Special Issue "Forensic Genetics and Genomics"

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

Deadline for manuscript submissions: closed (31 July 2020).

Special Issue Editor

Prof. Dr. Emiliano Giardina
Website1 Website2 Website3
Guest Editor
1. Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00142 Rome, Italy
2. Forensic Genetics Laboratoty, Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
Interests: Forensic Genetics; Genetic Counselling; Human Identification; Neurogenetics; Prenatal and postnatal genetic diagnosis;

Special Issue Information

Dear Colleagues,

Over the last 30 years, technological progress has led to the development of ultra-sensitive methods that can be applied to different fields of molecular genetics, including forensic genetics. Indeed, the availability of an -omic platform for the comprehensive and in-depth analysis of DNA or RNA is revolutionizing forensic investigations and can play a crucial role in improving current methods to find offenders, exonerate wrongly accused individuals, and identify victims of crime and disasters. Basic and applied genomics are expected to modify and probably remodel the methods we currently use for the genetic characterization and interpretation of forensic evidence.

This Special Issue focuses on the relevant aspects of forensic DNA analysis, covering new trends in forensic genetics. In particular, this Special Issue covers:

  • Recent progress concerning individual identification based on genomic investigation;
  • New scientific and technological developments in forensic genetics;
  • Examination of forensic biostatistics applied to a real case;
  • New approaches for forensic biostatistical analysis;
  • Recent progress on the age estimation of biological evidence;
  • Recent progress on the ancestry estimation of biological evidence;
  • Current limits and perspectives of forensic DNA phenotyping;
  • Use of RNA/miRNA in the forensic identification of biological fluids;
  • Recent progress, methods, and perspectives of forensic epigenetics.

Kind regards,

Prof. Emiliano Giardina
Guest Editor

Manuscript Submission Information

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Keywords

  • age estimation of forensic evidence
  • ancestry estimation
  • DNA mixtures
  • DNA phenotyping
  • epigenomics
  • forensic biostatistics
  • forensic genetics
  • forensic genomics
  • human identification
  • missing person identification
  • next-generation sequencing (NGS)
  • transcriptomics

Published Papers (11 papers)

