Special Issue "Advances in Forensic Genetics"

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

Deadline for manuscript submissions: 15 December 2021.

Special Issue Editor

Prof. Dr. Niels Morling
E-Mail Website
Guest Editor
1. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
2. Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
Interests: forensic genetics; genetics of sudden cardiac death; biostatistics

Special Issue Information

Dear colleagues,

Forensic Genetics has—mainly due to the advent of modern DNA technologies—undergone an impressive development leading to exciting possibilities in forensic genetic work with criminal cases, relationship testing, identification of human remains, animal and plant forensics, etc. This Special Issue is dedicated to the presentation of the current status of forensic genetics and discussion of future challenges and goals through invited presentations. Colleagues are encouraged to submit manuscripts with original research in forensic genetics.

Prof. Dr. Niels Morling
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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 2000 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

  • Forensic genetics
  • Criminal cases
  • Relationship testing
  • Human identification
  • Animal forensic genetics
  • DNA
  • RNA
  • Short Tandem Repeats (STR)
  • Single Nucleotide Polymorphism (SNP)
  • Mitochondrial DNA (mtDNA)
  • Massively Parallel Sequencing (MPS)
  • Forensic statistics
  • Ethics in forensic genetics

Published Papers (9 papers)

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Research

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Article
Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing
Genes 2021, 12(9), 1362; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12091362 - 30 Aug 2021
Viewed by 625
Abstract
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful [...] Read more.
Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the ability to analyze a mixture by separating single cells and obtaining CE-based STR profiles. This indicates a potential use of the method in other forensic investigations, like forensic DNA phenotyping, in which using mixed traces is not fully recommended. For this study, we collected single-source autopsy blood from which the white cells were first stained and later separated with the DEPArray™ N×T System. Groups of 20, 10, and 5 cells, as well as 20 single cells, were collected and submitted for DNA extraction. Libraries were prepared using the Ion AmpliSeq™ PhenoTrivium Panel, which includes both phenotype (HIrisPlex-S: eye, hair, and skin color) and ancestry-associated SNP-markers. Prior to sequencing, half of the single-cell-based libraries were additionally amplified and purified in order to improve the library concentrations. Ancestry and phenotype analysis resulted in nearly full consensus profiles resulting in correct predictions not only for the cells groups but also for the ten re-amplified single-cell libraries. Our results suggest that sequencing of single cells can be a promising tool used to deconvolute mixed traces submitted for forensic DNA phenotyping. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Article
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool
Genes 2021, 12(8), 1284; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081284 - 22 Aug 2021
Viewed by 1033
Abstract
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) [...] Read more.
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Article
Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs
Genes 2021, 12(6), 908; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060908 - 11 Jun 2021
Viewed by 1444
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime [...] Read more.
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog’s appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses’ testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Article
Prediction of Eye Colour in Scandinavians Using the EyeColour 11 (EC11) SNP Set
Genes 2021, 12(6), 821; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060821 - 27 May 2021
Cited by 2 | Viewed by 515
Abstract
Description of a perpetrator’s eye colour can be an important investigative lead in a forensic case with no apparent suspects. Herein, we present 11 SNPs (Eye Colour 11-EC11) that are important for eye colour prediction and eye colour prediction models for a two-category [...] Read more.
Description of a perpetrator’s eye colour can be an important investigative lead in a forensic case with no apparent suspects. Herein, we present 11 SNPs (Eye Colour 11-EC11) that are important for eye colour prediction and eye colour prediction models for a two-category reporting system (blue and brown) and a three-category system (blue, intermediate, and brown). The EC11 SNPs were carefully selected from 44 pigmentary variants in seven genes previously found to be associated with eye colours in 757 Europeans (Danes, Swedes, and Italians). Mathematical models using three different reporting systems: a quantitative system (PIE-score), a two-category system (blue and brown), and a three-category system (blue, intermediate, brown) were used to rank the variants. SNPs with a sufficient mean variable importance (above 0.3%) were selected for EC11. Eye colour prediction models using the EC11 SNPs were developed using leave-one-out cross-validation (LOOCV) in an independent data set of 523 Norwegian individuals. Performance of the EC11 models for the two- and three-category system was compared with models based on the IrisPlex SNPs and the most important eye colour locus, rs12913832. We also compared model performances with the IrisPlex online tool (IrisPlex Web). The EC11 eye colour prediction models performed slightly better than the IrisPlex and rs12913832 models in all reporting systems and better than the IrisPlex Web in the three-category system. Three important points to consider prior to the implementation of eye colour prediction in a forensic genetic setting are discussed: (1) the reference population, (2) the SNP set, and (3) the reporting strategy. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Article
Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch
Genes 2021, 12(5), 733; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050733 - 13 May 2021
Viewed by 707
Abstract
Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, [...] Read more.
Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals also had an average proportion of Sub-Saharan African ancestry of approximately 10%, whereas it was <1% in the Punjabi and Pashtun individuals. The pairwise genetic distances between the Pashtun, Punjabi, and Baloch subpopulations based on the ancestry markers were statistically significantly different. Individuals from the Pashtun subpopulation had statistically significantly lower skin pigmentation than individuals from the Punjabi and Baloch subpopulations (p < 0.05). The proportions of European and Sub-Saharan African ancestry and five SNPs (rs1042602, rs10831496, rs1426654, rs16891982, and rs12913832) were statistically significantly associated with skin pigmentation at either the upper arm, lower arm or forehead in the Pakistani population after correction for multiple testing (p < 10−3). A model based on four of these SNPs (rs1426654, rs1042602, rs16891982, and rs12913832) explained 33% of the upper arm skin pigmentation. The four SNPs and the proportions of European and Sub-Saharan African ancestry explained 37% of the upper arm skin pigmentation. Our results indicate that the four likely causative SNPs, rs1426654, rs1042602, rs16891982, and rs12913832 located in SLC24A5, TYR, SLC45A2, and HERC2, respectively, are essential for skin color variation in the admixed Pakistani subpopulations. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Article
Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification
Genes 2021, 12(2), 221; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020221 - 03 Feb 2021
Cited by 1 | Viewed by 930
Abstract
A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP [...] Read more.
A custom plate of OpenArray™ technology was evaluated to test 60 single-nucleotide polymorphisms (SNPs) validated for the prediction of eye color, hair color, and skin pigmentation, and for personal identification. The SNPs were selected from already validated subsets (Hirisplex-s, Precision ID Identity SNP Panel, and ForenSeq DNA Signature Prep Kit). The concordance rate and call rate for every SNP were calculated by analyzing 314 sequenced DNA samples. The sensitivity of the assay was assessed by preparing a dilution series of 10.0, 5.0, 1.0, and 0.5 ng. The OpenArray™ platform obtained an average call rate of 96.9% and a concordance rate near 99.8%. Sensitivity testing performed on serial dilutions demonstrated that a sample with 0.5 ng of total input DNA can be correctly typed. The profiles of the 19 SNPs selected for human identification reached a random match probability (RMP) of, on average, 10−8. An analysis of 21 examples of biological evidence from 8 individuals, that generated single short tandem repeat profiles during the routine workflow, demonstrated the applicability of this technology in real cases. Seventeen samples were correctly typed, revealing a call rate higher than 90%. Accordingly, the phenotype prediction revealed the same accuracy described in the corresponding validation data. Despite the reduced discrimination power of this system compared to STR based kits, the OpenArray™ System can be used to exclude suspects and prioritize samples for downstream analyses, providing well-established information about the prediction of eye color, hair color, and skin pigmentation. More studies will be needed for further validation of this technology and to consider the opportunity to implement this custom array with more SNPs to obtain a lower RMP and to include markers for studies of ancestry and lineage. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)

