Genes

Research

Jump to: Review

23 pages, 7330 KiB

Open AccessArticle

Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family

by Odile Loreille, Andreas Tillmar, Michael D. Brandhagen, Linda Otterstatter and Jodi A. Irwin

Genes 2022, 13(2), 202; https://doi.org/10.3390/genes13020202 - 23 Jan 2022

Cited by 9 | Viewed by 10598

Abstract

This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome [...] Read more.

This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina’s lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the locket were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas’ maternal lineage, including the well-known point heteroplasmy at position 16169. Full article

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

► Show Figures

Figure 1

9 pages, 3104 KiB

Open AccessEditor’s ChoiceArticle

Evaluation of Different Cleaning Strategies for Removal of Contaminating DNA Molecules

by Martina Nilsson, Hanne De Maeyer and Marie Allen

Genes 2022, 13(1), 162; https://doi.org/10.3390/genes13010162 - 17 Jan 2022

Cited by 20 | Viewed by 8414

Abstract

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. [...] Read more.

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the different sodium hypochlorite solutions and Trigene^®, for which a maximum of 0.3% DNA was recovered on all three surfaces. For blood, a maximum of 0.8% of the deposited DNA was recovered after using Virkon^® for decontamination. The recoveries after using these cleaning strategies correspond to DNA from only a few cells, out of 60 ng of cell-free DNA or thousands of deposited blood cells. Full article

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

► Show Figures

Figure 1

19 pages, 3098 KiB

Open AccessEditor’s ChoiceArticle

Ancient DNA Methods Improve Forensic DNA Profiling of Korean War and World War II Unknowns

by Elena I. Zavala, Jacqueline Tyler Thomas, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Kerriann K. Meyers, Suzanne Barrit-Ross, Ayinuer Aximu-Petri, Julia Richter, Birgit Nickel, Gregory E. Berg, Timothy P. McMahon, Matthias Meyer and Charla Marshall

Genes 2022, 13(1), 129; https://doi.org/10.3390/genes13010129 - 11 Jan 2022

Cited by 25 | Viewed by 8054

Abstract

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial [...] Read more.

The integration of massively parallel sequencing (MPS) technology into forensic casework has been of particular benefit to the identification of unknown military service members. However, highly degraded or chemically treated skeletal remains often fail to provide usable DNA profiles, even with sensitive mitochondrial (mt) DNA capture and MPS methods. In parallel, the ancient DNA field has developed workflows specifically for degraded DNA, resulting in the successful recovery of nuclear DNA and mtDNA from skeletal remains as well as sediment over 100,000 years old. In this study we use a set of disinterred skeletal remains from the Korean War and World War II to test if ancient DNA extraction and library preparation methods improve forensic DNA profiling. We identified an ancient DNA extraction protocol that resulted in the recovery of significantly more human mtDNA fragments than protocols previously used in casework. In addition, utilizing single-stranded rather than double-stranded library preparation resulted in increased attainment of reportable mtDNA profiles. This study emphasizes that the combination of ancient DNA extraction and library preparation methods evaluated here increases the success rate of DNA profiling, and likelihood of identifying historical remains. Full article

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

► Show Figures

Figure 1

13 pages, 1135 KiB

Open AccessArticle

Individual Identification with Short Tandem Repeat Analysis and Collection of Secondary Information Using Microbiome Analysis

by Solip Lee, Heesang You, Songhee Lee, Yeongju Lee, Hee-Gyoo Kang, Ho-Joong Sung, Jiwon Choi and Sunghee Hyun

Genes 2022, 13(1), 85; https://doi.org/10.3390/genes13010085 - 29 Dec 2021

Cited by 4 | Viewed by 2571

Abstract

Forensic investigation is important to analyze evidence and facilitate the search for key individuals, such as suspects and victims in a criminal case. The forensic use of genomic DNA has increased with the development of DNA sequencing technology, thereby enabling additional analysis during [...] Read more.

