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Advances and Challenges in Forensic Genetics

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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: 15 June 2026 | Viewed by 11410

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Special Issue Editors

Dr. Maria Helena Correia Dias

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Guest Editor

1. Departamento de Ciências da Vida, Centro de Investigação em Antropologia e Saúde, Universidade de Coimbra, Coimbra, Portugal
2. Departamento de Ciências da Vida, Laboratório de Antropologia Forense, Universidade de Coimbra, Coimbra, Portugal
3. Instituto Nacional de Medicina Legal e Ciências Forenses, Coimbra, Portugal
Interests: forensic genetics; forensic epigenetics; DNA methylation age estimation; forensic anthropology

Dr. Venusia Cortellini

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Guest Editor

Forensic Genetics Laboratory, Institute of Legal Medicine, University of Brescia, Brescia, Italy
Interests: forensic genetics; DNA analysis; trace and evidence analysis; legal medicine

Special Issue Information

Dear Colleagues,

Forensic genetics is one of the most important areas of forensics. It is based on DNA analysis, which allows for the unique identification of individuals, except for identical twins, who share the same genetic profile. The most commonly used method is the analysis of short tandem repeats (STRs), which is considered the gold-standard approach to DNA profiling.

DNA analysis can also provide information on physical traits, such as skin and hair color, sex, ancestry (through biogeographic markers), and age estimation through an epigenetic approach. These traits help in the identification process and can guide entire criminal investigations.

In recent years, new methodologies and laboratory techniques have greatly improved DNA analysis, making it more efficient, more accurate, and faster. Advances such as massive parallel sequencing (MPS), rapid DNA analysis, artificial intelligence, and 3D genomics, while offering many benefits, also add challenges to forensic geneticists’ routine casework, requiring them to constantly learn new skills and adapt to employing novel techniques.

A particularly interesting development is forensic epigenetics, a growing area within forensic genetics with potential applications in forensics, which could help in the resolution of cases in a new way.

Our main aim for this Special Issue is to provide in-depth knowledge on the advances and challenges in forensic genetics, focusing on laboratory advances and the emerging field of forensic epigenetics. We hope that this Special Issue will encourage further research in this evolving field.

Dr. Maria Helena Correia Dias
Dr. Venusia Cortellini
Guest Editors

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Keywords

DNA analysis
DNA methylation applications
biogeographic ancestry
age estimation approaches
discrimination of monozygotic twins
discrimination of tissues
next-generation sequencing
forensic cases

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Published Papers (8 papers)

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Research

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34 pages, 20484 KB

Open AccessArticle

A Fast-Fourier-Transform-Based Dynamic Likelihood Ratio Framework for Controlling False Positives in DNA Database Matching

by François-Xavier Laurent, Willem Burgers, Wim Wiegerinck, Cyril Gout and Susan Hitchin

Genes 2026, 17(5), 499; https://doi.org/10.3390/genes17050499 - 23 Apr 2026

Viewed by 636

Abstract

Background/Objectives: Operational DNA databases traditionally rely on static locus-count thresholds to determine search eligibility and report matches. While computationally straightforward, these rigid criteria routinely discard high-value investigative leads from degraded forensic profiles while simultaneously permitting adventitious matches when common alleles are involved. To overcome the limitations of static rules, this study introduces an automated framework for dynamic likelihood ratio (LR) thresholding. Methods: Utilizing a Fast Fourier Transform (FFT) algorithm, the system calculates the Probability Mass Function (PMF) for any specific combination of shared loci in real-time, natively incorporating the Balding–Nichols model to account for population substructure. Instead of applying an arbitrary locus count or fixed LR cutoff, the framework defines admissibility based on a user-defined maximum upper bound of acceptable false positives at a specified confidence (probability) level (e.g., 95%). Results: This empowers database custodians to precisely predict and adapt their search criteria to match an acceptable administrative workload, dynamically adjusting the required LR threshold to the exact size of the searched database. This approach was validated through massive-scale empirical simulations across five reference population groups. Receiver Operating Characteristic (ROC) and Poisson distribution analyses reveal that static thresholds inevitably collapse under the multiplicity effect of large-scale comparisons; for instance, a static locus rule that maintains safety within a small DNA database yields an unmanageable false positive risk when scaled to larger DNA databases or international networks like the Prüm DNA Exchange. Conclusions: By explicitly coupling the decision threshold to the database size and the genetic rarity of the evidence, this dynamic framework provides a mathematically rigorous and scalable solution. Most notably, it identifies rare, low-locus matches that static rules typically discard, offering a method to maintain a predefined expected false positive rate. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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11 pages, 1147 KB

