomarkers such as microRNAs (miRNAs), which, with their small size, are a promising tool in various fields in forensic medicine. Another goal is to speed up forensic investigations by using faster, automated techniques, such as AI-assisted data analysis, to reduce turnaround times. This is particularly valuable in resolving cold cases. Lastly, the evaluation of the results of forensic genetic analyses is vital, given that activity level propositions represent an emerging discipline in forensic genetics; today, this is considered a critically important topic for the field of forensics. The increasing sensitivity of analysis techniques and advances in data interpretation using probabilistic models ('probabilistic genotyping') is increasing the demands on forensic biologists to share specialized knowledge to help recipients of expert information to address the mode and timing of the transfer and persistence of traces in court.

In launching this Special Issue, we aim to gather the most advanced research currently available in forensic genetics, to showcase the most interesting work in our field.

Dr. Mauro Pesaresi
Guest Editor

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Keywords

forensic genetics
massive parallel sequencing (MPS)
DNA quantification methods
DNA extraction methods
sudden cardiac death
post-mortem interval
microRNA
DNA phenotyping
individual identification
genetic markers
short tandem repeats (STRs)
single-nucleotide polymorphism (SNP)
mitochondrial DNA (mtDNA)
microhaplotype
forensic statistics
artificial intelligence
activity level in forensics

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Published Papers (8 papers)

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Research

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17 pages, 741 KB

Open AccessArticle

Performance of the ForenSeq^TM Imagen Kit for Forensic DNA Phenotyping Under Partial Genotyping Conditions

by Nayeli González-Ortiz, Mariano Guardado-Estrada, Nahum Zepeta-Flores, José Miguel Moreno-Ortiz, Adrián Ramírez-de-Arellano, Héctor Rangel-Villalobos, José Francisco Muñoz-Valle and José Alonso Aguilar-Velázquez

Genes 2026, 17(3), 354; https://doi.org/10.3390/genes17030354 - 23 Mar 2026

Viewed by 599

Abstract

Background: Forensic DNA phenotyping (FDP) enables the inference of externally visible characteristics (EVCs) and biogeographic ancestry when conventional STR profiling is inconclusive. The ForenSeq™ Imagen kit (107 SNPs) integrates phenotype-, ancestry-, and Y-SNPs markers; however, its performance under partial genotyping conditions has not been systematically evaluated. Methods: Ninety-four samples from a Mexican mestizo population were analyzed using the ForenSeq™ Imagen kit on the MiSeq FGx™ platform. Due to incomplete genotype recovery, 41 samples with >60% locus detection were selected for downstream analyses. Phenotype prediction was performed using the HIrisPlex-S model, and ancestry inference was assessed through principal component analysis. In silico simulations were conducted to evaluate locus-specific dropout effects. Results: Eye color prediction showed both reduced feasibility (68.3%) and lower overall accuracy (56.1%), primarily driven by systematic prediction failure when rs12913832 (HERC2) was absent, although accuracy among successfully predicted samples remained high (82.1%). In contrast, hair and skin color inference remained feasible in >97% and 100% of evaluable samples, respectively; however, classification accuracy was moderate (70% for hair and 61% for skin), improving substantially when allowing adjacent-category concordance (90.2% for skin). Ancestry inference was robust when at least 27 aiSNPs were detected, and Y-SNPs reliably distinguished male and female samples. In silico analyses confirmed the critical contribution of rs12913832 to eye color model operability. Conclusions: FDP performance under partial genotyping reflects a trade-off between prediction feasibility and accuracy and depends on locus-specific integrity rather than overall genotype completeness. The ForenSeq™ Imagen kit shows robustness for ancestry, sex, hair, and skin prediction, although with variable accuracy, whereas eye color inference remains structurally vulnerable to drop out of high-impact variants. Evaluating FDP systems under realistic non-ideal conditions is essential to define their true operational limits and ensure scientifically robust and responsible implementation. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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12 pages, 2576 KB

Open AccessArticle

Genetic Diversity of 27 Y-STRs in Two Jordanian Subpopulations: Bedouins and Fellahin

by Almuthanna K. Alkaraki, Mohammad B. Alsliman, Mohammad M. Twait, Miguel A. Alfonso-Sánchez and Jose A. Peña

Genes 2026, 17(2), 194; https://doi.org/10.3390/genes17020194 - 4 Feb 2026

Cited by 1 | Viewed by 1838

Abstract

Background/Objectives: The Bedouins (nomads) and the Fellahin (farmers) of Jordan represent two distinct subpopulations, characterized by unique lifestyles, settlement patterns, and linguistic features. This study aims to estimate the frequency of 27 Y-STRs in these two Jordanian subpopulations, along with various forensic parameters and paternal lineage comparisons with neighboring populations. Methods: Twenty-seven Y-STRs were typed in two major Jordanian subpopulations: Bedouin nomads (n = 101) and Fellahin farmers (n = 98). The forensic and paternal genetic lineage parameters and Y-haplogroup predictions were estimated. In addition, we conducted multidimensional scaling (MDS) and centroid analyses based on the Fst distance matrix to compare the sampled communities with neighboring populations from the MENA region, East Africa, Southeast Europe, and South Asia. Results: The Y-haplogroup predictions revealed differences in the predicted lineage composition based on the Y-STR profiles. The predicted J1a2a1a2 haplogroup predominated among the Bedouins (74.3%), whereas the Fellahin displayed a more heterogeneous profile, with notable frequencies of J1 (40%) and J2 (17.3%). Furthermore, the Fellahin exhibited remarkable genetic diversity and significant gene flow, providing plausible evidence of kinship with neighboring Levantine and Arabian groups. In contrast, the Bedouins showed consistently lower diversity across multiple loci, indicating long-term tribal isolation and, therefore, the potential effects of genetic drift. The MDS and centroid analyses positioned the Fellahin among the genetically interconnected Middle Eastern populations, while the Bedouins were clustered with the Arabian Peninsula populations. Conclusions: Overall, the contrasting genetic signatures of the two Jordanian subpopulations reflect their settlement patterns and sociocultural practices. In addition, the Y-STR dataset generated in this study enhances the Jordanian forensic database and to extends our understanding of paternal lineage structures in the West Asian/Levantine region. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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10 pages, 209 KB

Open AccessArticle

Cardiac Genetic Variants in Sudden, Unexpected Death in Epilepsy: From Challenging DNA Extraction Methods to Updated NGS Panels for Improved Genetic Analysis

by Alessia Bernini Di Michele, Valerio Onofri, Filomena Melchionda, Lucia Fiordelmondo, Eleonora Ciarimboli, Marco Palpacelli, Sara Sablone, Chiara Turchi and Mauro Pesaresi

Genes 2025, 16(11), 1272; https://doi.org/10.3390/genes16111272 - 28 Oct 2025

Cited by 1 | Viewed by 760

Abstract

Background/Objectives: SUDEP is the sudden, unexpected death of someone with epilepsy, and occurs mainly during sleep or at rest, or when the individual does not seem to have experienced a convulsive seizure. The cause of death in SUDEP is still unknown, and it may differ between cases. Cardiac factors are among the most prevalent causes observed in SUDEP. Therefore, within the forensic medicine framework, identifying well-known DNA markers involved in cardiac sudden and unexpected death would aid in understanding the cause of SUDEP, as well as in finding cardiac risk markers in patients with epilepsy. The purpose of this study was to identify any genetic variants by analyzing blood and formalin-fixed paraffin-embedded (FFPE) tissue samples, utilizing next-generation sequencing techniques. Methods: We investigated five cases of SUDEP that were examined at the Legal Medicine department of Ancona (Italy). Peripheral blood or FFPE cardiac tissues were collected, and different DNA extraction methods were performed. In particular, this study underlines a new extraction method from FFPE tissue, adapting the Casework kit for forensic application to our purpose. Later, about one hundred genes correlated to inherited cardiac diseases were sequenced through the Ion PGM System and Ion GeneStudio S5 Systems. Results: Bioinformatic analysis showed some genetic variants of unknown significance (VUS) on genes involved in SUDEP: RYR2, SCN8A, and AKAP9. Conclusions: As expected, very low coverage of the target base was observed for FFPE tissue samples because of the complexity of the biological material. Therefore, the presence of any significant variants in unamplified regions cannot be excluded in the FFPE samples. As suggested by the literature, the variants found in the blood samples are potentially associated with SUDEP. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

16 pages, 644 KB

Open AccessArticle

Forensic DNA Recovery from FFPE Tissue Using the Maxwell^® RSC Xcelerate Kit: Optimization, Challenges, and Limitations

by Dagmara Lisman, Andrzej Ossowski, Aleksandra Tołoczko-Grabarek, Mateusz Kozłowski and Aneta Cymbaluk-Płoska