Review

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Review
A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™
Genes 2021, 12(10), 1559; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101559 - 30 Sep 2021
Viewed by 634
Abstract
Probabilistic genotyping has become widespread. EuroForMix and DNAStatistX are both based upon maximum likelihood estimation using a γ model, whereas STRmix™ is a Bayesian approach that specifies prior distributions on the unknown model parameters. A general overview is provided of the historical development [...] Read more.
Probabilistic genotyping has become widespread. EuroForMix and DNAStatistX are both based upon maximum likelihood estimation using a γ model, whereas STRmix™ is a Bayesian approach that specifies prior distributions on the unknown model parameters. A general overview is provided of the historical development of probabilistic genotyping. Some general principles of interpretation are described, including: the application to investigative vs. evaluative reporting; detection of contamination events; inter and intra laboratory studies; numbers of contributors; proposition setting and validation of software and its performance. This is followed by details of the evolution, utility, practice and adoption of the software discussed. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Review
Assessing the Forensic Value of DNA Evidence from Y Chromosomes and Mitogenomes
Genes 2021, 12(8), 1209; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081209 - 05 Aug 2021
Viewed by 932
Abstract
Y chromosome and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent), which presents different interpretation challenges [...] Read more.
Y chromosome and mitochondrial DNA profiles have been used as evidence in courts for decades, yet the problem of evaluating the weight of evidence has not been adequately resolved. Both are lineage markers (inherited from just one parent), which presents different interpretation challenges compared with standard autosomal DNA profiles (inherited from both parents). We review approaches to the evaluation of lineage marker profiles for forensic identification, focussing on the key roles of profile mutation rate and relatedness (extending beyond known relatives). Higher mutation rates imply fewer individuals matching the profile of an alleged contributor, but they will be more closely related. This makes it challenging to evaluate the possibility that one of these matching individuals could be the true source, because relatives may be plausible alternative contributors, and may not be well mixed in the population. These issues reduce the usefulness of profile databases drawn from a broad population: larger populations can have a lower profile relative frequency because of lower relatedness with the alleged contributor. Many evaluation methods do not adequately take account of distant relatedness, but its effects have become more pronounced with the latest generation of high-mutation-rate Y profiles. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
Review
Animal Forensic Genetics
Genes 2021, 12(4), 515; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12040515 - 01 Apr 2021
Cited by 1 | Viewed by 915
Abstract
Animal forensic genetics, where the focus is on non-human species, is broadly divided in two: domestic species and wildlife. When traces of a domestic species are relevant to a forensic investigation the question of species identification is less important, as the material comes [...] Read more.
Animal forensic genetics, where the focus is on non-human species, is broadly divided in two: domestic species and wildlife. When traces of a domestic species are relevant to a forensic investigation the question of species identification is less important, as the material comes from either a dog or a cat for instance, but more relevant may be the identification of the actual pet. Identification of a specific animal draws on similar methods to those used in human identification by using microsatellite markers. The use of cat short tandem repeats to link a cat hair to a particular cat paved the way for similar identification of dogs. Wildlife forensic science is becoming accepted as a recognised discipline. There is growing acceptance that the illegal trade in wildlife is having devasting effects on the numbers of iconic species. Loci on the mitochondrial genome are used to identify the most likely species present. Sequencing the whole locus may not be needed if specific bases can be targeted. There can be benefits of increased sensitivity using mitochondrial loci for species testing, but occasionally there is an issue if hybrids are present. The use of massively parallel DNA sequencing has a role in the identification of the ingredients of traditional medicines where studies found protected species to be present, and a potential role in future species assignments. Non-human animal forensic testing can play a key role in investigations provided that it is performed to the same standards as all other DNA profiling processes. Full article
(This article belongs to the Special Issue Advances in Forensic Genetics)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1. DNA-assisted identification of historical remains: a review of methods and recent developments

2. Age estimation in forensic genetics

3. The human genome in policing. Key ethical aspects of advances in forensic genetics

4. Development and evaluation of the ancestry informative marker panel of the VISAGE AmpliSeq Basic Tool.

5. X-Chromosomal STRs: metapopulations and mutation rates   

6. Recent Advances in Wildlife Forensic Science

7. Strategies for kinship analyses using dense SNP data for identifying missing persons

8. Methods for assessing the forensic value of DNA evidence from Y chromosomes and mitogenomes

9. The forensic use of polymorphic loci on the human Y‐chromosome

10.A review of probabilistic genotyping: DNAxs, Euroformix, and STRmix

11. Software and Algorithms for Sequencing Analysis in Forensic Genetics

12. DNA transfer in forensic science: recent progress towards meeting the challenges

13. Technology for the identification of body fluids and tissues, a crucial link in the investigation and solution of crime

14. Review of biostatistical methods for inferring ancestry from genetic markers

15. Interlaboratory Mitochondrial DNA Heteroplasmy Detection using Sanger and Massiv Parallel Sequencing

16. Prediction of physical appearance traits in forensic DNA intelligence

 

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