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Research

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Open AccessArticle
A Highly Polymorphic Panel Consisting of Microhaplotypes and Compound Markers with the NGS and Its Forensic Efficiency Evaluations in Chinese Two Groups
Genes 2020, 11(9), 1027; https://doi.org/10.3390/genes11091027 - 01 Sep 2020
Abstract
Novel genetic markers like microhaplotypes and compound markers show promising potential in forensic research. Based on previously reported single nucleotide polymorphism (SNP) and insertion/deletion (InDel) polymorphism loci, 29 genetic markers including 22 microhaplotypes and seven compound markers were identified. Genetic distributions of the [...] Read more.
Novel genetic markers like microhaplotypes and compound markers show promising potential in forensic research. Based on previously reported single nucleotide polymorphism (SNP) and insertion/deletion (InDel) polymorphism loci, 29 genetic markers including 22 microhaplotypes and seven compound markers were identified. Genetic distributions of the 29 loci in five continental populations, Kazak and Mongolian groups in China were investigated. We found that the expected heterozygosity values of these 29 loci were >0.4 in these populations, indicating these loci were relatively high polymorphisms. Population genetic analyses of five continental populations showed that five loci displayed relatively high genetic variations among these continental populations and could be useful markers for ancestry analysis. In summary, the 29 loci displayed relatively high genetic diversities in continental populations and Chinese two groups and could be informative loci for forensic research. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
The STRidER Report on Two Years of Quality Control of Autosomal STR Population Datasets
Genes 2020, 11(8), 901; https://doi.org/10.3390/genes11080901 - 07 Aug 2020
Abstract
STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates [...] Read more.
STRidER, the STRs for Identity ENFSI Reference Database, is a curated, freely publicly available online allele frequency database, quality control (QC) and software platform for autosomal Short Tandem Repeats (STRs) developed under the endorsement of the International Society for Forensic Genetics. Continuous updates comprise additional STR loci and populations in the frequency database and many further STR-related aspects. One significant innovation is the autosomal STR data QC provided prior to publication of datasets. Such scrutiny was lacking previously, leaving QC to authors, reviewers and editors, which led to an unacceptably high error rate in scientific papers. The results from scrutinizing 184 STR datasets containing >177,000 individual genotypes submitted in the first two years of STRidER QC since 2017 revealed that about two-thirds of the STR datasets were either being withdrawn by the authors after initial feedback or rejected based on a conservative error rate. Almost no error-free submissions were received, which clearly shows that centralized QC and data curation are essential to maintain the high-quality standard required in forensic genetics. While many errors had minor impact on the resulting allele frequencies, multiple error categories were commonly found within single datasets. Several datasets contained serious flaws. We discuss the factors that caused the errors to draw the attention to redundant pitfalls and thus contribute to better quality of autosomal STR datasets and allele frequency reports. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs
Genes 2020, 11(7), 743; https://doi.org/10.3390/genes11070743 - 03 Jul 2020
Abstract
Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating [...] Read more.
Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
Interpreting Mixture Profiles: Comparison Between Precision ID GlobalFiler™ NGS STR Panel v2 and Traditional Methods
Genes 2020, 11(6), 591; https://doi.org/10.3390/genes11060591 - 26 May 2020
Abstract
Forensic investigation for the identification of offenders, recognition of human remains, and verification of family relationships requires the analysis of particular types of highly informative DNA markers, which have high discriminatory power and are efficient for typing degraded samples. These markers, called STRs [...] Read more.
Forensic investigation for the identification of offenders, recognition of human remains, and verification of family relationships requires the analysis of particular types of highly informative DNA markers, which have high discriminatory power and are efficient for typing degraded samples. These markers, called STRs (Short Tandem Repeats), can be amplified by multiplex-PCR (Polymerase Chain Reaction) allowing attainment of a unique profile through which it is possible to distinguish one individual from another with a high statistical significance. The rapid and progressive evolution of analytical techniques and the advent of Next-Generation Sequencing (NGS) have completely revolutionized the DNA sequencing approach. This technology, widely used today in the diagnostic field, has the advantage of being able to process several samples in parallel, producing a huge volume of data in a short time. At this time, although default parameters of interpretation software are available, there is no general agreement on the interpretation rules of forensic data produced via NGS technology. Here we report a pilot study aimed for a comparison between NGS (Precision ID GlobalFiler™ NGS STR Panel v2, Thermo Fisher Scientific, Waltham, MA, USA) and traditional methods in their ability to identify major and minor contributors in DNA mixtures from saliva and urine samples. A quantity of six mixed samples were prepared for both saliva and urine samples from donors. A total of 12 mixtures were obtained in the ratios of 1:2; 1:4; 1:6; 1:8; 1:10; and 1:20 between minor and major contributors. Although the number of analyzed mixtures is limited, our results confirm that NGS technology offers a huge range of additional information on samples, but cannot ensure a higher sensitivity in respect to traditional methods. Finally, the Precision ID GlobalFiler™ NGS STR Panel v2 is a powerful method for kinship analyses and typing reference samples, but its use in biological evidence should be carefully considered on the basis of the characteristics of the evidence. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods
Genes 2020, 11(5), 582; https://doi.org/10.3390/genes11050582 - 22 May 2020
Cited by 1
Abstract
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This “swab in—profile out” method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary [...] Read more.
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This “swab in—profile out” method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessCommunication
Characterizing Y-STRs in the Evaluation of Population Differentiation Using the Mean of Allele Frequency Difference between Populations
Genes 2020, 11(5), 566; https://doi.org/10.3390/genes11050566 - 19 May 2020
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each [...] Read more.
Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure. In this study, a total of 20,927 haplotypes of a Yfiler Plus set were collected from 41 global populations. Different configurations were observed in multidimensional scaling (MDS) plots based on pairwise genetic distances evaluated using a Yfiler set and a Yfiler Plus set, respectively. Subsequently, 23 single-copy Y-STRs were characterized in the evaluation of population differentiation using the mean of allele frequency difference (mAFD) between populations. Our results indicated that DYS392 had the largest mAFD value (0.3802) and YGATAH4 had the smallest value (0.1845). On the whole, larger pairwise genetic distances could be obtained using the set with the top fifteen markers from these 23 single-copy Y-STRs, and clear clustering or separation of populations could be observed in the MDS plot in comparison with those using the set with the minimum fifteen markers. In conclusion, the mAFD value is reliable to characterize Y-STRs for efficiency in the evaluation of population differentiation. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China
Genes 2020, 11(5), 564; https://doi.org/10.3390/genes11050564 - 18 May 2020
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of [...] Read more.
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
Ancestry Prediction Comparisons of Different AISNPs for Five Continental Populations and Population Structure Dissection of the Xinjiang Hui Group via a Self-Developed Panel
Genes 2020, 11(5), 505; https://doi.org/10.3390/genes11050505 - 04 May 2020
Cited by 1
Abstract
Ancestry informative markers are genetic markers that show distinct genetic divergences among different populations. These markers can be utilized to discern population substructures and estimate the ancestral origins of unknown individuals. Previously, we developed a multiplex system of 30 ancestry informative single nucleotide [...] Read more.
Ancestry informative markers are genetic markers that show distinct genetic divergences among different populations. These markers can be utilized to discern population substructures and estimate the ancestral origins of unknown individuals. Previously, we developed a multiplex system of 30 ancestry informative single nucleotide polymorphism (AISNP) loci to facilitate ancestral inferences in different continental populations. In the current study, we first compared the ancestry resolutions of the 30 AISNPs and the other previously reported AISNP panels for African, European, East Asian, South Asian and American populations. Next, the genetic components of the Xinjiang Hui group were further explored in comparison to these continental populations based on the 30 AISNPs. Genetic divergence analyses of the 30 AISNPs in these five continental populations revealed that most of the AISNPs showed high genetic differentiations between these populations. Ancestry analysis comparisons of the 30 AISNPs and other published AISNPs revealed that these 30 AISNPs had comparable efficiency to other AISNP panels. Genetic relationship analyses among the studied Hui group and other continental populations demonstrated that the Hui group had close genetic affinities with East Asian populations and might share the genetic ancestries with East Asian populations. Overall, the 30 AISNPs can be used to predict the bio-geographical origins of different continental populations. Moreover, the obtained genetic data of 30 AISNPs in the Hui group can further enrich the extant reference data, which can be used as reference data for ancestry analyses of the Hui group. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Open AccessArticle
Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling
Genes 2020, 11(4), 381; https://doi.org/10.3390/genes11040381 - 01 Apr 2020
Cited by 2
Abstract
Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the occurrence of homopolymers in STR loci. The [...] Read more.
Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the occurrence of homopolymers in STR loci. The goal of this study was to apply the latest progress in nanopore sequencing by Oxford Nanopore Technologies in the field of STR genotyping. The experiments were performed using the state of the art R9.4 flow cell and the most recent R10 flow cell, which was specifically designed to improve consensus accuracy of homopolymers. Two single-contributor samples and one mixture sample were genotyped using Illumina sequencing, Nanopore R9.4 sequencing, and Nanopore R10 sequencing. The accuracy of genotyping was comparable for both types of flow cells, although the R10 flow cell provided improved data quality for loci characterized by the presence of homopolymers. We identify locus-dependent characteristics hindering accurate STR genotyping, providing insights for the design of a panel of STR loci suited for nanopore sequencing. Repeat number, the number of different reference alleles for the locus, repeat pattern complexity, flanking region complexity, and the presence of homopolymers are identified as unfavorable locus characteristics. For single-contributor samples and for a limited set of the commonly used STR loci, nanopore sequencing could be applied. However, the technology is not mature enough yet for implementation in routine forensic workflows. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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Review

