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Strategies and Techniques in DNA Forensic Investigations
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Strategies and Techniques in DNA Forensic Investigations

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

Deadline for manuscript submissions: closed (15 December 2024) | Viewed by 9551

Special Issue Editors

Dr. Claus Børsting

E-Mail Website
Guest Editor
Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
Interests: forensic genetics; SNP analysis; STR analysis; microhaplotype analysis; whole genome sequencing; whole transcriptome sequencing; forensic investigative genetic genealogy
Dr. Vania Alves e Silva Pereira

E-Mail Website
Guest Editor
Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
Interests: population genetics; forensic genetics; mtDNA analysis; Y chromosome analysis; X-chromosomal diversity; genetic markers; massively parallel sequencing; ancestry; age estimation

Special Issue Information

Dear Colleagues,

High-throuput sequencing quickly changed the landscape of genetic research by introducing vast new possibilities, ranging from single-cell sequencing to microbiome analyses and the whole-genome sequencing of ancient samples. In forensic genetic case work the revolution has evolved slowly, most likely because of the highly optimized and highly sensitive PCR-CE methods already in place in most laboratories. Nevertheless, high-throughput sequencing has had a large impact on forensic genetic research during the last 10–15 years and some of the techniques are gradually being introduced into case work. It has led to new methods, new markers, new applications, and new ways of performing statistical analyses.

The aim of this Special Issue, entitled “Strategies and Techniques in DNA Forensic Investigations", is to highlight the state of the forensic genetic techniques used today and debate their future objectives as well as challenges. Colleagues are encouraged to submit manuscripts of original articles or reviews on forensic genetics.

Dr. Claus Børsting
Dr. Vania Alves e Silva Pereira
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • human identification
  • relationship testing
  • forensic investigative genetic genealogy
  • next-generation sequencing/massively parallel sequencing
  • DNA
  • haploid markers
  • RNA
  • DNA methylation
  • non-human forensic genetics

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Published Papers (6 papers)

