State-of-the-Art in Forensic Genetics Volume II

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: closed (20 August 2024) | Viewed by 4894

Special Issue Editor


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Guest Editor
Section of Legal Medicine, Marche Polytechnic University, Ancona, Italy
Interests: forensic genetics; massive parallel sequencing; individual identification; kinship analysis; mtDNA analysis in forensics; microhaplotypes analysis
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Special Issue Information

Dear Colleagues,

Since its first use 35 years ago, the field of forensic genetics has undergone many advancements in knowledge and technology, resulting in faster results, a higher sensitivity and information content, and stronger conclusions, mostly for challenging specimens.

Great improvements in DNA extraction methods have been observed, especially through the introduction of robotic workstations. Automation is now also involved in all laboratory steps through the development of rapid and portable fully automated DNA-profiling systems, which allow results in less than 90 min and also immediately at the crime scene.

A higher information content in forensic DNA analysis has been achieved using expanded sets of core STR loci and deeper information from the sequence analysis of alleles. Several SNP panels for different purposes, as well as novel types of molecular markers, such as the microhaplotype loci that are useful for individual identification, ancestry inference, estimating relationships, and deconvoluting mixtures, have been developed. Supplemental genetic markers that are not only related to personal identification and parental testing but also to other important issues, such as body fluid identification, postmortem interval (PMI) estimation, and forensic DNA phenotyping for investigative purposes (appearance, age, and biogeographic prediction), have been introduced into forensic practice.

Mitochondrial DNA polymorphisms have been widely used in addition to nuclear STR loci, especially for challenging forensic samples. Among the new technologies introduced in recent years, massive parallel sequencing (MPS) has had a great impact on the forensic field, both in terms of data quantity and of the type of markers and allele discrimination.

In addition, non-human DNA has demonstrated its utility in the forensic field. Microbioma analysis may aid investigations, allowing the discrimination of environmental samples, postmortem interval estimation (PMI), geolocation, non-sterile body fluid and tissue characterization, and human identification.

Strong improvements have been made in the last years with respect to improving the ability to decipher and interpret all data obtained from DNA analysis, and this not only remains the greatest challenge but also provides the most exciting opportunities for future advances in forensic DNA analysis. Probabilistic approaches are constantly under development, not only for the statistical evaluation of a genetic profile match and a complex DNA mixture but also for familial searching, and they are useful for finding close relatives and for the prediction of age, external visible traits, and PMI. Moreover, particular attention has been paid to the relevance of DNA evidence in relation to an activity, and much progress has been made in the evaluation of biological traces, considering activity level propositions.

The aim of this Special Issue is to illustrate the principal advancements in the forensic genetic field, both in terms of the research efforts and of casework and current practice, by covering all the laboratory steps related to obtaining DNA profiles and data interpretation.

Dr. Chiara Turchi
Guest Editor

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Keywords

  • forensic genetic
  • DNA profiling
  • short tandem repeats
  • mitochondrial DNA
  • DNA phenotyping
  • massive parallel sequencing
  • SNPs
  • forensic DNA extraction
  • DNA quantification
  • individual identification
  • parentage testing
  • activity level evaluation
  • molecular autopsy

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Published Papers (3 papers)