Open AccessArticle

Genetic Characterization and Statistical Interpretation of 16 STR Markers in South-West Bulgaria: Implications for Forensic Identification and Kinship Analysis

by Vera Djeliova, Bogdan Mirchev, Ekaterina Angelova, Milka Mileva, Dimo Krastev, Atanas Hristov, Yanko Kolev and Aleksandar Apostolov

Genes 2026, 17(4), 493; https://doi.org/10.3390/genes17040493 - 21 Apr 2026

Viewed by 187

Abstract

Background/Objectives: The widespread adoption of short tandem repeat (STR) marker technology in genetic analysis has led to the collection of substantial STR data from diverse populations. Allele-frequency data provide robust forensic utility and support accurate likelihood ratio calculations, highlighting the importance of regional databases. Methods: The presented study aimed to determine the allelic frequencies and statistical parameters for 16 autosomal genetic STR markers included in the NGM Detect^TM PCR Amplification Kit in a population sample of 220 unrelated individuals from the South-West region of the Republic of Bulgaria. Results: We found that the most polymorphic and informative marker for the Bulgarian population in the southwestern region is SE33, with the next most informative markers being D1S1656, D12S391, D18S51, and FGA. In contrast, D22S1045, D16S539, and D2S441 showed comparatively lower genetic variability and informativeness. At the same time, no deviations from the Hardy–Weinberg equilibrium were observed for the 16 loci studied. Conclusions: This work not only enriches knowledge of the genetic diversity of the Bulgarian population but also provides the Bulgarian and international justice systems with an objective, scientifically sound basis for expert decision-making. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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8 pages, 437 KB

Open AccessArticle

Preparing for Shotgun Sequencing in Forensic Genetics—A Workflow for Analysis of Monozygotic Twins

by Olivia Luxford Meyer, Claus Børsting, Jeppe Dyrberg Andersen and Marie-Louise Kampmann

Genes 2026, 17(4), 409; https://doi.org/10.3390/genes17040409 - 31 Mar 2026

Viewed by 528

Abstract

Background/Objectives: Identifying the true perpetrator among monozygotic (MZ) twins has long posed a challenge in forensic genetics and for police investigations because MZ twins are likely identical in their short tandem repeat (STR) profile. In this study, we propose a workflow to address this issue, anchored in a case study involving MZ twins. Methods: The workflow includes shotgun sequencing of reference samples from one twin and trace samples, followed by a targeted amplicon-based approach (AmpliSeq™ Custom Panel) to validate the identified variants. Results: Biological traces from the crime scene, identified as blood, were available for analysis along with reference material from one twin, collected as a buccal swab. The samples underwent shotgun sequencing, and the resulting reads were aligned to the human reference genome. The sequencing yielded 2.91 and 2.85 billion mapped positions (corresponding to a breadth of coverage of 91% and 89%), with mean depths of coverage of 39.7× and 25.8× for the trace and reference samples, respectively. To minimise the risk of detecting somatic variants in the two different tissues, a stringent heterozygosity balance threshold (Hb: 0.4–0.6) was applied, and 2,047,077 single nucleotide variants (SNVs) were identified, of which 28 showed inconsistencies between the trace and reference samples. These candidate variants were subjected to validation using an AmpliSeq™ Custom Panel. Conclusions: No detectable SNV differences were observed between the reference and trace samples, and it was not possible to determine whether the trace originated from the reference twin or from his monozygotic co-twin. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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18 pages, 1239 KB

Open AccessArticle

Bone Marrow as a Source of DNA in Forensic Genetics: An Optimized Nucleic Acids Extraction Protocol

by Mattia Porcu, Noemi Argirò, Venusia Cortellini, Antonio De Luca, Camilla Tettamanti, Lorenzo Franceschetti, Francesco Ventura and Andrea Verzeletti