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Open AccessReview
Challenges in Human Skin Microbial Profiling for Forensic Science: A Review
Genes 2020, 11(9), 1015; https://doi.org/10.3390/genes11091015 - 28 Aug 2020
Cited by 1
Abstract
The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a [...] Read more.
The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a personal microbiome. This review highlights some important aspects of recent studies, many of which have revealed issues involving the effect of contamination of microbial samples from both technical and environmental sources and their impacts on microbiome research and the potential forensic applications of microbial profiling. It is imperative that these challenges be discussed and evaluated within a forensic context to better understand the future directions and potential applications of microbial profiling for human identification. It is necessary that the limitations identified be resolved prior to the adoption of microbial profiling, or, at a minimum, acknowledged by those applying this new approach. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)

Other

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Open AccessCommentary
Autosomal STR Profiling and Databanking in Malaysia: Current Status and Future Prospects
Genes 2020, 11(10), 1112; https://doi.org/10.3390/genes11101112 - 23 Sep 2020
Abstract
Science and technology are extensively used in criminal investigation. From the mid- to late-1980s, one of the scientific discoveries that has had a particularly remarkable impact on this field has been the use of highly variable DNA sequence regions (minisatellites) in the human [...] Read more.
Science and technology are extensively used in criminal investigation. From the mid- to late-1980s, one of the scientific discoveries that has had a particularly remarkable impact on this field has been the use of highly variable DNA sequence regions (minisatellites) in the human genome for individual identification. The technique was initially referred to as DNA fingerprinting, but is now more widely referred to as DNA profiling. Since then, many new developments have occurred within this area of science. These include the introduction of new genetic markers (microsatellites also known as short tandem repeats/STRs), the use of the polymerase chain reaction for target amplification, the development of DNA databases (databanking), and the advancement and/or improvement of genotyping protocols and technologies. In 2019, we described the progress of DNA profiling and DNA databanking in Malaysia for the first time. This report included information on DNA analysis regulations and legislation, STR genotyping protocols, database management, and accreditation status. Here, we provide an update on the performance of our DNA databank (numbers of DNA profiles and hits) plus the technical issues associated with correctly assigning the weight of evidence for DNA profiles in an ethnically diverse population, and the potential application of rapid DNA testing in the country. A total of 116,534 DNA profiles were obtained and stored in the Forensic DNA Databank of Malaysia (FDDM) by 2019, having increased from 70,570 in 2017. The number of hits increased by more than three-fold in just two years, where 17 and 69 hits between the DNA profiles stored in the FDDM and those from crime scenes, suspects, detainees, drug users, convicts, missing persons, or volunteers were recorded in 2017 and 2019, respectively. Forensic DNA analysis and databanking are thus progressing well in Malaysia and have already contributed to many criminal investigations. However, several other issues are discussed here, including the need for STR population data for uncharacterized population groups, and pilot trials for adopting rapid DNA profiling technology. These aspects should be considered by policy makers and law enforcement agencies in order to increase the reliability and efficiency of DNA profiling in criminal cases and in kinship analysis in Malaysia. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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