Forensic investigation is important to analyze evidence and facilitate the search for key individuals, such as suspects and victims in a criminal case. The forensic use of genomic DNA has increased with the development of DNA sequencing technology, thereby enabling additional analysis during criminal investigations when additional legal evidence is required. In this study, we used next-generation sequencing to facilitate the generation of complementary data in order to analyze human evidence obtained through short tandem repeat (STR) analysis. We examined the applicability and potential of analyzing microbial genome communities. Microbiological supplementation information was confirmed for two of four failed STR samples. Additionally, the accuracy of the gargle sample was confirmed to be as high as 100% and was highly likely to be classified as a body fluid sample. Our experimental method confirmed that anthropological and microbiological evidence can be obtained by performing two experiments with one extraction. We discuss the advantages and disadvantages of using these techniques, explore prospects in the forensic field, and highlight suggestions for future research. Full article

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

► Show Figures

Figure 1

8 pages, 1682 KiB

Open AccessArticle

Efficient DNA Sampling in Burglary Investigations

by Colin Charles Tièche, Markus Dubach and Martin Zieger

Genes 2022, 13(1), 26; https://doi.org/10.3390/genes13010026 - 23 Dec 2021

Cited by 8 | Viewed by 3850

Abstract

In terms of crime scene investigations by means of forensic DNA-analyses, burglaries are the number one mass crime in Switzerland. Around one third of the DNA trace profiles registered in the Swiss DNA database are related to burglaries. However, during the collection of [...] Read more.

In terms of crime scene investigations by means of forensic DNA-analyses, burglaries are the number one mass crime in Switzerland. Around one third of the DNA trace profiles registered in the Swiss DNA database are related to burglaries. However, during the collection of potential DNA traces within someone’s residence after a burglary, it is not known whether the sampled DNA originated from the perpetrator or from an inhabitant of said home. Because of the high incidence of burglaries, crime scene investigators usually do not collect reference samples from all the residents for economical and administrative reasons. Therefore, the presumably high probability that a DNA profile belonging to a person authorized to be at the crime scene ends up being sent to a DNA database for comparison, has to be taken into account. To our knowledge, no investigation has been made to evaluate the percentage of these non-perpetrator profiles straying into DNA databases. To shed light on this question, we collected reference samples from residents who had been victims of recent burglaries in their private homes. By comparing the profiles established from these reference samples with the profiles generated from trace DNA, we can show that the majority of the DNA samples collected in burglary investigations belong to the residents. Despite the limited number of cases included in the study, presumably due to a crime decline caused by the pandemic, we further show that trace DNA collection in the vicinity of the break and entry area, in particular window and door glasses, is most promising for sampling perpetrator instead of inhabitant DNA. Full article

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

► Show Figures

Figure 1

19 pages, 2192 KiB

Open AccessArticle

Who Packed the Drugs? Application of Bayesian Networks to Address Questions of DNA Transfer, Persistence, and Recovery from Plastic Bags and Tape

by Ane Elida Fonneløp, Sara Faria, Gnanagowry Shanthan and Peter Gill

Genes 2022, 13(1), 18; https://doi.org/10.3390/genes13010018 - 22 Dec 2021

Cited by 15 | Viewed by 4016

Abstract

When DNA from a suspect is detected in a sample collected at a crime scene, there can be alternative explanations about the activity that may have led to the transfer, persistence and recovery of his/her DNA. Previous studies have shown that DNA can [...] Read more.