Genes 2025, 16(9), 1074; https://doi.org/10.3390/genes16091074 - 12 Sep 2025

Cited by 1 | Viewed by 1937

Abstract

Background/Objectives: Obtaining reliable DNA profiles from archival tissue preserved as formalin-fixed, paraffin-embedded (FFPE) samples remains a major challenge in both forensic and medical evaluations. The quality of DNA isolated from FFPE material is frequently compromised due to formalin-induced fragmentation and chemical modifications. These limitations are particularly relevant in cases of suspected medical malpractice related to cancer diagnosis or treatment, where retrospective molecular analyses may provide critical evidence. The aim of this study was to evaluate the performance of the Maxwell^® RSC Xcelerate DNA FFPE Kit (Promega) in generating DNA profiles from archival FFPE tissue blocks of endometrial cancer and to identify the limitations associated with this approach. Methods: Archival FFPE blocks of endometrial cancer were analyzed using the Maxwell^® RSC Xcelerate DNA FFPE Kit. DNA yield, purity, and degradation indices were assessed using standard real-time PCR-based quantification methods. Short tandem repeat (STR) profiling was performed with forensic genotyping kits, and the completeness, allele balance, and reliability of obtained profiles were evaluated. The obtained results were compared with reference quality thresholds commonly used in forensic practice. Results: The Maxwell^® RSC Xcelerate Kit allowed for recovery of relatively high DNA yields with consistently low degradation indices, confirming good extraction efficiency from FFPE samples. Nevertheless, despite favorable quantitative values, the generation of complete STR profiles was often unsuccessful. Partial or incomplete profiles were frequent, characterized by allele dropout and imbalance, which substantially reduced their evidentiary value. These findings suggest that DNA fragmentation and fixation-related artifacts impair amplification efficiency and limit the usefulness of STR analysis. Conclusions: This study emphasizes the persistent challenges of DNA profiling from FFPE tissue in forensic-medical contexts. Although the Maxwell^® RSC Xcelerate Kit demonstrated effective DNA recovery, the ability to generate complete and interpretable STR profiles remained limited. Further refinement of extraction protocols, as well as improved interpretative strategies, are required to enhance the reliability and evidentiary significance of molecular analyses based on archival FFPE material. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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13 pages, 1507 KB

Open AccessArticle

DNA Transfer Between Items Within an Evidence Package

by Yong Sheng Lee and Christopher Kiu-Choong Syn

Genes 2025, 16(8), 894; https://doi.org/10.3390/genes16080894 - 28 Jul 2025

Cited by 3 | Viewed by 2240

Abstract

Background/Objectives: Advancements in DNA profiling have made it possible to retrieve intact DNA profiles from increasingly minute biological samples. This increased sensitivity in DNA detection has highlighted crucial considerations to be made when handling and packing items from the crime scene to minimize potential contamination from either direct or indirect transfer of DNA. To investigate potential DNA transfer between items stored within the same evidence package, we conducted a simulation study with items commonly encountered during forensic casework. Methods: Participants were grouped in pairs, each of them handling the same type of item to simulate the activity conducted at the crime scene. The items were then collected from each pair of participants and stored in the same evidence package for 4 to 5 days. To evaluate the basal DNA transfer between items within the same package, the packed items were not subjected to friction, force, or long-distance movement in this study. Results: We have observed the occurrence of DNA transfer on 39% of the studied items inside the package, which changed the source attribution of the DNA profiles for 10% of the recovered samples. Our results showed that the types of items were associated with the number of transferred alleles and the amount of DNA recovered, while no association was found between the number of transferred alleles and the amount of DNA on the studied items. Conclusions: Taken together, the results from this study reiterate the importance of packing each item from the crime scene separately, especially when packing items together may impact the interpretation of source attribution. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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19 pages, 449 KB

Open AccessArticle

An Upper Bound on the Power of DNA to Distinguish Pedigree Relationships

by Maarten Kruijver

Genes 2025, 16(5), 492; https://doi.org/10.3390/genes16050492 - 26 Apr 2025

Cited by 5 | Viewed by 2568

Abstract

Background/Objectives: Dense genetic marker panels are increasingly used in kinship analysis for the identification of distant relatives. As more markers are available, it is possible to pinpoint IBD segments more precisely and more reliably, ultimately approaching close to continuously observed IBD. This study investigates the evidential value obtained for discrimination between common pedigree relationships if IBD is observed continuously across the autosomal genome without error. In the continuous case, the evidential value is limited only by the pedigree relationship and the recombination rates. Methods: We conducted simulations to generate IBD segments across the autosomal genome for individuals with defined pedigree relationships. The evidential value for relationship discrimination was then calculated exactly from the underlying model, assuming no genotyping error and full genome coverage. Results: The simulations show that the ability to distinguish pedigree relationships quickly diminishes as relationships become more distant. First cousins can be distinguished from second cousins with 99.9% accuracy which drops to 94% when distinguishing second and third cousins. Relationships with the same expected degree of relatedness can be discriminated using continuously observed IBD, although the effectiveness decreases with more distant relationships. Conclusions: Continuous IBD observation establishes a theoretical upper bound on the power to distinguish relationships if a large but finite number of markers is used. The findings provide a benchmark for evaluating kinship analyses based on finite genetic marker panels. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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Review

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12 pages, 453 KB

Open AccessReview

A Mini Narrative Review on Human DNA Transfer Involving Dogs and Cats and Their Role in Forensic Investigation

by Carla Bini, Alessia Trasatti, Arianna Giorgetti, Sara Amurri, Giulia Fazio and Susi Pelotti

Genes 2026, 17(4), 423; https://doi.org/10.3390/genes17040423 - 2 Apr 2026

Viewed by 446

Abstract

Background/Objectives: The potential role of domestic animals in DNA transfer, persistence, prevalence and recovery (TPPR) warrants careful consideration in forensic contexts. This mini narrative review aims to provide an updated overview of human DNA transfer involving household dogs and cats as vectors, to clarify their forensic relevance, and to identify key considerations for the design of future experimental research. Methods: A narrative review was conducted using multiple electronic databases as search engines without restriction related to the timing of publication. Results: Experimental evidence shows that dogs and cats readily acquire human DNA following even brief contact, acting as reservoirs for primary DNA transfer. Once acquired, human DNA can be redistributed via secondary transfer to a wide range of substrates, such as gloved hands, vehicle interiors, clothing, and surfaces. Moreover, multi-step and higher-order transfer events have been documented, highlighting the complexity of DNA transfer involving household animals. Conclusions: The sampling on pets may be included in certain scenarios and may contribute to building a Bayesian network together with the experimental data. To deal with uncertainty during probability assignment, more experimental data, especially addressing the main variables impacting DNA TPPR involving pets, should be generated and are highly needed to assist in activity level evaluation. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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34 pages, 1365 KB

Open AccessReview

Predicting Physical Appearance from Low Template: State of the Art and Future Perspectives

by Francesco Sessa, Emina Dervišević, Massimiliano Esposito, Martina Francaviglia, Mario Chisari, Cristoforo Pomara and Monica Salerno

Genes 2026, 17(1), 59; https://doi.org/10.3390/genes17010059 - 5 Jan 2026

Cited by 1 | Viewed by 1242

Abstract

Background/Objectives: Forensic DNA phenotyping (FDP) enables the prediction of externally visible characteristics (EVCs) such as eye, hair, and skin color, ancestry, and age from biological traces. However, low template DNA (LT-DNA), often derived from degraded or trace samples, poses significant challenges due to allelic dropout, contamination, and incomplete profiles. This review evaluates recent advances in FDP from LT-DNA, focusing on the integration of machine learning (ML) models to improve predictive accuracy and operational readiness, while addressing ethical and population-related considerations. Methods: A comprehensive literature review was conducted on FDP and ML applications in forensic genomics. Key areas examined include SNP-based trait modeling, genotype imputation, epigenetic age estimation, and probabilistic inference. Comparative performance of ML algorithms (Random Forests, Support Vector Machines, Gradient Boosting, and deep learning) was assessed using datasets such as the 1000 Genomes Project, UK Biobank, and forensic casework samples. Ethical frameworks and validation standards were also analyzed. Results: ML approaches significantly enhance phenotype prediction from LT-DNA, achieving AUC > 0.9 for eye color and improving SNP recovery by up to 15% through imputation. Tools like HIrisPlex-S and VISAGE panels remain robust for eye and hair color, with moderate accuracy for skin tone and emerging capabilities for age and facial morphology. Limitations persist in admixed populations and traits with polygenic complexity. Interpretability and bias mitigation remain critical for forensic admissibility. Conclusions: L integration strengthens FDP from LT-DNA, offering valuable investigative leads in challenging scenarios. Future directions include multi-omics integration, portable sequencing platforms, inclusive reference datasets, and explainable AI to ensure accuracy, transparency, and ethical compliance in forensic applications. Full article

(This article belongs to the Special Issue Advanced Research in Forensic Genetics)

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