Genes 2026, 17(3), 332; https://doi.org/10.3390/genes17030332 - 18 Mar 2026

Viewed by 513

Abstract

Background: low-quantity or degraded samples are often studied in forensic genetics. Therefore, it is important to efficiently obtain all the available DNA from the biological sample analyzed to provide the most reliable results. This is particularly challenging in bone marrow processing due to its hydrophobic molecular structure, as for other lipid-rich tissues, especially if rancid. In fact, during adipose tissue decomposition, the putrefaction of fatty acids can in some instances give a compact cerous consistency to the lipidic tissue, hardly susceptible to the nucleic acid extraction mechanisms. According to environmental circumstances, this condition is notably observable in submerged bodies or in putrefied bone marrow. Thus, this study is focused on developing an optimized nucleic acids extraction protocol for putrefied bone marrow. Methods: genetic analyses were performed on putrefied yellow bone marrow collected from 20 human femora recovered from bodies in different decomposition stages. The optimized method was developed by integrating additional steps, reagents and time intervals on a silica-based column commercial kit. This strategy was compared in DNA yield to a standard extraction protocol, represented by the same commercial kit, but following the manufacturer’s directions. Both these strategies were tested in nucleic acid isolation efficiency by performing DNA typing, including real-time PCR quantification, Short Tandem Repeats (STR) amplification and fragments analysis steps. The analytical parameters evaluated were allele count, DNA concentration (ng/µL) and Degradation Index (DI). Results: for allele count and DNA concentration parameters, the optimized protocol showed clear and significant qualitative and quantitative improvements compared with the standard protocol, supporting its potential applicability in forensic casework and laying the foundation for future studies. Conclusions: prior to appropriate laboratory internal validation, the optimized protocol can be used for tough lipid-rich tissues processing without the need to purchase a dedicated system and using a same commercial kit routinely adopted for other forensic genetics matrices. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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25 pages, 1609 KB

Open AccessArticle

Forensic Validation of the 95K SNP Panel and the Parabon Fx Forensic Analysis Platform for Identification of US Military Unknowns Using Extended Kinship Inference

by Jacqueline Tyler Thomas, Courtney L. Cavagnino, Kimberly Sturk-Andreaggi, Ellen M. Greytak, Julie A. Demarest, Suzanne M. Barritt-Ross, Timothy P. McMahon and Charla Marshall

Genes 2026, 17(3), 306; https://doi.org/10.3390/genes17030306 - 3 Mar 2026

Cited by 1 | Viewed by 2073

Abstract

Background/Objectives: To identify US military unknowns, the Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory has historically relied upon mitochondrial DNA and Y-chromosomal short tandem repeat testing. Where no appropriate family reference sample (FRS) is available or skeletal samples are degraded, autosomal single nucleotide polymorphism (SNP) testing with next-generation sequencing could assist. Methods: A method utilizing hybridization capture enrichment of a 95,000 (95K) SNP panel, amenable to FRS and extremely challenging samples, was validated. The Parabon Fx Forensic Analysis Platform was used for analysis and extended kinship inference. Skeletal samples (n = 65) and associated FRS (n = 64) were selected for a performance evaluation and case-type sample study. Results: Considering FRS with ≥7 ng DNA input into library preparation, 94% yielded ≥66,320 SNPs at ≥5X coverage. SNP recovery for skeletal samples at ≥1X coverage ranged from 5 to 94,197 SNPs, averaging 40,770 SNPs. When skeletal samples resulted in ≥13,000 SNPs, the most likely relationship category was consistent with the expected relationship. A log10 likelihood ratio of ≥4 and a posterior probability of ≥99.99% were established as thresholds for strong statistical support, and 87% of inferences met these thresholds while 13% were considered inconclusive. Pairwise kinship inference between unrelated individuals yielded an unrelated result in 85% of comparisons, 66% with strong statistical support. There were 170 instances of false positive 4th degree relationship inferences with strong statistical support. All false positives involved skeletal samples from individuals of admixed ancestry. Conclusions: With this approach, autosomal SNP testing can result in reliable kinship inferences between related individuals out to 3rd, and in some cases 4th, degree relationships, increasing the scope of eligible FRS to aid in identifications. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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13 pages, 1141 KB

Open AccessArticle

Pedigree-Based Estimation of Y-STR Mutation and Male Differentiation Rates: Application to Historical Remains Identification

by Jasmine R. Connell, Toni White, Thais Zielke, Luke Armstrong, Natasha Mitchell and Lyn R. Griffiths