When DNA from a suspect is detected in a sample collected at a crime scene, there can be alternative explanations about the activity that may have led to the transfer, persistence and recovery of his/her DNA. Previous studies have shown that DNA can be indirectly transferred via intermediate surfaces and that DNA on a previously used object can persist after subsequent use of another individual. In addition, it has been shown that a person’s shedder status may influence transfer, persistence, prevalence, and recovery of DNA. In this study we have investigated transfer persistence and recovery on zip-lock bags and tape, which are commonly encountered in drug cases and how the shedder status of the participants influenced the results. A probabilistic framework was developed which was based on a previously described Bayesian network with case-specific modifications. Continuous modelling of data was used to inform the Bayesian networks and two case scenarios were investigated. In the specific scenarios only moderate to low support for H_p was obtained. Applying a continuous model based on the profile quality can change the LRs. Full article

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

► Show Figures

Figure 1

24 pages, 2880 KiB

Open AccessArticle

The FORCE Panel: An All-in-One SNP Marker Set for Confirming Investigative Genetic Genealogy Leads and for General Forensic Applications

by Andreas Tillmar, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Jacqueline Tyler Thomas and Charla Marshall

Genes 2021, 12(12), 1968; https://doi.org/10.3390/genes12121968 - 10 Dec 2021

Cited by 42 | Viewed by 7838

Abstract

The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3931 autosomal SNPs for extended kinship analysis, and [...] Read more.

The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3931 autosomal SNPs for extended kinship analysis, and no clinically relevant/disease markers. The FORCE panel was developed as a custom hybridization capture assay utilizing ~20,000 baits to target the selected SNPs. Five non-probative, previously identified World War II (WWII) cases were used to assess the kinship panel. Each case included one bone sample and associated family reference DNA samples. Additionally, seven reference quality samples, two 200-year-old bone samples, and four control DNAs were processed for kit performance and concordance assessments. SNP recovery after capture resulted in a mean of ~99% SNPs exceeding 10X coverage for reference and control samples, and 44.4% SNPs for bone samples. The WWII case results showed that the FORCE panel could predict first to fifth degree relationships with strong statistical support (likelihood ratios over 10,000 and posterior probabilities over 99.99%). To conclude, SNPs will be important for further advances in forensic DNA analysis. The FORCE panel shows promising results and demonstrates the utility of a 5000 SNP panel for forensic applications. Full article

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

► Show Figures

Figure 1

17 pages, 316 KiB

Open AccessArticle

Ethics as Lived Practice. Anticipatory Capacity and Ethical Decision-Making in Forensic Genetics

by Matthias Wienroth, Rafaela Granja, Veronika Lipphardt, Emmanuel Nsiah Amoako and Carole McCartney

Genes 2021, 12(12), 1868; https://doi.org/10.3390/genes12121868 - 24 Nov 2021

Cited by 13 | Viewed by 4370

Abstract

Greater scrutiny and demands for innovation and increased productivity place pressures on scientists. Forensic genetics is advancing at a rapid pace but can only do so responsibly, usefully, and acceptably within ethical and legal boundaries. We argue that such boundaries require that forensic [...] Read more.

Greater scrutiny and demands for innovation and increased productivity place pressures on scientists. Forensic genetics is advancing at a rapid pace but can only do so responsibly, usefully, and acceptably within ethical and legal boundaries. We argue that such boundaries require that forensic scientists embrace ‘ethics as lived practice’. As a starting point, we critically discuss ‘thin’ ethics in forensic genetics, which lead to a myopic focus on procedures, and to seeing ‘privacy’ as the sole ethical concern and technology as a mere tool. To overcome ‘thin’ ethics in forensic genetics, we instead propose understanding ethics as an intrinsic part of the lived practice of a scientist. Therefore, we explore, within the context of three case studies of emerging forensic genetics technologies, ethical aspects of decision-making in forensic genetics research and in technology use. We discuss the creation, curation, and use of databases, and the need to engage with societal and policing contexts of forensic practice. We argue that open communication is a vital ethical aspect. Adoption of ‘ethics as lived practice’ supports the development of anticipatory capacity—empowering scientists to understand, and act within ethical and legal boundaries, incorporating the operational and societal impacts of their daily decisions, and making visible ethical decision making in scientific practice. Full article

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

19 pages, 1314 KiB

Open AccessArticle

Cross-Amplification in Strigiformes: A New STR Panel for Forensic Purposes

by Patrizia Giangregorio, Lorenzo Naldi, Chiara Mengoni, Claudia Greco, Anna Padula, Marco Zaccaroni, Renato Fani, Giovanni Argenti and Nadia Mucci

Genes 2021, 12(11), 1721; https://doi.org/10.3390/genes12111721 - 28 Oct 2021

Cited by 1 | Viewed by 2413

Abstract

Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation [...] Read more.

Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations. Full article

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

► Show Figures

Figure 1

27 pages, 5257 KiB

Open AccessArticle

Precision DNA Mixture Interpretation with Single-Cell Profiling

by Jianye Ge, Jonathan L. King, Amy Smuts and Bruce Budowle

Genes 2021, 12(11), 1649; https://doi.org/10.3390/genes12111649 - 20 Oct 2021

Cited by 8 | Viewed by 3542

Abstract

Wet-lab based studies have exploited emerging single-cell technologies to address the challenges of interpreting forensic mixture evidence. However, little effort has been dedicated to developing a systematic approach to interpreting the single-cell profiles derived from the mixtures. This study is the first attempt [...] Read more.

Wet-lab based studies have exploited emerging single-cell technologies to address the challenges of interpreting forensic mixture evidence. However, little effort has been dedicated to developing a systematic approach to interpreting the single-cell profiles derived from the mixtures. This study is the first attempt to develop a comprehensive interpretation workflow in which single-cell profiles from mixtures are interpreted individually and holistically. In this approach, the genotypes from each cell are assessed, the number of contributors (NOC) of the single-cell profiles is estimated, followed by developing a consensus profile of each contributor, and finally the consensus profile(s) can be used for a DNA database search or comparing with known profiles to determine their potential sources. The potential of this single-cell interpretation workflow was assessed by simulation with various mixture scenarios and empirical allele drop-out and drop-in rates, the accuracies of estimating the NOC, the accuracies of recovering the true alleles by consensus, and the capabilities of deconvolving mixtures with related contributors. The results support that the single-cell based mixture interpretation can provide a precision that cannot beachieved with current standard CE-STR analyses. A new paradigm for mixture interpretation is available to enhance the interpretation of forensic genetic casework. Full article

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

► Show Figures

Figure 1

18 pages, 5919 KiB

Open AccessArticle

Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing

by Marta Diepenbroek, Birgit Bayer and Katja Anslinger

Genes 2021, 12(9), 1362; https://doi.org/10.3390/genes12091362 - 30 Aug 2021

Cited by 12 | Viewed by 4885

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)

► Show Figures

Figure 1

19 pages, 2561 KiB

Open AccessArticle

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

by María de la Puente, Jorge Ruiz-Ramírez, Adrián Ambroa-Conde, Catarina Xavier, Jacobo Pardo-Seco, Jose Álvarez-Dios, Ana Freire-Aradas, Ana Mosquera-Miguel, Theresa E. Gross, Elaine Y. Y. Cheung, Wojciech Branicki, Michael Nothnagel, Walther Parson, Peter M. Schneider, Manfred Kayser, Ángel Carracedo, Maria Victoria Lareu, Christopher Phillips and on behalf of the VISAGE Consortium

Genes 2021, 12(8), 1284; https://doi.org/10.3390/genes12081284 - 22 Aug 2021

Cited by 21 | Viewed by 5388

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)

► Show Figures

Figure 1

18 pages, 1358 KiB

Open AccessArticle

Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs

by Cordula Berger, Josephin Heinrich, Burkhard Berger, Werner Hecht, Walther Parson and on behalf of CaDNAP

Genes 2021, 12(6), 908; https://doi.org/10.3390/genes12060908 - 11 Jun 2021

Cited by 5 | Viewed by 10066

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)

► Show Figures

Figure 1

14 pages, 525 KiB

Open AccessArticle

Prediction of Eye Colour in Scandinavians Using the EyeColour 11 (EC11) SNP Set

by Olivia Strunge Meyer, Nina Mjølsnes Salvo, Anne Kjærbye, Marianne Kjersem, Mikkel Meyer Andersen, Erik Sørensen, Henrik Ullum, Kirstin Janssen, Niels Morling, Claus Børsting, Gunn-Hege Olsen and Jeppe Dyrberg Andersen