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Research

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12 pages, 2086 KiB  
Article
Development of Publicly Available Forensic DNA Sequence Mixture Data
by Erica L. Romsos, Kevin M. Kiesler, Carolyn R. Steffen, Lisa A. Borsuk, Sarah Riman, Lauren E. Mullen, Jodi A. Irwin, Peter M. Vallone and Katherine B. Gettings
Genes 2025, 16(3), 333; https://doi.org/10.3390/genes16030333 - 12 Mar 2025
Viewed by 653
Abstract
Background: In 2018, the Next-Generation Sequencing Committee of SWGDAM queried bioinformatic and statistical interpretation method developers regarding data needs for the development of sequence-based probabilistic genotyping software. Methods: Based on this engagement, a set of 74 mixture samples was conceived and [...] Read more.
Background: In 2018, the Next-Generation Sequencing Committee of SWGDAM queried bioinformatic and statistical interpretation method developers regarding data needs for the development of sequence-based probabilistic genotyping software. Methods: Based on this engagement, a set of 74 mixture samples was conceived and created using 11 single-source samples. The allelic overlap among these samples was evaluated and sample combinations of varying complexity were selected, aiming to represent the variability observed in forensic casework. Results: The samples were distributed into a 96-well plate design containing several features: (1) three-person mixtures of 1% to 5% minor components in triplicate with varying levels of input DNA to provide information on sensitivity and reproducibility, (2) three-person mixtures containing degraded DNA of either only the major contributor or all three contributors, (3) four- and five-person mixtures with varying ratios and donors, (4) a single-source dilution series. Conclusions: Mixture samples were prepared and have been sequenced thus far with three commercially available kits targeting forensic short tandem repeat (STR) and single nucleotide polymorphism (SNP) markers, with FASTQ data files and metadata publicly available at doi.org/10.18434/M32157. Full article
(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)
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20 pages, 1945 KiB  
Article
Considerations for the Implementation of Massively Parallel Sequencing into Routine Kinship Analysis
by Lucinda Davenport, Laurence Devesse, Somruetai Satmun, Denise Syndercombe Court and David Ballard
Genes 2025, 16(3), 238; https://doi.org/10.3390/genes16030238 - 20 Feb 2025
Viewed by 911
Abstract
Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve [...] Read more.
Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve more distant or complex relationships can be limited. Massively parallel sequencing (MPS) has become a popular alternative method to CE for analysing genetic markers for forensic applications, including kinship analysis. Data workflows used in kinship testing are well-characterised for CE-based methodologies but are much less established for MPS. When incorporating this technology into routine relationship casework, modifications to existing procedures will be required to ensure that the full power of MPS can be utilised whilst maintaining the authenticity of results. Methods: Empirical data generated with MPS for forensically relevant STRs and SNPs and real-world case experience have been used to determine the necessary workflow adaptations. Results: The four considerations highlighted in this work revolve around the distinctive properties of sequence-based data and the need to adapt CE-based data analysis workflows to ensure compatibility with existing kinship software. These considerations can be summarised as the need for a suitable sequence-based allele nomenclature; methods to account for mutational events; appropriate population databases; and procedures for dealing with rare allele frequencies. Additionally, a practical outline of the statistical adjustments required to account for genetic linkage between loci, within the expanded marker sets associated with MPS, has been presented. Conclusions: This article provides a framework for laboratories wishing to implement MPS into routine kinship analysis, with guidance on aspects of the data analysis and statistical interpretation processes. Full article
(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)
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21 pages, 29667 KiB  
Article
Enhancement of the Precision ID Mitochondrial DNA Whole Genome System for Challenging Unidentified Human Remains
by Lauren C. Canale, Mavis Date-Chong, Jeanette Wallin, Sandra Sheehan, Jessica Battaglia, Michelle Halsing and Daniela Cuenca
Genes 2025, 16(2), 119; https://doi.org/10.3390/genes16020119 - 22 Jan 2025
Viewed by 904
Abstract
Background: The Precision ID mitochondrial (mt) DNA Whole Genome system is a fully automated massively parallel sequencing (MPS) solution for the whole mitochondrial genome. While extremely sensitive, the Precision ID system is susceptible to inhibitors and microbial DNA that are often co-extracted from [...] Read more.
Background: The Precision ID mitochondrial (mt) DNA Whole Genome system is a fully automated massively parallel sequencing (MPS) solution for the whole mitochondrial genome. While extremely sensitive, the Precision ID system is susceptible to inhibitors and microbial DNA that are often co-extracted from human remains. Methods: DNA templates spiked with varying amounts of hematin, humic acid, and calcium, along with bones containing degraded and non-human DNA, were sequenced using the Precision ID system with and without the addition of bovine serum albumin (BSA). Results: BSA added to the initial PCR reaction successfully improved the robustness of the Precision ID system while not negatively impacting the sequencing success of uninhibited samples. The success of BSA is inhibitor-concentration dependent and is effective for templates containing at least 50 ng/μL humic acid, 50 μM hematin, and 1500 μM calcium ions. Furthermore, the presence of microbial DNA in addition to an inhibitor, results in non-specific adaptor ligation to the non-human DNA; BSA can alleviate the inhibition, allowing the human mtDNA to be amplified and sequenced. Conclusions: The addition of BSA to the Precision ID mtDNA system can yield successful sequencing results from challenging case samples that would otherwise fail. Full article
(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)
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11 pages, 632 KiB  
Article
Performance of a 74-Microhaplotype Assay in Kinship Analyses
by Carmen Tomas, Pedro Rodrigues, Carina G. Jønck, Zohal Barekzay, Halimureti Simayijiang, Vania Pereira and Claus Børsting
Genes 2024, 15(2), 224; https://doi.org/10.3390/genes15020224 - 10 Feb 2024
Cited by 3 | Viewed by 2205
Abstract
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic [...] Read more.
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory. Full article
(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)
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17 pages, 3710 KiB  
Article
Optimizing Analytical Thresholds for Low-Template DNA Analysis: Insights from Multi-Laboratory Negative Controls
by Dezhi Chen, Mengyu Tan, Jiaming Xue, Mengna Wu, Jinlong Song, Qiushuo Wu, Guihong Liu, Yazi Zheng, Yuanyuan Xiao, Meili Lv, Miao Liao, Shengqiu Qu and Weibo Liang
Genes 2024, 15(1), 117; https://doi.org/10.3390/genes15010117 - 18 Jan 2024
Viewed by 1926
Abstract
When analyzing challenging samples, such as low-template DNA, analysts aim to maximize information while minimizing noise, often by adjusting the analytical threshold (AT) for optimal results. A potential approach involves calculating the AT based on the baseline signal distribution in electrophoresis results. This [...] Read more.
When analyzing challenging samples, such as low-template DNA, analysts aim to maximize information while minimizing noise, often by adjusting the analytical threshold (AT) for optimal results. A potential approach involves calculating the AT based on the baseline signal distribution in electrophoresis results. This study investigates the impact of reagent kits, testing quarters, environmental conditions, and amplification cycles on baseline signals using historical records and experimental data on low-template DNA. Variations in these aspects contribute to differences in baseline signal patterns. Analysts should remain vigilant regarding routine instrument maintenance and reagent replacement, as these may affect baseline signals. Prompt analysis of baseline status and tailored adjustments to ATs under specific laboratory conditions are advised. A comparative analysis of published methods for calculating the optimal AT from a negative signal distribution highlighted the efficiency of utilizing baseline signals to enhance forensic genetic analysis, with the exception of extremely low-template samples and high-amplification cycles. Moreover, a user-friendly program for real-time analysis was developed, enabling prompt adjustments to ATs based on negative control profiles. In conclusion, this study provides insights into baseline signals, aiming to enhance genetic analysis accuracy across diverse laboratories. Practical recommendations are offered for optimizing ATs in forensic DNA analysis. Full article
(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)
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Review

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36 pages, 2063 KiB  
Review
Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics
by Sharlize Pedroza Matute and Sasitaran Iyavoo
Genes 2024, 15(9), 1133; https://doi.org/10.3390/genes15091133 - 28 Aug 2024
Cited by 2 | Viewed by 1991
Abstract
Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some [...] Read more.
Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs). Nonetheless, these methods are still under optimization, and their adoption into practice is limited. Among the available kits, Thermo Fisher Scientific (Waltham, MA, USA) produces three Precision ID Panels: GlobalFiler NGS STR, Identity, and Ancestry. A clear review of these kits, providing information useful for the promotion of their use, is, however, lacking. To close the gap, a literature review was performed to investigate the popularity, applications, and performance of these kits. Following the PRISMA guidelines, 89 publications produced since 2015 were identified. China was the most active country in the field, and the Identity Panel was the most researched. All kits appeared robust and useful for low-quality and low-quantity samples, while performance with mixtures varied. The need for more population data was highlighted, as well as further research surrounding variables affecting the quality of the sequencing results. Full article
(This article belongs to the Special Issue Strategies and Techniques in DNA Forensic Investigations)
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