Genes 2025, 16(10), 1211; https://doi.org/10.3390/genes16101211 - 14 Oct 2025

Viewed by 1506

Abstract

Background/Objectives: High differentiation rates provided by Y-chromosomal short tandem repeats (Y-STRs) are highly advantageous in most forensic and genealogical casework, as they enhance the ability to exclude close or moderately related individuals, refine an individual’s position within a pedigree, and uncover the population substructure in otherwise homogeneous groups. However, the impact for historical remains identification casework is underexplored. Methods: We present a pedigree analysis of 366 males from 183 pedigrees, separated by 4 to 16 meioses at 27 Y-STR loci, from the Yfiler Plus kit. The differentiation rate for a given degree of separation was defined as the proportion of pairs at that specific number of meioses showing at least one allelic difference, relative to the total number of such pairs. Results: Our pedigree-based locus-specific mutation rates were consistent with published father–son values for 22 of 25 loci, with 3 loci (DYS389II, DYS449, and DYS570) being significantly different (p < 0.05). These results were consistent with previous pedigree-based estimates, and the strong agreement between father–son and pedigree-based mutation rates supports the use of pedigrees as a reliable method for estimating mutation rates. The probability of differentiating male relatives reached 60.1%, which is similar to previous studies using the Yfiler Plus kit. Conclusions: This high male differentiation rate is advantageous for distinguishing unrelated individuals within the same population, reducing false inclusions. However, when comparing distantly related individuals, excessive mutations accumulated over many generations may obscure genuine patrilineal relationships, increasing the risk of false exclusions. Our findings are likely to be highly valuable for future interpretation of Y-STR haplotypes from patrilineal relatives across a wide range of applications, with significant relevance to historical remains identification casework. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

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Review

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20 pages, 345 KB

Open AccessReview

Integrative Forensic Genetics, Biochemical, and Histological Methods for Reconstructing Biological Profiles from Aged Human Skeletal Remains

by Irena Zupanič Pajnič and Tamara Leskovar

Genes 2026, 17(3), 258; https://doi.org/10.3390/genes17030258 - 25 Feb 2026

Viewed by 648

Abstract

The reconstruction of biological profiles from aged or degraded human skeletal remains represents a major challenge in both forensic and bioarcheological contexts, particularly when conventional identification approaches fail. Recent advances in molecular genetics, biochemical and histological analyses, and biomolecular anthropology have substantially expanded the range of information that can be recovered from compromised remains. This review synthesizes current integrative approaches combining genomic analyses, stable isotope investigations, epigenetic age estimation, proteomic sex determination, and complementary histological techniques to infer sex, ancestry, kinship, age, diet, mobility, and geographic origin. Genetic methods, including next-generation sequencing (NGS), enable increasingly robust inference even from highly degraded samples. Stable isotope analyses provide insights into dietary patterns and mobility, while DNA methylation markers improve age estimation accuracy. Tooth cementum annulation (TCA), although a histological rather than molecular method, contributes an additional chronological indicator within an integrative analytical framework. Rather than treating these approaches independently, this review proposes a multidisciplinary perspective in which complementary datasets collectively support biological profile reconstruction. Integrative interpretation enhances identification potential and provides more nuanced life-history reconstructions, demonstrating the value of combining molecular, biochemical, and histological evidence in forensic and archaeological investigations. Full article

(This article belongs to the Special Issue Advances and Challenges in Forensic Genetics)

20 pages, 354 KB

Open AccessReview

Analysis of Human Degraded DNA in Forensic Genetics

by Irena Zupanič Pajnič

Genes 2025, 16(11), 1375; https://doi.org/10.3390/genes16111375 - 11 Nov 2025

Cited by 8 | Viewed by 4323

Abstract

Upon an organism’s death, enzymatic DNA repair ceases, exposing the genome to destructive factors such as free cellular nucleases and proliferating microorganisms, which can cause DNA loss. DNA preservation is highly dependent on environmental conditions, and less favorable environments accelerate degradation. Despite this, advanced extraction and analytical methods now enable the study of poorly preserved and degraded DNA. DNA typing is a foundation of forensic genomics, enabling the identification of individuals and the individualization of biological evidence through the generation of unique genetic profiles. Although DNA is relatively stable, environmental exposure initiates its degradation into progressively shorter fragments, complicating analysis. The extent of DNA preservation in biological evidence depends on numerous factors, and this review focuses on the environmental factors—including temperature, humidity, ultraviolet radiation, pH, chemical agents, and microbial activity—as the most influential variables. In samples with degraded DNA, the maximum amplicon length achievable through polymerase chain reaction (PCR) is inherently limited. This review discusses genetic markers and analytical strategies improvements that enable the examination of highly degraded samples, particularly when conventional short tandem repeat (STR) typing fails. In these situations, successful identification requires targeting short DNA fragments, which are more likely to persist. Single-nucleotide polymorphisms (SNPs) are a valuable alternative, as their high allelic variability and short amplicon requirements make them more amenable to amplification from fragmented templates than STRs. Advances in next-generation sequencing (NGS) technologies have further enhanced this capacity by enabling high-resolution SNP profiling, thereby improving outcomes in challenging forensic cases. Full article

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