Genes 2021, 12(6), 821; https://doi.org/10.3390/genes12060821 - 27 May 2021

Cited by 12 | Viewed by 3640

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)

► Show Figures

Figure 1

13 pages, 1491 KiB

Open AccessArticle

Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch

by Muhammad Adnan Shan, Olivia Strunge Meyer, Mie Refn, Niels Morling, Jeppe Dyrberg Andersen and Claus Børsting

Genes 2021, 12(5), 733; https://doi.org/10.3390/genes12050733 - 13 May 2021

Cited by 6 | Viewed by 5820

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)

► Show Figures

Figure 1

10 pages, 243 KiB

Open AccessArticle

Evaluation of OpenArray™ as a Genotyping Method for Forensic DNA Phenotyping and Human Identification

by Michele Ragazzo, Giulio Puleri, Valeria Errichiello, Laura Manzo, Laura Luzzi, Saverio Potenza, Claudia Strafella, Cristina Peconi, Fabio Nicastro, Valerio Caputo and Emiliano Giardina

Genes 2021, 12(2), 221; https://doi.org/10.3390/genes12020221 - 3 Feb 2021

Cited by 10 | Viewed by 3858

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

Jump to: Research

26 pages, 547 KiB

Open AccessReview

A Logical Framework for Forensic DNA Interpretation

by Tacha Hicks, John Buckleton, Vincent Castella, Ian Evett and Graham Jackson

Genes 2022, 13(6), 957; https://doi.org/10.3390/genes13060957 - 27 May 2022

Cited by 10 | Viewed by 4393

Abstract

The forensic community has devoted much effort over the last decades to the development of a logical framework for forensic interpretation, which is essential for the safe administration of justice. We review the research and guidelines that have been published and provide examples [...] Read more.

The forensic community has devoted much effort over the last decades to the development of a logical framework for forensic interpretation, which is essential for the safe administration of justice. We review the research and guidelines that have been published and provide examples of how to implement them in casework. After a discussion on uncertainty in the criminal trial and the roles that the DNA scientist may take, we present the principles of interpretation for evaluative reporting. We show how their application helps to avoid a common fallacy and present strategies that DNA scientists can apply so that they do not transpose the conditional. We then discuss the hierarchy of propositions and explain why it is considered a fundamental concept for the evaluation of biological results and the differences between assessing results given propositions that are at the source level or the activity level. We show the importance of pre-assessment, especially when the questions relate to the alleged activities, and when transfer and persistence need to be considered by the scientists to guide the court. We conclude with a discussion on statement writing and testimony. This provides guidance on how DNA scientists can report in a balanced, transparent, and logical way. Full article

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

► Show Figures

Figure 1

11 pages, 688 KiB

Open AccessReview

Review of the Forensic Applicability of Biostatistical Methods for Inferring Ancestry from Autosomal Genetic Markers

by Torben Tvedebrink

Genes 2022, 13(1), 141; https://doi.org/10.3390/genes13010141 - 14 Jan 2022

Cited by 7 | Viewed by 3109

Abstract

The inference of ancestry has become a part of the services many forensic genetic laboratories provide. Interest in ancestry may be to provide investigative leads or identify the region of origin in cases of unidentified missing persons. There exist many biostatistical methods developed [...] Read more.