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Research

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13 pages, 1907 KiB  
Article
Biogeographical Ancestry Analyses Using the ForenSeqTM DNA Signature Prep Kit and Multiple Prediction Tools
by Nina Mjølsnes Salvo, Gunn-Hege Olsen, Thomas Berg and Kirstin Janssen
Genes 2024, 15(4), 510; https://doi.org/10.3390/genes15040510 - 18 Apr 2024
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Abstract
The inference of biogeographical ancestry (BGA) can assist in police investigations of serious crime cases and help to identify missing people and victims of mass disasters. In this study, we evaluated the typing performance of 56 ancestry-informative SNPs in 177 samples using the [...] Read more.
The inference of biogeographical ancestry (BGA) can assist in police investigations of serious crime cases and help to identify missing people and victims of mass disasters. In this study, we evaluated the typing performance of 56 ancestry-informative SNPs in 177 samples using the ForenSeq™ DNA Signature Prep Kit on the MiSeq FGx system. Furthermore, we compared the prediction accuracy of the tools Universal Analysis Software v1.2 (UAS), the FROG-kb, and GenoGeographer when inferring the ancestry of 503 Europeans, 22 non-Europeans, and 5 individuals with co-ancestry. The kit was highly sensitive with complete aiSNP profiles in samples with as low as 250pg input DNA. However, in line with others, we observed low read depth and occasional drop-out in some SNPs. Therefore, we suggest not using less than the recommended 1ng of input DNA. FROG-kb and GenoGeographer accurately predicted both Europeans (99.6% and 91.8% correct, respectively) and non-Europeans (95.4% and 90.9% correct, respectively). The UAS was highly accurate when predicting Europeans (96.0% correct) but performed poorer when predicting non-Europeans (40.9% correct). None of the tools were able to correctly predict individuals with co-ancestry. Our study demonstrates that the use of multiple prediction tools will increase the prediction accuracy of BGA inference in forensic casework. Full article
(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics Volume II)
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17 pages, 952 KiB  
Article
Transferability of Human and Environmental Microbiome on Clothes as a Tool for Forensic Investigations
by Noemi Procopio, Giulia Sguazzi, Emma V. Eriksson, Nengi Ogbanga, Frazer C. McKell, Eleanor P. Newton, Paola A. Magni, Andrea Bonicelli and Sarah Gino
Genes 2024, 15(3), 375; https://doi.org/10.3390/genes15030375 - 19 Mar 2024
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Abstract
Considering the growing importance of microbiome analyses in forensics for identifying individuals, this study explores the transfer of the skin microbiome onto clothing, its persistence on fabrics over time, and its transferability from the environment and between different garments. Furthermore, this project compares [...] Read more.
Considering the growing importance of microbiome analyses in forensics for identifying individuals, this study explores the transfer of the skin microbiome onto clothing, its persistence on fabrics over time, and its transferability from the environment and between different garments. Furthermore, this project compares three specific QIAGEN microbiome extraction kits to test their extraction efficiency on fabric samples. Additionally, this study aims to check if these extracts contain human DNA, providing a chance to obtain more information from the same evidence for personal identification. The results obtained show: (1) variations in the skin microbiome between the volunteers, potentially due to their different sex; (2) differences in microbial composition between worn and unworn clothing; (3) the influence of the environment on the microbial signature of unworn clothing; (4) the potential use of certain phyla as biomarkers to differentiate between worn and unworn garments, even over extended periods; (5) a tendency towards extraction biases in the QIAampMP® DNA microbiome kit among the three tested ones; and (6) none of the extraction kits allow for the typing of human genetic profiles suitable for comparison. In conclusion, our study offers supplementary insights into the potential utility of time-transferred microbiome analysis on garments for forensic applications. Full article
(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics Volume II)
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Review

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12 pages, 259 KiB  
Review
Sudden Cardiac Death and Channelopathies: What Lies behind the Clinical Significance of Rare Splice-Site Alterations in the Genes Involved?
by Mauro Pesaresi, Alessia Bernini Di Michele, Filomena Melchionda, Valerio Onofri, Federica Alessandrini and Chiara Turchi
Genes 2024, 15(10), 1272; https://doi.org/10.3390/genes15101272 - 27 Sep 2024
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Abstract
Background and objectives: Sudden cardiac death (SCD) is a natural and unexpected death of cardiac origin that occurs within 1 h from the onset of acute symptoms. The major leading causes of SCD are cardiomyopathies and channelopathies. In this review, we focus [...] Read more.
Background and objectives: Sudden cardiac death (SCD) is a natural and unexpected death of cardiac origin that occurs within 1 h from the onset of acute symptoms. The major leading causes of SCD are cardiomyopathies and channelopathies. In this review, we focus on channelopathies, inherited diseases caused by mutations affecting genes encoding membrane ion channels (sodium, potassium or calcium channels) or cellular structures that affect Ca2+ availability. The diagnosis of diseases such as long QT, Brugada syndrome, short QT and catecholaminergic polymorphic ventricular tachycardia (CPVT) is still challenging. Currently, genetic testing and next-generation sequencing allow us to identify many rare alterations. However, some non-coding variants, e.g., splice-site variants, are usually difficult to interpret and to classify. Methods: In our review, we searched for splice-site variants of genes involved in channelopathies, focusing on variants of unknown significance (VUSs) registered on ClinVar up to now. Results: The research led to a high number of splice-site VUSs of genes involved in channelopathies, suggesting the performance of deeper studies. Conclusions: In order to interpret the correlation between variants and pathologies, we discuss experimental studies, such as RNA sequencing and functional analysis of proteins. Unfortunately, as these in vitro analyses cannot always be performed, we draw attention to in silico studies as future perspectives in genetics. This review has the aim of discussing the potential methods of detection and interpretation of VUSs, bringing out the need for a future reclassification of variants with currently unknown significance. Full article
(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics Volume II)
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