The inference of ancestry has become a part of the services many forensic genetic laboratories provide. Interest in ancestry may be to provide investigative leads or identify the region of origin in cases of unidentified missing persons. There exist many biostatistical methods developed for the study of population structure in the area of population genetics. However, the challenges and questions are slightly different in the context of forensic genetics, where the origin of a specific sample is of interest compared to the understanding of population histories and genealogies. In this paper, the methodologies for modelling population admixture and inferring ancestral populations are reviewed with a focus on their strengths and weaknesses in relation to ancestry inference in the forensic context. Full article

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

► Show Figures

Figure 1

28 pages, 1141 KiB

Open AccessReview

Predicting Physical Appearance from DNA Data—Towards Genomic Solutions

by Ewelina Pośpiech, Paweł Teisseyre, Jan Mielniczuk and Wojciech Branicki

Genes 2022, 13(1), 121; https://doi.org/10.3390/genes13010121 - 10 Jan 2022

Cited by 10 | Viewed by 7222

Abstract

The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data [...] Read more.

The idea of forensic DNA intelligence is to extract from genomic data any information that can help guide the investigation. The clues to the externally visible phenotype are of particular practical importance. The high heritability of the physical phenotype suggests that genetic data can be easily predicted, but this has only become possible with less polygenic traits. The forensic community has developed DNA-based predictive tools by employing a limited number of the most important markers analysed with targeted massive parallel sequencing. The complexity of the genetics of many other appearance phenotypes requires big data coupled with sophisticated machine learning methods to develop accurate genomic predictors. A significant challenge in developing universal genomic predictive methods will be the collection of sufficiently large data sets. These should be created using whole-genome sequencing technology to enable the identification of rare DNA variants implicated in phenotype determination. It is worth noting that the correctness of the forensic sketch generated from the DNA data depends on the inclusion of an age factor. This, however, can be predicted by analysing epigenetic data. An important limitation preventing whole-genome approaches from being commonly used in forensics is the slow progress in the development and implementation of high-throughput, low DNA input sequencing technologies. The example of palaeoanthropology suggests that such methods may possibly be developed in forensics. Full article

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

► Show Figures

Figure 1

35 pages, 1689 KiB

Open AccessReview

DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges

by Roland A. H. van Oorschot, Georgina E. Meakin, Bas Kokshoorn, Mariya Goray and Bianca Szkuta

Genes 2021, 12(11), 1766; https://doi.org/10.3390/genes12111766 - 7 Nov 2021

Cited by 35 | Viewed by 10708

Abstract

Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance [...] Read more.

Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA. Full article

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

► Show Figures

Figure 1

16 pages, 572 KiB

Open AccessReview

An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data

by Tunde I. Huszar, Katherine B. Gettings and Peter M. Vallone

Genes 2021, 12(11), 1739; https://doi.org/10.3390/genes12111739 - 29 Oct 2021

Cited by 5 | Viewed by 4658

Abstract

The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic [...] Read more.

The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing. Full article

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

► Show Figures

Figure 1

32 pages, 780 KiB

Open AccessReview

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime

by Titia Sijen and SallyAnn Harbison

Genes 2021, 12(11), 1728; https://doi.org/10.3390/genes12111728 - 28 Oct 2021

Cited by 53 | Viewed by 12239

Abstract

Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds [...] Read more.

Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime. Full article

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

► Show Figures

Figure 1

40 pages, 2967 KiB

Open AccessReview

A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™

by Peter Gill, Corina Benschop, John Buckleton, Øyvind Bleka and Duncan Taylor

Genes 2021, 12(10), 1559; https://doi.org/10.3390/genes12101559 - 30 Sep 2021

Cited by 38 | Viewed by 6271

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)

► Show Figures

Figure 1

13 pages, 318 KiB

Open AccessReview

Assessing the Forensic Value of DNA Evidence from Y Chromosomes and Mitogenomes

by Mikkel M. Andersen and David J. Balding

Genes 2021, 12(8), 1209; https://doi.org/10.3390/genes12081209 - 5 Aug 2021

Cited by 8 | Viewed by 4165

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)

15 pages, 32444 KiB

Open AccessReview

Animal Forensic Genetics

by Adrian Linacre

Genes 2021, 12(4), 515; https://doi.org/10.3390/genes12040515 - 1 Apr 2021

Cited by 24 | Viewed by 6580

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)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Advances in Forensic Genetics

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (25 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI